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Cervia-Hasler C, Brüningk SC, Hoch T, Fan B, Muzio G, Thompson RC, Ceglarek L, Meledin R, Westermann P, Emmenegger M, Taeschler P, Zurbuchen Y, Pons M, Menges D, Ballouz T, Cervia-Hasler S, Adamo S, Merad M, Charney AW, Puhan M, Brodin P, Nilsson J, Aguzzi A, Raeber ME, Messner CB, Beckmann ND, Borgwardt K, Boyman O. Persistent complement dysregulation with signs of thromboinflammation in active Long Covid. Science 2024; 383:eadg7942. [PMID: 38236961 DOI: 10.1126/science.adg7942] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of >6500 proteins in 268 longitudinal samples revealed dysregulated activation of the complement system, an innate immune protection and homeostasis mechanism, in individuals experiencing Long Covid. Thus, active Long Covid was characterized by terminal complement system dysregulation and ongoing activation of the alternative and classical complement pathways, the latter associated with increased antibody titers against several herpesviruses possibly stimulating this pathway. Moreover, markers of hemolysis, tissue injury, platelet activation, and monocyte-platelet aggregates were increased in Long Covid. Machine learning confirmed complement and thromboinflammatory proteins as top biomarkers, warranting diagnostic and therapeutic interrogation of these systems.
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Affiliation(s)
- Carlo Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah C Brüningk
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Hoch
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Bowen Fan
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Giulia Muzio
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Ceglarek
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Roman Meledin
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Westermann
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Marc Emmenegger
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Michele Pons
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Tala Ballouz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Sara Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander W Charney
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Milo Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Petter Brodin
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institute, 17165 Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Data Driven and Digital Medicine (D3M), Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Faculty of Medicine and Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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2
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Pan AL, Audrain M, Sakakibara E, Joshi R, Zhu X, Wang Q, Wang M, Beckmann ND, Schadt EE, Gandy S, Zhang B, Ehrlich ME, Salton SR. Dual-specificity protein phosphatase 6 (DUSP6) overexpression reduces amyloid load and improves memory deficits in male 5xFAD mice. bioRxiv 2023:2023.08.24.554335. [PMID: 37662269 PMCID: PMC10473733 DOI: 10.1101/2023.08.24.554335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Dual specificity protein phosphatase 6 (DUSP6) was recently identified as a key hub gene in a causal network that regulates late-onset Alzheimer's disease. Importantly, decreased DUSP6 levels are correlated with an increased clinical dementia rating in human subjects, and DUSP6 levels are additionally decreased in the 5xFAD amyloidopathy mouse model. Methods AAV5-DUSP6 or AAV5-GFP (control) were stereotactically injected into the dorsal hippocampus (dHc) of female and male 5xFAD or wild type mice to overexpress DUSP6 or GFP. Spatial learning memory of these mice was assessed in the Barnes maze, after which hippocampal tissues were isolated for downstream analysis. Results Barnes maze testing indicated that DUSP6 overexpression in the dHc of 5xFAD mice improved memory deficits and was associated with reduced amyloid plaque load, Aß 1-40 and Aß 1-42 levels, and amyloid precursor protein processing enzyme BACE1, in male but not in female mice. Microglial activation and microgliosis, which are increased in 5xFAD mice, were significantly reduced by dHc DUSP6 overexpression in both males and females. Transcriptomic profiling of female 5xFAD hippocampus revealed upregulated expression of genes involved in inflammatory and extracellular signal-regulated kinase (ERK) pathways, while dHc DUSP6 overexpression in female 5xFAD mice downregulated a subset of genes in these pathways. A limited number of differentially expressed genes (DEGs) (FDR<0.05) were identified in male mice; gene ontology analysis of DEGs (p<0.05) identified a greater number of synaptic pathways that were regulated by DUSP6 overexpression in male compared to female 5xFAD. Notably, the msh homeobox 3 gene, Msx3 , previously shown to regulate microglial M1/M2 polarization and reduce neuroinflammation, was one of the most robustly upregulated genes in female and male wild type and 5xFAD mice overexpressing DUSP6. Conclusions In summary, our data indicate that DUSP6 overexpression in dHc reduced amyloid deposition and memory deficits in male but not female 5xFAD mice, whereas reduced neuroinflammation and microglial activation were observed in both males and females. The sex-dependent regulation of synaptic pathways by DUSP6 overexpression, however, correlated with the improvement of spatial memory deficits in male but not female 5xFAD.
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3
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Liharska LE, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Vornholt E, Sullivan B, Cohen V, Kota P, Feng C, Cheng E, Moya E, Thompson RC, Johnson JS, Rieder MK, Huang J, Scarpa J, Hashemi A, Polanco J, Levin MA, Nadkarni GN, Sebra R, Crary J, Schadt EE, Beckmann ND, Kopell BH, Charney AW. A study of gene expression in the living human brain. medRxiv 2023:2023.04.21.23288916. [PMID: 37163086 PMCID: PMC10168405 DOI: 10.1101/2023.04.21.23288916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A goal of medical research is to determine the molecular basis of human brain health and illness. One way to achieve this goal is through observational studies of gene expression in human brain tissue. Due to the unavailability of brain tissue from living people, most such studies are performed using tissue from postmortem brain donors. An assumption underlying this practice is that gene expression in the postmortem human brain is an accurate representation of gene expression in the living human brain. Here, this assumption - which, until now, had not been adequately tested - is tested by comparing human prefrontal cortex gene expression between 275 living samples and 243 postmortem samples. Expression levels differed significantly for nearly 80% of genes, and a systematic examination of alternative explanations for this observation determined that these differences are not a consequence of cell type composition, RNA quality, postmortem interval, age, medication, morbidity, symptom severity, tissue pathology, sample handling, batch effects, or computational methods utilized. Analyses integrating the data generated for this study with data from earlier landmark studies that used tissue from postmortem brain donors showed that postmortem brain gene expression signatures of neurological and mental illnesses, as well as of normal traits such as aging, may not be accurate representations of these gene expression signatures in the living brain. By using tissue from large cohorts living people, future observational studies of human brain biology have the potential to (1) determine the medical research questions that can be addressed using postmortem tissue as a proxy for living tissue and (2) expand the scope of medical research to include questions about the molecular basis of human brain health and illness that can only be addressed in living people (e.g., "What happens at the molecular level in the brain as a person experiences an emotion?").
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4
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Su CY, Zhou S, Gonzalez-Kozlova E, Butler-Laporte G, Brunet-Ratnasingham E, Nakanishi T, Jeon W, Morrison DR, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg MA, Langenberg C, Forgetta V, Pineau J, Mooser V, Marron T, Beckmann ND, Kim-Schulze S, Charney AW, Gnjatic S, Kaufmann DE, Merad M, Richards JB. Circulating proteins to predict COVID-19 severity. Sci Rep 2023; 13:6236. [PMID: 37069249 PMCID: PMC10107586 DOI: 10.1038/s41598-023-31850-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict COVID-19 severity in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different COVID-19 severity were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of COVID-19 severity. Further research is needed to understand how to incorporate protein measurement into clinical care.
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Affiliation(s)
- Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Computer Science, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Wonseok Jeon
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - David R Morrison
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Laetitia Laurent
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Jonathan Afilalo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marc Afilalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Danielle Henry
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Maik Pietzner
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Nardin Rezk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Meriem Bouab
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Louis Petitjean
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Charlotte Guzman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Xiaoqing Xue
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chris Tselios
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Branka Vulesevic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Olumide Adeleye
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Tala Abdullah
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Noor Almamlouk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yara Moussa
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chantal DeLuca
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Naomi Duggan
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ieisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | | | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Joelle Pineau
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas Marron
- Immunotherapy and Phase 1 Trials, Mount Sinai Hospital, New York, NY, USA
| | - Noam D Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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5
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Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Cervia C, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang YC, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo MA, Yuan D, Huckins L, Roussos P, Marron TU, Glicksberg BS, Nadkarni G, Heath JR, Gonzalez-Kozlova E, Boyman O, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt EE, Charney AW, Beckmann ND. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nat Med 2023; 29:236-246. [PMID: 36482101 PMCID: PMC9873574 DOI: 10.1038/s41591-022-02107-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/25/2022] [Indexed: 12/13/2022]
Abstract
Post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are debilitating, clinically heterogeneous and of unknown molecular etiology. A transcriptome-wide investigation was performed in 165 acutely infected hospitalized individuals who were followed clinically into the post-acute period. Distinct gene expression signatures of post-acute sequelae were already present in whole blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell-associated gene expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in individuals with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.
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Affiliation(s)
- Ryan C Thompson
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Marie Del Valle
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy J Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lauren Lepow
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Laura Huckins
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Thomas U Marron
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin S Glicksberg
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Edgar Gonzalez-Kozlova
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Seunghee Kim-Schulze
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Noam D Beckmann
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Pan AL, Audrain M, Sakakibara E, Joshi R, Zhu X, Wang Q, Wang M, Beckmann ND, Schadt EE, Gandy S, Zhang B, Ehrlich ME, Salton SR. Dual-Specificity Protein Phosphatase 4 (DUSP4) Overexpression Improves Learning Behavior Selectively in Female 5xFAD Mice, and Reduces β-Amyloid Load in Males and Females. Cells 2022; 11:3880. [PMID: 36497141 PMCID: PMC9737364 DOI: 10.3390/cells11233880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer's disease converged on VGF (non-acronymic) as a key hub or driver. Within this computational VGF network, we identified the dual-specificity protein phosphatase 4 (DUSP4) [also known as mitogen-activated protein kinase (MAPK) phosphatase 2] as an important node. Importantly, DUSP4 gene expression, like that of VGF, is downregulated in postmortem Alzheimer's disease (AD) brains. We investigated the roles that this VGF/DUSP4 network plays in the development of learning behavior impairment and neuropathology in the 5xFAD amyloidopathy mouse model. We found reductions in DUSP4 expression in the hippocampi of male AD subjects, correlating with increased CDR scores, and in 4-month-old female and 12-18-month-old male 5xFAD hippocampi. Adeno-associated virus (AAV5)-mediated overexpression of DUSP4 in 5xFAD mouse dorsal hippocampi (dHc) rescued impaired Barnes maze performance in females but not in males, while amyloid loads were reduced in both females and males. Bulk RNA sequencing of the dHc from 5-month-old mice overexpressing DUSP4, and Ingenuity Pathway and Enrichr analyses of differentially expressed genes (DEGs), revealed that DUSP4 reduced gene expression in female 5xFAD mice in neuroinflammatory, interferon-gamma (IFNγ), programmed cell death protein-ligand 1/programmed cell death protein 1 (PD-L1/PD-1), and extracellular signal-regulated kinase (ERK)/MAPK pathways, via which DUSP4 may modulate AD phenotype with gender-specificity.
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Affiliation(s)
- Allen L. Pan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Mickael Audrain
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Emmy Sakakibara
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Rajeev Joshi
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xiaodong Zhu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry and Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen R. Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Brookdale Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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7
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- 409511 CIHR
- RG/13/13/30194 British Heart Foundation
- C18281/A29019 Cancer Research UK
- 100558 CIHR
- MC_PC_20004 Medical Research Council
- 365825 CIHR
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- * E-mail:
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Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, Patel A, Hendry C, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MY, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I. Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. Cell Stem Cell 2022; 29:1505. [DOI: 10.1016/j.stem.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Chen ST, Park MD, Del Valle DM, Buckup M, Tabachnikova A, Thompson RC, Simons NW, Mouskas K, Lee B, Geanon D, D'Souza D, Dawson T, Marvin R, Nie K, Zhao Z, LeBerichel J, Chang C, Jamal H, Akturk G, Chaddha U, Mathews K, Acquah S, Brown SA, Reiss M, Harkin T, Feldmann M, Powell CA, Hook JL, Kim-Schulze S, Rahman AH, Brown BD, Beckmann ND, Gnjatic S, Kenigsberg E, Charney AW, Merad M. A shift in lung macrophage composition is associated with COVID-19 severity and recovery. Sci Transl Med 2022; 14:eabn5168. [PMID: 36103512 PMCID: PMC10117220 DOI: 10.1126/scitranslmed.abn5168] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although it has been more than 2 years since the start of the coronavirus disease 2019 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, therapies to treat COVID-19 and other inflammatory diseases remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and mortality to develop tailored immunotherapy strategies to halt disease progression. We assembled the Mount Sinai COVID-19 Biobank, which was composed of almost 600 hospitalized patients followed longitudinally through the peak of the pandemic in 2020. Moderate disease and survival were associated with a stronger antigen presentation and effector T cell signature. In contrast, severe disease and death were associated with an altered antigen presentation signature, increased numbers of inflammatory immature myeloid cells, and extrafollicular activated B cells that have been previously associated with autoantibody formation. In severely ill patients with COVID-19, lung tissue-resident alveolar macrophages not only were drastically depleted but also had an altered antigen presentation signature, which coincided with an influx of inflammatory monocytes and monocyte-derived macrophages. In addition, we found that the size of the alveolar macrophage pool correlated with patient outcome and that alveolar macrophage numbers and functionality were restored to homeostasis in patients who recovered from COVID-19. These data suggest that local and systemic myeloid cell dysregulation are drivers of COVID-19 severity and modulation of alveolar macrophage numbers and activity in the lung may be a viable therapeutic strategy for the treatment of critical inflammatory lung diseases.
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Affiliation(s)
- Steven T Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diane Marie Del Valle
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ryan C Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Nicole W Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Darwin D'Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhen Zhao
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica LeBerichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hajra Jamal
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guray Akturk
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Udit Chaddha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kusum Mathews
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel Acquah
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stacey-Ann Brown
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle Reiss
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy Harkin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaime L Hook
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adeeb H Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian D Brown
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | -
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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10
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Voloudakis G, Vicari JM, Venkatesh S, Hoffman GE, Dobrindt K, Zhang W, Beckmann ND, Higgins CA, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee KM, Bian J, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Lynch JA, Merad M, tenOever BR, Charney AW, Brennand KJ, Fullard JF, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. NPJ Genom Med 2022; 7:52. [PMID: 36064543 PMCID: PMC9441828 DOI: 10.1038/s41525-022-00324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/19/2022] [Indexed: 02/06/2023] Open
Abstract
Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that reduce COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX), and perturbagen signatures, we identified IL10RB as the top candidate gene target for COVID-19 host susceptibility. In a series of validation steps, we show that predicted GReX upregulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
| | - James M Vicari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Dobrindt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Wen Zhang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina A Higgins
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University, New York, NY, USA
| | - Stathis Argyriou
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | | | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Jiantao Bian
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Jennifer S Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- VA Northeast Ohio Healthcare System, Cleveland VA Medical Center, Cleveland, OH, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, OR, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Striker
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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11
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Chen ST, Park MD, Del Valle DM, Buckup M, Tabachnikova A, Simons NW, Mouskas K, Lee B, Geanon D, D’Souza D, Dawson T, Marvin R, Nie K, Thompson RC, Zhao Z, LeBerichel J, Chang C, Jamal H, Chaddha U, Mathews K, Acquah S, Brown SA, Reiss M, Harkin T, Feldmann M, Powell CA, Hook JL, Kim-Schulze S, Rahman AH, Brown BD, Beckmann ND, Gnjatic S, Kenigsberg E, Charney AW, Merad M. Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. bioRxiv 2022:2022.01.11.475918. [PMID: 35043110 PMCID: PMC8764718 DOI: 10.1101/2022.01.11.475918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoMΦ). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.
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Affiliation(s)
- Steven T. Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew D. Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Marie Del Valle
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Darwin D’Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Zhen Zhao
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica LeBerichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hajra Jamal
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Udit Chaddha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kusum Mathews
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Samuel Acquah
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stacey-Ann Brown
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michelle Reiss
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Timothy Harkin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaime L. Hook
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adeeb H. Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Immunai, New York, NY, USA
| | - Brian D. Brown
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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13
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Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang YC, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo MA, Huckins L, Roussos P, Marron TU, Glicksberg BS, Nadkarni G, Gonzalez-Kozlova E, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt EE, Charney AW, Beckmann ND. Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae. medRxiv 2021:2021.10.04.21264434. [PMID: 34642700 PMCID: PMC8509101 DOI: 10.1101/2021.10.04.21264434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.
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Affiliation(s)
- Ryan C. Thompson
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Marie Del Valle
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Gabriel E. Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessy
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy J. Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Lauren Lepow
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Christie Chang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Ying-chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicholas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Vanessa Barcessat
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
| | - Mario A. Cedillo
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panagiotis Roussos
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas U. Marron
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Benjamin S. Glicksberg
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10065, USA
| | - Girish Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Division of Data Driven and Digital Medicine (D3M), Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10065, USA
| | - Edgar Gonzalez-Kozlova
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Mount Sinai, New York, NY 10029, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D. Beckmann
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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14
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Landi I, Kaji DA, Cotter L, Van Vleck T, Belbin G, Preuss M, Loos RJF, Kenny E, Glicksberg BS, Beckmann ND, O'Reilly P, Schadt EE, Achtyes ED, Buckley PF, Lehrer D, Malaspina DP, McCarroll SA, Rapaport MH, Fanous AH, Pato MT, Pato CN, Bigdeli TB, Nadkarni GN, Charney AW. Prognostic value of polygenic risk scores for adults with psychosis. Nat Med 2021; 27:1576-1581. [PMID: 34489608 PMCID: PMC8446329 DOI: 10.1038/s41591-021-01475-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/22/2021] [Indexed: 12/31/2022]
Abstract
Polygenic risk scores (PRS) summarize genetic liability to a disease at the individual level, and the aim is to use them as biomarkers of disease and poor outcomes in real-world clinical practice. To date, few studies have assessed the prognostic value of PRS relative to standards of care. Schizophrenia (SCZ), the archetypal psychotic illness, is an ideal test case for this because the predictive power of the SCZ PRS exceeds that of most other common diseases. Here, we analyzed clinical and genetic data from two multi-ethnic cohorts totaling 8,541 adults with SCZ and related psychotic disorders, to assess whether the SCZ PRS improves the prediction of poor outcomes relative to clinical features captured in a standard psychiatric interview. For all outcomes investigated, the SCZ PRS did not improve the performance of predictive models, an observation that was generally robust to divergent case ascertainment strategies and the ancestral background of the study participants.
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Affiliation(s)
- Isotta Landi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Deepak A Kaji
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liam Cotter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian Belbin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Eric D Achtyes
- Cherry Health, Grand Rapids, MI, USA
- Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Peter F Buckley
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Douglas Lehrer
- Department of Psychiatry, Wright State University, Dayton, OH, USA
| | - Dolores P Malaspina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mark H Rapaport
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Ayman H Fanous
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Girish N Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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15
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Beckmann ND, Comella PH, Cheng E, Lepow L, Beckmann AG, Tyler SR, Mouskas K, Simons NW, Hoffman GE, Francoeur NJ, Del Valle DM, Kang G, Do A, Moya E, Wilkins L, Le Berichel J, Chang C, Marvin R, Calorossi S, Lansky A, Walker L, Yi N, Yu A, Chung J, Hartnett M, Eaton M, Hatem S, Jamal H, Akyatan A, Tabachnikova A, Liharska LE, Cotter L, Fennessy B, Vaid A, Barturen G, Shah H, Wang YC, Sridhar SH, Soto J, Bose S, Madrid K, Ellis E, Merzier E, Vlachos K, Fishman N, Tin M, Smith M, Xie H, Patel M, Nie K, Argueta K, Harris J, Karekar N, Batchelor C, Lacunza J, Yishak M, Tuballes K, Scott I, Kumar A, Jaladanki S, Agashe C, Thompson R, Clark E, Losic B, Peters L, Roussos P, Zhu J, Wang W, Kasarskis A, Glicksberg BS, Nadkarni G, Bogunovic D, Elaiho C, Gangadharan S, Ofori-Amanfo G, Alesso-Carra K, Onel K, Wilson KM, Argmann C, Bunyavanich S, Alarcón-Riquelme ME, Marron TU, Rahman A, Kim-Schulze S, Gnjatic S, Gelb BD, Merad M, Sebra R, Schadt EE, Charney AW. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children. Nat Commun 2021; 12:4854. [PMID: 34381049 PMCID: PMC8357784 DOI: 10.1038/s41467-021-24981-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and pathology of multiple organs in individuals under 21 years of age in the weeks following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although an autoimmune pathogenesis has been proposed, the genes, pathways and cell types causal to this new disease remain unknown. Here we perform RNA sequencing of blood from patients with MIS-C and controls to find disease-associated genes clustered in a co-expression module annotated to CD56dimCD57+ natural killer (NK) cells and exhausted CD8+ T cells. A similar transcriptome signature is replicated in an independent cohort of Kawasaki disease (KD), the related condition after which MIS-C was initially named. Probing a probabilistic causal network previously constructed from over 1,000 blood transcriptomes both validates the structure of this module and reveals nine key regulators, including TBX21, a central coordinator of exhausted CD8+ T cell differentiation. Together, this unbiased, transcriptome-wide survey implicates downregulation of NK cells and cytotoxic T cell exhaustion in the pathogenesis of MIS-C.
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Affiliation(s)
- Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren Lepow
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aviva G Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy J Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | | | - Gurpawan Kang
- Department of Medicine, Division of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anh Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Emily Moya
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lillian Wilkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharlene Calorossi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alona Lansky
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Walker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nancy Yi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan Chung
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Melody Eaton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandra Hatem
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hajra Jamal
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alara Akyatan
- Department of of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lora E Liharska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liam Cotter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fennessy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Akhil Vaid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guillermo Barturen
- Department of Medical Genomics, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government (GENYO), Granada, Spain
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shwetha Hara Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Swaroop Bose
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Elyze Merzier
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Konstantinos Vlachos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Nataly Fishman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Manying Tin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Hui Xie
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neha Karekar
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Craig Batchelor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose Lacunza
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mahlet Yishak
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ieisha Scott
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arvind Kumar
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suraj Jaladanki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charuta Agashe
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
| | - Evan Clark
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panagiotis Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wenhui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- Mount Sinai COVID Informatics Center, New York, NY, USA
- Department of Medicine, Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Dusan Bogunovic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cordelia Elaiho
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandeep Gangadharan
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George Ofori-Amanfo
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kasey Alesso-Carra
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karen M Wilson
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marta E Alarcón-Riquelme
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas U Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA
- Black Family Stem Cell Institute, New York, NY, USA
- Sema4, a Mount Sinai Venture, Stamford, CT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
- Sema4, a Mount Sinai Venture, Stamford, CT, USA.
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Data Science and Genomics Technology, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai COVID Informatics Center, New York, NY, USA.
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16
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Voloudakis G, Hoffman G, Venkatesh S, Lee KM, Dobrindt K, Vicari JM, Zhang W, Beckmann ND, Jiang S, Hoagland D, Bian J, Gao L, Corvelo A, Cho K, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Merad M, tenOever BR, Charney AW, Brennand KJ, Lynch JA, Fullard JF, Roussos P. IL10RB as a key regulator of COVID-19 host susceptibility and severity. medRxiv 2021:2021.05.31.21254851. [PMID: 34100031 PMCID: PMC8183086 DOI: 10.1101/2021.05.31.21254851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes and readily available compounds that reduce COVID-19 host susceptibility is a critical next step. METHODS We integrate COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX) and perturbargen signatures to identify candidate genes and compounds that reverse the predicted gene expression dysregulation associated with COVID-19 susceptibility. The top candidate gene is validated by testing both its GReX and observed blood transcriptome association with COVID-19 severity, as well as by in vitro perturbation to quantify effects on viral load and molecular pathway dysregulation. We validate the in silico drug repositioning analysis by examining whether the top candidate compounds decrease COVID-19 incidence based on epidemiological evidence. RESULTS We identify IL10RB as the top key regulator of COVID-19 host susceptibility. Predicted GReX up-regulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes. In vitro IL10RB overexpression is associated with increased viral load and activation of immune-related molecular pathways. Azathioprine and retinol are prioritized as candidate compounds to reduce the likelihood of testing positive for COVID-19. CONCLUSIONS We establish an integrative data-driven approach for gene target prioritization. We identify and validate IL10RB as a suitable molecular target for modulation of COVID-19 host susceptibility. Finally, we provide evidence for a few readily available medications that would warrant further investigation as drug repositioning candidates.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Gabriel Hoffman
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Sanan Venkatesh
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kyung Min Lee
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kristina Dobrindt
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - James M Vicari
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Wen Zhang
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Noam D Beckmann
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Shan Jiang
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Daisy Hoagland
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Jiantao Bian
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Lina Gao
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - André Corvelo
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kelly Cho
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Jennifer S Lee
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Sudha K Iyengar
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Shiuh-Wen Luoh
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Schahram Akbarian
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Robert Striker
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Themistocles L Assimes
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Eric E Schadt
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Miriam Merad
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Benjamin R tenOever
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Alexander W Charney
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kristen J Brennand
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Julie A Lynch
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - John F Fullard
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Panos Roussos
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
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17
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Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, Torre D, Moscati A, Wojcik GL, Shemirani R, Beckmann ND, Cohain A, Sorokin EP, Park DS, Ambite JL, Ellis S, Auton A, Bottinger EP, Cho JH, Loos RJF, Abul-Husn NS, Zaitlen NA, Gignoux CR, Kenny EE. Toward a fine-scale population health monitoring system. Cell 2021; 184:2068-2083.e11. [PMID: 33861964 DOI: 10.1016/j.cell.2021.03.034] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/18/2020] [Accepted: 03/12/2021] [Indexed: 12/22/2022]
Abstract
Understanding population health disparities is an essential component of equitable precision health efforts. Epidemiology research often relies on definitions of race and ethnicity, but these population labels may not adequately capture disease burdens and environmental factors impacting specific sub-populations. Here, we propose a framework for repurposing data from electronic health records (EHRs) in concert with genomic data to explore the demographic ties that can impact disease burdens. Using data from a diverse biobank in New York City, we identified 17 communities sharing recent genetic ancestry. We observed 1,177 health outcomes that were statistically associated with a specific group and demonstrated significant differences in the segregation of genetic variants contributing to Mendelian diseases. We also demonstrated that fine-scale population structure can impact the prediction of complex disease risk within groups. This work reinforces the utility of linking genomic data to EHRs and provides a framework toward fine-scale monitoring of population health.
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Affiliation(s)
- Gillian M Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephane Wenric
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arden Moscati
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ruhollah Shemirani
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariella Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Danny S Park
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jose-Luis Ambite
- Information Science Institute, University of Southern California, Marina del Rey, CA 90089, USA
| | - Steve Ellis
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | -
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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- Regeneron Genetics Center, Tarrytown, New York, NY 10591, USA
| | - Erwin P Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Judy H Cho
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J F Loos
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah A Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90033, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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18
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Comella PH, Gonzalez-Kozlova E, Kosoy R, Charney AW, Peradejordi IF, Chandrasekar S, Tyler SR, Wang W, Losic B, Zhu J, Hoffman GE, Kim-Schulze S, Qi J, Patel M, Kasarskis A, Suarez-Farinas M, Gümüş ZH, Argmann C, Merad M, Becker C, Beckmann ND, Schadt EE. A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. medRxiv 2021:2021.01.29.21250755. [PMID: 33564792 PMCID: PMC7872387 DOI: 10.1101/2021.01.29.21250755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
IntroThe molecular mechanisms of chronic fatigue syndrome (CFS, or Myalgic encephalomyelitis), a disease defined by extreme, long-term fatigue, remain largely uncharacterized, and presently no molecular diagnostic test and no specific treatments exist to diagnose and treat CFS patients. While CFS has historically had an estimated prevalence of 0.1-0.5% [1], concerns of a “long hauler” version of Coronavirus disease 2019 (COVID-19) that symptomatically overlaps CFS to a significant degree(Supplemental Table-1)and appears to occur in 10% of COVID-19 patients[2], has raised concerns of a larger spike in CFS [3]. Here, we established molecular signatures of CFS and a corresponding network-based disease context from RNA-sequencing data generated on whole blood and FACs sorted specific peripheral blood mononuclear cells (PBMCs) isolated from CFS cases and non-CFS controls. The immune cell type specific molecular signatures of CFS we identified, overlapped molecular signatures from other fatiguing illnesses, demonstrating a common molecular etiology. Further, after constructing a probabilistic causal model of the CFS gene expression data, we identified master regulator genes modulating network states associated with CFS, suggesting potential therapeutic targets for CFS.
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Affiliation(s)
- Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Irene Font Peradejordi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Shreya Chandrasekar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Cornell Tech at Cornell University, New York, NY, 10044, USA
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jingjing Qi
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Population Health Science and Policy at the Icahn School of Medicine at Mount Sinai
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Zeynep H. Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
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19
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Cohain AT, Barrington WT, Jordan DM, Beckmann ND, Argmann CA, Houten SM, Charney AW, Ermel R, Sukhavasi K, Franzen O, Koplev S, Whatling C, Belbin GM, Yang J, Hao K, Kenny EE, Tu Z, Zhu J, Gan LM, Do R, Giannarelli C, Kovacic JC, Ruusalepp A, Lusis AJ, Bjorkegren JLM, Schadt EE. An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease. Nat Commun 2021; 12:547. [PMID: 33483510 PMCID: PMC7822923 DOI: 10.1038/s41467-020-20750-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/08/2020] [Indexed: 01/30/2023] Open
Abstract
Elevated plasma cholesterol and type 2 diabetes (T2D) are associated with coronary artery disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explore the relationship between lipid and glucose control by constructing network models from the STARNET study with sequencing data from seven cardiometabolic tissues obtained from CAD patients during coronary artery by-pass grafting surgery. By integrating gene expression, genotype, metabolomic, and clinical data, we identify a glucose and lipid determining (GLD) regulatory network showing inverse relationships with lipid and glucose traits. Master regulators of the GLD network also impact lipid and glucose levels in inverse directions. Experimental inhibition of one of the GLD network master regulators, lanosterol synthase (LSS), in mice confirms the inverse relationships to glucose and lipid levels as predicted by our model and provides mechanistic insights.
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Affiliation(s)
- Ariella T Cohain
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - William T Barrington
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Daniel M Jordan
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen A Argmann
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Raili Ermel
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | | | - Oscar Franzen
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Simon Koplev
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carl Whatling
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Gillian M Belbin
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jialiang Yang
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ke Hao
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eimear E Kenny
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhidong Tu
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li-Ming Gan
- Early Clinical Development, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ron Do
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jason C Kovacic
- Cardiovascular Research Centre, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Johan L M Bjorkegren
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Clinical Gene Networks AB, Stockholm, Sweden.
| | - Eric E Schadt
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Sema4, Stamford, CT, USA.
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20
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Wang M, Li A, Sekiya M, Beckmann ND, Quan X, Schrode N, Fernando MB, Yu A, Zhu L, Cao J, Lyu L, Horgusluoglu E, Wang Q, Guo L, Wang YS, Neff R, Song WM, Wang E, Shen Q, Zhou X, Ming C, Ho SM, Vatansever S, Kaniskan HÜ, Jin J, Zhou MM, Ando K, Ho L, Slesinger PA, Yue Z, Zhu J, Katsel P, Gandy S, Ehrlich ME, Fossati V, Noggle S, Cai D, Haroutunian V, Iijima KM, Schadt E, Brennand KJ, Zhang B. Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits, Key Regulators, and Potential Therapeutics for Alzheimer's Disease. Neuron 2021; 109:257-272.e14. [PMID: 33238137 PMCID: PMC7855384 DOI: 10.1016/j.neuron.2020.11.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/16/2020] [Accepted: 10/30/2020] [Indexed: 01/11/2023]
Abstract
To identify the molecular mechanisms and novel therapeutic targets of late-onset Alzheimer's Disease (LOAD), we performed an integrative network analysis of multi-omics profiling of four cortical areas across 364 donors with varying cognitive and neuropathological phenotypes. Our analyses revealed thousands of molecular changes and uncovered neuronal gene subnetworks as the most dysregulated in LOAD. ATP6V1A was identified as a key regulator of a top-ranked neuronal subnetwork, and its role in disease-related processes was evaluated through CRISPR-based manipulation in human induced pluripotent stem cell-derived neurons and RNAi-based knockdown in Drosophila models. Neuronal impairment and neurodegeneration caused by ATP6V1A deficit were improved by a repositioned compound, NCH-51. This study provides not only a global landscape but also detailed signaling circuits of complex molecular interactions in key brain regions affected by LOAD, and the resulting network models will serve as a blueprint for developing next-generation therapeutic agents against LOAD.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Aiqun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,These authors contributed equally
| | - Michiko Sekiya
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,These authors contributed equally
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,These authors contributed equally
| | - Xiuming Quan
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,These authors contributed equally
| | - Nadine Schrode
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Michael B. Fernando
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Alex Yu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Li Zhu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Jiqing Cao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Liwei Lyu
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Emrin Horgusluoglu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yuan-shuo Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qi Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Seok-Man Ho
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - H. Ümit Kaniskan
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Jian Jin
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Kanae Ando
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan 192-0397
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Paul A. Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Zhenyu Yue
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Sam Gandy
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York NY 10029
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Scott Noggle
- The New York Stem Cell Foundation Research Institute, New York, NY 10019
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York NY 10029,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Neurology, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York NY 10029,Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Koichi M. Iijima
- Department of Alzheimer’s Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan 474-8511,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan 467-8603,Senior author
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author
| | - Kristen J. Brennand
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Senior author
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA,Senior author,Lead Contact,Correspondence: (B.Z.)
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21
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Carcamo-Orive I, Henrion MYR, Zhu K, Beckmann ND, Cundiff P, Moein S, Zhang Z, Alamprese M, D’Souza SL, Wabitsch M, Schadt EE, Quertermous T, Knowles JW, Chang R. Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PLoS Comput Biol 2020; 16:e1008491. [PMID: 33362275 PMCID: PMC7790417 DOI: 10.1371/journal.pcbi.1008491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/07/2021] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. Thus, new approaches are necessary to explore the genetic architecture of insulin resistance. To that end, we generated an iPSC library across the spectrum of insulin sensitivity in humans. RNA-seq based analysis of 310 induced pluripotent stem cell (iPSC) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive iPSC lines. Analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. Functional validation in human adipocytes and skeletal muscle cells (SKMCs) confirmed the relevance of the key driver candidate genes for insulin responsiveness. Insulin resistance is characterized by a defective response (“resistance”) to normal insulin concentrations to uptake the glucose present in the blood, and is the underlying condition that leads to type 2 diabetes (T2D) and increases the risk of cardiovascular disease. It is estimated that 25–33% of the US population are insulin resistant enough to be at risk of serious clinical consequences. For more than a decade, large population studies have tried to discover the genes that participate in the development of insulin resistance, but without much success. It is now increasingly clear that the complex genetic nature of insulin resistance requires novel approaches centered in patient specific cellular models. To fill this gap, we have generated an induced pluripotent stem cell (iPSC) library from individuals with accurate measurements of insulin sensitivity, and performed gene expression and key driver analyses. Our work demonstrates that iPSCs can be used as a revolutionary technology to model insulin resistance and to discover key genetic drivers. Moreover, they can develop our basic knowledge of the disease, and are ultimately expected to increase the therapeutic targets to treat insulin resistance and type 2 diabetes.
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Affiliation(s)
- Ivan Carcamo-Orive
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Marc Y. R. Henrion
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
- Malawi—Liverpool—Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kuixi Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Paige Cundiff
- Vertex Pharmaceuticals, Boston, Massachusetts, United States of America
| | - Sara Moein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Zenan Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Melissa Alamprese
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Sunita L. D’Souza
- Department of Cellular, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology, Ulm University, Ulm, Germany
| | - Eric E. Schadt
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Thomas Quertermous
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
| | - Joshua W. Knowles
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Rui Chang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
- INTelico Therapeutics LLC, Tucson, Arizona, United States of America
- * E-mail: (ICO); (JWK); (RC)
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22
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Vaid A, Somani S, Russak AJ, De Freitas JK, Chaudhry FF, Paranjpe I, Johnson KW, Lee SJ, Miotto R, Richter F, Zhao S, Beckmann ND, Naik N, Kia A, Timsina P, Lala A, Paranjpe M, Golden E, Danieletto M, Singh M, Meyer D, O'Reilly PF, Huckins L, Kovatch P, Finkelstein J, Freeman RM, Argulian E, Kasarskis A, Percha B, Aberg JA, Bagiella E, Horowitz CR, Murphy B, Nestler EJ, Schadt EE, Cho JH, Cordon-Cardo C, Fuster V, Charney DS, Reich DL, Bottinger EP, Levin MA, Narula J, Fayad ZA, Just AC, Charney AW, Nadkarni GN, Glicksberg BS. Machine Learning to Predict Mortality and Critical Events in a Cohort of Patients With COVID-19 in New York City: Model Development and Validation. J Med Internet Res 2020; 22:e24018. [PMID: 33027032 PMCID: PMC7652593 DOI: 10.2196/24018] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND COVID-19 has infected millions of people worldwide and is responsible for several hundred thousand fatalities. The COVID-19 pandemic has necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods to meet these needs are lacking. OBJECTIVE The aims of this study were to analyze the electronic health records (EHRs) of patients who tested positive for COVID-19 and were admitted to hospitals in the Mount Sinai Health System in New York City; to develop machine learning models for making predictions about the hospital course of the patients over clinically meaningful time horizons based on patient characteristics at admission; and to assess the performance of these models at multiple hospitals and time points. METHODS We used Extreme Gradient Boosting (XGBoost) and baseline comparator models to predict in-hospital mortality and critical events at time windows of 3, 5, 7, and 10 days from admission. Our study population included harmonized EHR data from five hospitals in New York City for 4098 COVID-19-positive patients admitted from March 15 to May 22, 2020. The models were first trained on patients from a single hospital (n=1514) before or on May 1, externally validated on patients from four other hospitals (n=2201) before or on May 1, and prospectively validated on all patients after May 1 (n=383). Finally, we established model interpretability to identify and rank variables that drive model predictions. RESULTS Upon cross-validation, the XGBoost classifier outperformed baseline models, with an area under the receiver operating characteristic curve (AUC-ROC) for mortality of 0.89 at 3 days, 0.85 at 5 and 7 days, and 0.84 at 10 days. XGBoost also performed well for critical event prediction, with an AUC-ROC of 0.80 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. In external validation, XGBoost achieved an AUC-ROC of 0.88 at 3 days, 0.86 at 5 days, 0.86 at 7 days, and 0.84 at 10 days for mortality prediction. Similarly, the unimputed XGBoost model achieved an AUC-ROC of 0.78 at 3 days, 0.79 at 5 days, 0.80 at 7 days, and 0.81 at 10 days. Trends in performance on prospective validation sets were similar. At 7 days, acute kidney injury on admission, elevated LDH, tachypnea, and hyperglycemia were the strongest drivers of critical event prediction, while higher age, anion gap, and C-reactive protein were the strongest drivers of mortality prediction. CONCLUSIONS We externally and prospectively trained and validated machine learning models for mortality and critical events for patients with COVID-19 at different time horizons. These models identified at-risk patients and uncovered underlying relationships that predicted outcomes.
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Affiliation(s)
- Akhil Vaid
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sulaiman Somani
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adam J Russak
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jessica K De Freitas
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Fayzan F Chaudhry
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ishan Paranjpe
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samuel J Lee
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Riccardo Miotto
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Felix Richter
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Shan Zhao
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nidhi Naik
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Arash Kia
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Prem Timsina
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Anuradha Lala
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Eddye Golden
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matteo Danieletto
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Manbir Singh
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dara Meyer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Paul F O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Laura Huckins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Patricia Kovatch
- Mount Sinai Data Warehouse, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert M Freeman
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Edgar Argulian
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Data Office, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bethany Percha
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Judith A Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Emilia Bagiella
- Institute for Healthcare Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Carol R Horowitz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Barbara Murphy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Valentin Fuster
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dennis S Charney
- Office of the Dean, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David L Reich
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Erwin P Bottinger
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Matthew A Levin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zahi A Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Girish N Nadkarni
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin S Glicksberg
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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23
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Del Valle DM, Kim-Schulze S, Huang HH, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz TH, Madduri D, Stock A, Marron TU, Xie H, Patel M, Tuballes K, Van Oekelen O, Rahman A, Kovatch P, Aberg JA, Schadt E, Jagannath S, Mazumdar M, Charney AW, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med 2020. [PMID: 32839624 DOI: 10.1038/s41591-41020-41051-41599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Several studies have revealed that the hyper-inflammatory response induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major cause of disease severity and death. However, predictive biomarkers of pathogenic inflammation to help guide targetable immune pathways are critically lacking. We implemented a rapid multiplex cytokine assay to measure serum interleukin (IL)-6, IL-8, tumor necrosis factor (TNF)-α and IL-1β in hospitalized patients with coronavirus disease 2019 (COVID-19) upon admission to the Mount Sinai Health System in New York. Patients (n = 1,484) were followed up to 41 d after admission (median, 8 d), and clinical information, laboratory test results and patient outcomes were collected. We found that high serum IL-6, IL-8 and TNF-α levels at the time of hospitalization were strong and independent predictors of patient survival (P < 0.0001, P = 0.0205 and P = 0.0140, respectively). Notably, when adjusting for disease severity, common laboratory inflammation markers, hypoxia and other vitals, demographics, and a range of comorbidities, IL-6 and TNF-α serum levels remained independent and significant predictors of disease severity and death. These findings were validated in a second cohort of patients (n = 231). We propose that serum IL-6 and TNF-α levels should be considered in the management and treatment of patients with COVID-19 to stratify prospective clinical trials, guide resource allocation and inform therapeutic options.
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Affiliation(s)
- Diane Marie Del Valle
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hsin-Hui Huang
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- TCI Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharon Nirenberg
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Scientific Computing, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bo Wang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Talia H Swartz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepu Madduri
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aryeh Stock
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas U Marron
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oliver Van Oekelen
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Kovatch
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Scientific Computing, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judith A Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sundar Jagannath
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhu Mazumdar
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- TCI Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Firpo-Betancourt
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Damodara Rao Mendu
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Jhang
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Reich
- Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith Sigel
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Samir Parekh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Del Valle DM, Kim-Schulze S, Huang HH, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz TH, Madduri D, Stock A, Marron TU, Xie H, Patel M, Tuballes K, Van Oekelen O, Rahman A, Kovatch P, Aberg JA, Schadt E, Jagannath S, Mazumdar M, Charney AW, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med 2020; 26:1636-1643. [PMID: 32839624 PMCID: PMC7869028 DOI: 10.1038/s41591-020-1051-9] [Citation(s) in RCA: 1541] [Impact Index Per Article: 385.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Several studies have revealed that the hyper-inflammatory response induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major cause of disease severity and death. However, predictive biomarkers of pathogenic inflammation to help guide targetable immune pathways are critically lacking. We implemented a rapid multiplex cytokine assay to measure serum interleukin (IL)-6, IL-8, tumor necrosis factor (TNF)-α and IL-1β in hospitalized patients with coronavirus disease 2019 (COVID-19) upon admission to the Mount Sinai Health System in New York. Patients (n = 1,484) were followed up to 41 d after admission (median, 8 d), and clinical information, laboratory test results and patient outcomes were collected. We found that high serum IL-6, IL-8 and TNF-α levels at the time of hospitalization were strong and independent predictors of patient survival (P < 0.0001, P = 0.0205 and P = 0.0140, respectively). Notably, when adjusting for disease severity, common laboratory inflammation markers, hypoxia and other vitals, demographics, and a range of comorbidities, IL-6 and TNF-α serum levels remained independent and significant predictors of disease severity and death. These findings were validated in a second cohort of patients (n = 231). We propose that serum IL-6 and TNF-α levels should be considered in the management and treatment of patients with COVID-19 to stratify prospective clinical trials, guide resource allocation and inform therapeutic options.
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Affiliation(s)
- Diane Marie Del Valle
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hsin-Hui Huang
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- TCI Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sharon Nirenberg
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Scientific Computing, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bo Wang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Talia H Swartz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepu Madduri
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aryeh Stock
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas U Marron
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oliver Van Oekelen
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Kovatch
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Scientific Computing, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judith A Aberg
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sundar Jagannath
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhu Mazumdar
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- TCI Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Firpo-Betancourt
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Damodara Rao Mendu
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Jhang
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Reich
- Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith Sigel
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Samir Parekh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Beckmann ND, Comella PH, Cheng E, Lepow L, Beckmann AG, Mouskas K, Simons NW, Hoffman GE, Francoeur NJ, Del Valle DM, Kang G, Moya E, Wilkins L, Le Berichel J, Chang C, Marvin R, Calorossi S, Lansky A, Walker L, Yi N, Yu A, Hartnett M, Eaton M, Hatem S, Jamal H, Akyatan A, Tabachnikova A, Liharska LE, Cotter L, Fennessey B, Vaid A, Barturen G, Tyler SR, Shah H, Wang YC, Sridhar SH, Soto J, Bose S, Madrid K, Ellis E, Merzier E, Vlachos K, Fishman N, Tin M, Smith M, Xie H, Patel M, Argueta K, Harris J, Karekar N, Batchelor C, Lacunza J, Yishak M, Tuballes K, Scott L, Kumar A, Jaladanki S, Thompson R, Clark E, Losic B, Zhu J, Wang W, Kasarskis A, Glicksberg BS, Nadkarni G, Bogunovic D, Elaiho C, Gangadharan S, Ofori-Amanfo G, Alesso-Carra K, Onel K, Wilson KM, Argmann C, Alarcón-Riquelme ME, Marron TU, Rahman A, Kim-Schulze S, Gnjatic S, Gelb BD, Merad M, Sebra R, Schadt EE, Charney AW. Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children. medRxiv 2020:2020.08.29.20182899. [PMID: 32909006 PMCID: PMC7480058 DOI: 10.1101/2020.08.29.20182899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and multiple organ involvement in individuals under 21 years following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To identify genes, pathways and cell types driving MIS-C, we sequenced the blood transcriptomes of MIS-C cases, pediatric cases of coronavirus disease 2019, and healthy controls. We define a MIS-C transcriptional signature partially shared with the transcriptional response to SARS-CoV-2 infection and with the signature of Kawasaki disease, a clinically similar condition. By projecting the MIS-C signature onto a co-expression network, we identified disease gene modules and found genes downregulated in MIS-C clustered in a module enriched for the transcriptional signatures of exhausted CD8 + T-cells and CD56 dim CD57 + NK cells. Bayesian network analyses revealed nine key regulators of this module, including TBX21 , a central coordinator of exhausted CD8 + T-cell differentiation. Together, these findings suggest dysregulated cytotoxic lymphocyte response to SARS-Cov-2 infection in MIS-C.
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Affiliation(s)
- Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esther Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Lepow
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aviva G. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel E. Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nancy J. Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Diane Marie Del Valle
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gurpawan Kang
- Department of Medicine, division of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Moya
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lillian Wilkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica Le Berichel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Marvin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sharlene Calorossi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alona Lansky
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Laura Walker
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nancy Yi
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alex Yu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew Hartnett
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melody Eaton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sandra Hatem
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hajra Jamal
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alara Akyatan
- Department of of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra Tabachnikova
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lora E. Liharska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Liam Cotter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Fennessey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Akhil Vaid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Guillermo Barturen
- Department of Medical Genomics, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government (GENYO), 18007 Urb. los Vergeles, Granada, Spain
| | - Scott R. Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha Hara Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Swaroop Bose
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Ethan Ellis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Elyze Merzier
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Konstantinos Vlachos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Nataly Fishman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Manying Tin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Hui Xie
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimberly Argueta
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jocelyn Harris
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Neha Karekar
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Craig Batchelor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Lacunza
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mahlet Yishak
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Leisha Scott
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Arvind Kumar
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Suraj Jaladanki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
| | - Evan Clark
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenhui Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin S. Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Girish Nadkarni
- Mount Sinai COVID Informatics Center, New York, NY 10029, USA
- Department of Medicine, Mount Sinai, New York, NY 10029, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, New York, NY 10029, USA
| | - Dusan Bogunovic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Cordelia Elaiho
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandeep Gangadharan
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - George Ofori-Amanfo
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kasey Alesso-Carra
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen M. Wilson
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marta E. Alarcón-Riquelme
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas U. Marron
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adeeb Rahman
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departments of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mindich Child Health and Development Institute at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Black Family Stem Cell Institute, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Sema4, a Mount Sinai venture, Stamford CT, 06902, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai COVID Informatics Center, New York, NY 10029, USA
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26
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Beckmann ND, Lin WJ, Wang M, Cohain AT, Charney AW, Wang P, Ma W, Wang YC, Jiang C, Audrain M, Comella PH, Fakira AK, Hariharan SP, Belbin GM, Girdhar K, Levey AI, Seyfried NT, Dammer EB, Duong D, Lah JJ, Haure-Mirande JV, Shackleton B, Fanutza T, Blitzer R, Kenny E, Zhu J, Haroutunian V, Katsel P, Gandy S, Tu Z, Ehrlich ME, Zhang B, Salton SR, Schadt EE. Multiscale causal networks identify VGF as a key regulator of Alzheimer's disease. Nat Commun 2020; 11:3942. [PMID: 32770063 PMCID: PMC7414858 DOI: 10.1038/s41467-020-17405-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
Though discovered over 100 years ago, the molecular foundation of sporadic Alzheimer's disease (AD) remains elusive. To better characterize the complex nature of AD, we constructed multiscale causal networks on a large human AD multi-omics dataset, integrating clinical features of AD, DNA variation, and gene- and protein-expression. These probabilistic causal models enabled detection, prioritization and replication of high-confidence master regulators of AD-associated networks, including the top predicted regulator, VGF. Overexpression of neuropeptide precursor VGF in 5xFAD mice partially rescued beta-amyloid-mediated memory impairment and neuropathology. Molecular validation of network predictions downstream of VGF was also achieved in this AD model, with significant enrichment for homologous genes identified as differentially expressed in 5xFAD brains overexpressing VGF. Our findings support a causal role for VGF in protecting against AD pathogenesis and progression.
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Affiliation(s)
- Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Jye Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 510120, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ariella T Cohain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Cheng Jiang
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Mickael Audrain
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda K Fakira
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Siddharth P Hariharan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Gillian M Belbin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiran Girdhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Allan I Levey
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc Duong
- Department of Neurology and Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Jean-Vianney Haure-Mirande
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ben Shackleton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Tomas Fanutza
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Blitzer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Eimear Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Sema4, Stamford, CT, 06902, USA
| | - Vahram Haroutunian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Sam Gandy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY, 10468, USA
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Stephen R Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
- Sema4, Stamford, CT, 06902, USA.
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27
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Del Valle DM, Kim-Schulze S, Hsin-Hui H, Beckmann ND, Nirenberg S, Wang B, Lavin Y, Swartz T, Madduri D, Stock A, Marron T, Xie H, Patel MK, van Oekelen O, Rahman A, Kovatch P, Aberg J, Schadt E, Jagannath S, Mazumdar M, Charney A, Firpo-Betancourt A, Mendu DR, Jhang J, Reich D, Sigel K, Cordon-Cardo C, Feldmann M, Parekh S, Merad M, Gnjatic S. An inflammatory cytokine signature helps predict COVID-19 severity and death. medRxiv 2020. [PMID: 32511562 DOI: 10.1101/2020.05.28.20115758] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The COVID-19 pandemic caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to more than 100,000 deaths in the United States. Several studies have revealed that the hyper-inflammatory response induced by SARS-CoV-2 is a major cause of disease severity and death in infected patients. However, predictive biomarkers of pathogenic inflammation to help guide targetable immune pathways are critically lacking. We implemented a rapid multiplex cytokine assay to measure serum IL-6, IL-8, TNF-α, and IL-1β in hospitalized COVID-19 patients upon admission to the Mount Sinai Health System in New York. Patients (n=1484) were followed up to 41 days (median 8 days) and clinical information, laboratory test results and patient outcomes were collected. In 244 patients, cytokine measurements were repeated over time, and effect of drugs could be assessed. Kaplan-Meier methods were used to compare survival by cytokine strata, followed by Cox regression models to evaluate the independent predictive value of baseline cytokines. We found that high serum IL-6, IL-8, and TNF-α levels at the time of hospitalization were strong and independent predictors of patient survival. Importantly, when adjusting for disease severity score, common laboratory inflammation markers, hypoxia and other vitals, demographics, and a range of comorbidities, IL-6 and TNF-α serum levels remained independent and significant predictors of disease severity and death. We propose that serum IL-6 and TNF-α levels should be considered in the management and treatment of COVID-19 patients to stratify prospective clinical trials, guide resource allocation and inform therapeutic options. We also propose that patients with high IL-6 and TNF-α levels should be assessed for combinatorial blockade of pathogenic inflammation in this disease.
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28
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Joseph GA, Hung M, Goel AJ, Hong M, Rieder MK, Beckmann ND, Serasinghe MN, Chipuk JE, Devarakonda PM, Goldhamer DJ, Aldana-Hernandez P, Curtis J, Jacobs RL, Krauss RS. Late-onset megaconial myopathy in mice lacking group I Paks. Skelet Muscle 2019; 9:5. [PMID: 30791960 PMCID: PMC6383276 DOI: 10.1186/s13395-019-0191-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Group I Paks are serine/threonine kinases that function as major effectors of the small GTPases Rac1 and Cdc42, and they regulate cytoskeletal dynamics, cell polarity, and transcription. We previously demonstrated that Pak1 and Pak2 function redundantly to promote skeletal myoblast differentiation during postnatal development and regeneration in mice. However, the roles of Pak1 and Pak2 in adult muscle homeostasis are unknown. Choline kinase β (Chk β) is important for adult muscle homeostasis, as autosomal recessive mutations in CHKβ are associated with two human muscle diseases, megaconial congenital muscular dystrophy and proximal myopathy with focal depletion of mitochondria. METHODS We analyzed mice conditionally lacking Pak1 and Pak2 in the skeletal muscle lineage (double knockout (dKO) mice) over 1 year of age. Muscle integrity in dKO mice was assessed with histological stains, immunofluorescence, electron microscopy, and western blotting. Assays for mitochondrial respiratory complex function were performed, as was mass spectrometric quantification of products of choline kinase. Mice and cultured myoblasts deficient for choline kinase β (Chk β) were analyzed for Pak1/2 phosphorylation. RESULTS dKO mice developed an age-related myopathy. By 10 months of age, dKO mouse muscles displayed centrally-nucleated myofibers, fibrosis, and signs of degeneration. Disease severity occurred in a rostrocaudal gradient, hindlimbs more strongly affected than forelimbs. A distinctive feature of this myopathy was elongated and branched intermyofibrillar (megaconial) mitochondria, accompanied by focal mitochondrial depletion in the central region of the fiber. dKO muscles showed reduced mitochondrial respiratory complex I and II activity. These phenotypes resemble those of rmd mice, which lack Chkβ and are a model for human diseases associated with CHKβ deficiency. Pak1/2 and Chkβ activities were not interdependent in mouse skeletal muscle, suggesting a more complex relationship in regulation of mitochondria and muscle homeostasis. CONCLUSIONS Conditional loss of Pak1 and Pak2 in mice resulted in an age-dependent myopathy with similarity to mice and humans with CHKβ deficiency. Protein kinases are major regulators of most biological processes but few have been implicated in muscle maintenance or disease. Pak1/Pak2 dKO mice offer new insights into these processes.
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Affiliation(s)
- Giselle A Joseph
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.,Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.,Present address: Novartis Institutes for BioMedical Research, 181 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Margaret Hung
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.,Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - Aviva J Goel
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.,Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - Mingi Hong
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - Marysia-Kolbe Rieder
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - Noam D Beckmann
- Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - Madhavika N Serasinghe
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parvathi M Devarakonda
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David J Goldhamer
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Paulina Aldana-Hernandez
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Jonathan Curtis
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - René L Jacobs
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Robert S Krauss
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA. .,Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.
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29
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Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, Ming C, Neff R, Ma W, Fullard JF, Hauberg ME, Bendl J, Peters MA, Logsdon B, Wang P, Mahajan M, Mangravite LM, Dammer EB, Duong DM, Lah JJ, Seyfried NT, Levey AI, Buxbaum JD, Ehrlich M, Gandy S, Katsel P, Haroutunian V, Schadt E, Zhang B. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease. Sci Data 2018; 5:180185. [PMID: 30204156 PMCID: PMC6132187 DOI: 10.1038/sdata.2018.185] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/20/2018] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD) affects half the US population over the age of 85 and is universally fatal following an average course of 10 years of progressive cognitive disability. Genetic and genome-wide association studies (GWAS) have identified about 33 risk factor genes for common, late-onset AD (LOAD), but these risk loci fail to account for the majority of affected cases and can neither provide clinically meaningful prediction of development of AD nor offer actionable mechanisms. This cohort study generated large-scale matched multi-Omics data in AD and control brains for exploring novel molecular underpinnings of AD. Specifically, we generated whole genome sequencing, whole exome sequencing, transcriptome sequencing and proteome profiling data from multiple regions of 364 postmortem control, mild cognitive impaired (MCI) and AD brains with rich clinical and pathophysiological data. All the data went through rigorous quality control. Both the raw and processed data are publicly available through the Synapse software platform.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - John F. Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Mads E. Hauberg
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus 8000, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Aarhus, 8000, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, 8000, Denmark
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Mette A. Peters
- Sage Bionetworks, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Ben Logsdon
- Sage Bionetworks, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | | | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph D. Buxbaum
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Michelle Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York NY 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
| | - Sam Gandy
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York NY 10029, USA
- The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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30
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Petyuk VA, Chang R, Ramirez-Restrepo M, Beckmann ND, Henrion MYR, Piehowski PD, Zhu K, Wang S, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, De Jager P, Schneider JA, Morris CM, McKeith IG, Perry RH, Lovestone S, Woltjer RL, Beach TG, Sue LI, Serrano GE, Lieberman AP, Albin RL, Ferrer I, Mash DC, Hulette CM, Ervin JF, Reiman EM, Hardy JA, Bennett DA, Schadt E, Smith RD, Myers AJ. The human brainome: network analysis identifies HSPA2 as a novel Alzheimer’s disease target. Brain 2018; 141:2721-2739. [PMID: 30137212 PMCID: PMC6136080 DOI: 10.1093/brain/awy215] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 11/24/2022] Open
Abstract
Our hypothesis is that changes in gene and protein expression are crucial to the development of late-onset Alzheimer’s disease. Previously we examined how DNA alleles control downstream expression of RNA transcripts and how those relationships are changed in late-onset Alzheimer’s disease. We have now examined how proteins are incorporated into networks in two separate series and evaluated our outputs in two different cell lines. Our pipeline included the following steps: (i) predicting expression quantitative trait loci; (ii) determining differential expression; (iii) analysing networks of transcript and peptide relationships; and (iv) validating effects in two separate cell lines. We performed all our analysis in two separate brain series to validate effects. Our two series included 345 samples in the first set (177 controls, 168 cases; age range 65–105; 58% female; KRONOSII cohort) and 409 samples in the replicate set (153 controls, 141 cases, 115 mild cognitive impairment; age range 66–107; 63% female; RUSH cohort). Our top target is heat shock protein family A member 2 (HSPA2), which was identified as a key driver in our two datasets. HSPA2 was validated in two cell lines, with overexpression driving further elevation of amyloid-β40 and amyloid-β42 levels in APP mutant cells, as well as significant elevation of microtubule associated protein tau and phosphorylated-tau in a modified neuroglioma line. This work further demonstrates that studying changes in gene and protein expression is crucial to understanding late onset disease and further nominates HSPA2 as a specific key regulator of late-onset Alzheimer’s disease processes.10.1093/brain/awy215_video1awy215media15824729224001.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rui Chang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manuel Ramirez-Restrepo
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Noam D Beckmann
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc Y R Henrion
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kuixi Zhu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sven Wang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer Clarke
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Fang Xie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Victor Andreev
- Arbor Research Collaborative for Health, 340 E Huron St # 300, Ann Arbor, MI, USA
| | - Anzhelika Engel
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Loida Navarro
- Roche Sequencing, 4300 Hacienda Drive, Pleasanton, CA, USA
| | - Philip De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- New York Genome Center, New York NY, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Christopher M Morris
- Newcastle Brain Tissue Resource, Institute of Neuroscience, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, UK
| | - Ian G McKeith
- NIHR Biomedical Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK
| | - Robert H Perry
- Neuropathology and Cellular Pathology, Royal Victoria Infirmary, Queen Victoria Road, Newcastle upon Tyne, UK
| | - Simon Lovestone
- University of Oxford, Medical Sciences Division, Department of Psychiatry, Warneford Hospital, Oxford, UK
| | - Randall L Woltjer
- Neuropathology Core of the Layton Aging and Alzheimer’s Disease Center, Oregon Health and Science University, Portland, OR, USA
| | | | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | | | | | - Roger L Albin
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Geriatrics Research, Education, and Clinical Center, VAAAHS, Ann Arbor, MI, USA
| | - Isidre Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona; CIBERNED; Hospitalet de Llobregat, Spain
| | - Deborah C Mash
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Christine M Hulette
- Department of Pathology, Division of Neuropathology, Duke University Medical Center, Durham, NC, USA
| | - John F Ervin
- Kathleen Price Bryan Brain Bank, Department of Medicine, Division of Neurology, Duke University, Durham, NC, USA
| | - Eric M Reiman
- The Arizona Alzheimer’s Consortium, Phoenix, Arizona, USA
- Banner Alzheimer’s Institute, Phoenix, Arizona, USA
| | - John A Hardy
- Department of Molecular Neuroscience and Reta Lila Research Laboratories, University College London Institute of Neurology, London, UK
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Eric Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Amanda J Myers
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdepartmental Program in Neuroscience, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdepartmental Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
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31
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Readhead B, Haure-Mirande JV, Funk CC, Richards MA, Shannon P, Haroutunian V, Sano M, Liang WS, Beckmann ND, Price ND, Reiman EM, Schadt EE, Ehrlich ME, Gandy S, Dudley JT. Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus. Neuron 2018; 99:64-82.e7. [PMID: 29937276 PMCID: PMC6551233 DOI: 10.1016/j.neuron.2018.05.023] [Citation(s) in RCA: 418] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/05/2018] [Accepted: 05/15/2018] [Indexed: 12/13/2022]
Abstract
Investigators have long suspected that pathogenic microbes might contribute to the onset and progression of Alzheimer's disease (AD) although definitive evidence has not been presented. Whether such findings represent a causal contribution, or reflect opportunistic passengers of neurodegeneration, is also difficult to resolve. We constructed multiscale networks of the late-onset AD-associated virome, integrating genomic, transcriptomic, proteomic, and histopathological data across four brain regions from human post-mortem tissue. We observed increased human herpesvirus 6A (HHV-6A) and human herpesvirus 7 (HHV-7) from subjects with AD compared with controls. These results were replicated in two additional, independent and geographically dispersed cohorts. We observed regulatory relationships linking viral abundance and modulators of APP metabolism, including induction of APBB2, APPBP2, BIN1, BACE1, CLU, PICALM, and PSEN1 by HHV-6A. This study elucidates networks linking molecular, clinical, and neuropathological features with viral activity and is consistent with viral activity constituting a general feature of AD.
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Affiliation(s)
- Ben Readhead
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Jean-Vianney Haure-Mirande
- Department of Neurology, Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, 98109-5263, USA
| | | | - Paul Shannon
- Institute for Systems Biology, Seattle, WA, 98109-5263, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters VA Medical Center, 130 West Kingsbridge Road, New York, NY 10468, USA
| | - Mary Sano
- James J. Peters VA Medical Center, 130 West Kingsbridge Road, New York, NY 10468, USA; Department of Psychiatry, Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Winnie S Liang
- Arizona Alzheimer's Consortium, Phoenix, AZ 85014, USA; Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Noam D Beckmann
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, 98109-5263, USA
| | - Eric M Reiman
- Arizona Alzheimer's Consortium, Phoenix, AZ 85014, USA; Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Department of Psychiatry, University of Arizona, Phoenix, AZ 85721, USA; Banner Alzheimer's Institute, Phoenix, AZ 85006, USA
| | - Eric E Schadt
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, Stamford, CT 06902, USA
| | - Michelle E Ehrlich
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sam Gandy
- Department of Neurology, Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters VA Medical Center, 130 West Kingsbridge Road, New York, NY 10468, USA; Department of Psychiatry, Alzheimer's Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for NFL Neurological Care, Department of Neurology, New York, NY 10029, USA
| | - Joel T Dudley
- Departments of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomic Sciences and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85287-5001, USA.
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32
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Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics 2017; 32:i101-i110. [PMID: 27307606 PMCID: PMC4908366 DOI: 10.1093/bioinformatics/btw282] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Li Li
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marcus A Badgeley
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Khader Shameer
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Nam Pho
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02115 MA, USA
| | - Jörg Hakenberg
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Meng Ma
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Kristin L Ayers
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Shuyu Dan Li
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02115 MA, USA
| | - Rong Chen
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences Icahn Institute for Genomics and Multiscale Biology Harris Center for Precision Wellness, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA Department of Population Health Science and Policy, New York City, NY 10029, USA
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33
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Epel ES, Puterman E, Lin J, Blackburn EH, Lum PY, Beckmann ND, Zhu J, Lee E, Gilbert A, Rissman RA, Tanzi RE, Schadt EE. Meditation and vacation effects have an impact on disease-associated molecular phenotypes. Transl Psychiatry 2016; 6:e880. [PMID: 27576169 PMCID: PMC5022094 DOI: 10.1038/tp.2016.164] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 07/07/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023] Open
Abstract
Meditation is becoming increasingly practiced, especially for stress-related medical conditions. Meditation may improve cellular health; however, studies have not separated out effects of meditation from vacation-like effects in a residential randomized controlled trial. We recruited healthy women non-meditators to live at a resort for 6 days and randomized to either meditation retreat or relaxing on-site, with both groups compared with 'regular meditators' already enrolled in the retreat. Blood drawn at baseline and post intervention was assessed for transcriptome-wide expression patterns and aging-related biomarkers. Highly significant gene expression changes were detected across all groups (the 'vacation effect') that could accurately predict (96% accuracy) between baseline and post-intervention states and were characterized by improved regulation of stress response, immune function and amyloid beta (Aβ) metabolism. Although a smaller set of genes was affected, regular meditators showed post-intervention differences in a gene network characterized by lower regulation of protein synthesis and viral genome activity. Changes in well-being were assessed post intervention relative to baseline, as well as 1 and 10 months later. All groups showed equivalently large immediate post-intervention improvements in well-being, but novice meditators showed greater maintenance of lower distress over time compared with those in the vacation arm. Regular meditators showed a trend toward increased telomerase activity compared with randomized women, who showed increased plasma Aβ42/Aβ40 ratios and tumor necrosis factor alpha (TNF-α) levels. This highly controlled residential study showed large salutary changes in gene expression networks due to the vacation effect, common to all groups. For those already trained in the practice of meditation, a retreat appears to provide additional benefits to cellular health beyond the vacation effect.
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Affiliation(s)
- E S Epel
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - E Puterman
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - J Lin
- Departments of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - E H Blackburn
- Departments of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - P Y Lum
- Capella Biosciences Inc., Palo Alto, CA, USA
| | - N D Beckmann
- Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA
| | - J Zhu
- Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA
| | - E Lee
- Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA
| | - A Gilbert
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - R A Rissman
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - R E Tanzi
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, USA
| | - E E Schadt
- Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA
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34
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Myers A, Chang R, Petyuk VA, Ramirez-Restrepo M, Beckmann ND, Henrion MY, Zhu K, Wang S, Piehowski PD, Clarke J, Huentelman MJ, Xie F, Andreev V, Engel A, Guettoche T, Navarro L, Jager P, Schneider JA, Morris CM, McKeith IG, Perry RH, Lovestone S, Woltjer RL, Beach TG, Sue L, Lieberman AP, Albin RL, Abizanda IF, Mash DC, Hulette CM, Ervin JF, Hardy JA, Reiman EM, Bennett DA, Schadt E, Smith R. O2‐06‐01: The Human Brainome: Human Brain Genome, Transcriptome, and Proteome Integration. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Rui Chang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Vladislav A. Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National LaboratoryRichlandWA USA
| | - Manuel Ramirez-Restrepo
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of MedicineMiamiFL USA
| | - Noam D. Beckmann
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Marc Y.R. Henrion
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Kuixi Zhu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Sven Wang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Paul D. Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National LaboratoryRichlandWA USA
| | - Jennifer Clarke
- Food Science and Technology Department University of Nebraska-LincolnLincolnNE USA
| | - Matthew J. Huentelman
- Neurogenomics Division The Translational Genomics Research Institute (TGen)PhoenixAZ USA
| | - Fang Xie
- Amgen Inc One Amgen Center DriveThousand OaksCA USA
| | | | - Anzhelika Engel
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of MedicineMiamiFL USA
| | | | - Loida Navarro
- Oncogenomics Core Facility, Sylvester Comprehensive Cancer Center University of Miami, Miller School of MedicineMiamiFL USA
| | - Philip Jager
- Broad InstituteCambridgeMA USA
- Brigham and Women’s HospitalBostonMA USA
- Harvard Medical SchoolBostonMA USA
| | | | - Christopher M. Morris
- Medical Toxicology Centre Institute of Neuroscience and the Institute for Ageing and HealthNewcastle upon Tyne United Kingdom
| | - Ian G. McKeith
- Institute for Ageing and Health Newcastle University, Wolfson Research Centre, Campus for Ageing and VitalityNewcastle upon Tyne United Kingdom
| | - Robert H. Perry
- Neuropathology and Cellular Pathology Crawford House Royal Victoria InfirmaryQueen Victoria Road Newcastle upon Tyne United Kingdom
| | | | | | | | - Lucia Sue
- Banner Sun Health Research InstituteSun CityAZ USA
| | | | - Roger L. Albin
- Department of Neurology University of MichiganAnn ArborMI USA
- Geriatrics Research, Education and Clinical Center, VAAAHSAnn ArborMI USA
| | | | | | - Christine M. Hulette
- Department of Pathology, Division of Neuropathology Duke University Medical CenterDurhamNC USA
| | - John F. Ervin
- Kathleen Price Bryan Brain Bank, Department of Medicine, Division of Neurology Duke University, Duke University Medical CenterDurhamNC USA
| | - John A. Hardy
- Department of Molecular Neuroscience and Reta Lila Research Laboratories University College London Institute of NeurologyLondonUnited Kingdom
| | | | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical CenterChicagoIL USA
| | - Eric Schadt
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Richard Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National LaboratoryRichlandWA USA
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Rykunov D, Beckmann ND, Li H, Uzilov A, Schadt EE, Reva B. A new molecular signature method for prediction of driver cancer pathways from transcriptional data. Nucleic Acids Res 2016; 44:e110. [PMID: 27098033 PMCID: PMC4914110 DOI: 10.1093/nar/gkw269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 04/02/2016] [Indexed: 01/01/2023] Open
Abstract
Assigning cancer patients to the most effective treatments requires an understanding of the molecular basis of their disease. While DNA-based molecular profiling approaches have flourished over the past several years to transform our understanding of driver pathways across a broad range of tumors, a systematic characterization of key driver pathways based on RNA data has not been undertaken. Here we introduce a new approach for predicting the status of driver cancer pathways based on signature functions derived from RNA sequencing data. To identify the driver cancer pathways of interest, we mined DNA variant data from TCGA and nominated driver alterations in seven major cancer pathways in breast, ovarian and colon cancer tumors. The activation status of these driver pathways were then characterized using RNA sequencing data by constructing classification signature functions in training datasets and then testing the accuracy of the signatures in test datasets. The signature functions differentiate well tumors with nominated pathway activation from tumors with no signs of activation: average AUC equals to 0.83. Our results confirm that driver genomic alterations are distinctively displayed at the transcriptional level and that the transcriptional signatures can generally provide an alternative to DNA sequencing methods in detecting specific driver pathways.
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Affiliation(s)
- Dmitry Rykunov
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
| | - Noam D Beckmann
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
| | - Hui Li
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
| | - Andrew Uzilov
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
| | - Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
| | - Boris Reva
- Icahn Institute for Genomics and Multiscale Biology, New York, 10029, USA
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Abstract
Background It has recently become possible to rapidly and accurately detect epigenetic signatures in bacterial genomes using third generation sequencing data. Monitoring the speed at which a single polymerase inserts a base in the read strand enables one to infer whether a modification is present at that specific site on the template strand. These sites can be challenging to detect in the absence of high coverage and reliable reference genomes. Methods Here we provide a new method for detecting epigenetic motifs in bacteria on datasets with low-coverage, with incomplete references, and with mixed samples (i.e. metagenomic data). Our approach treats motif inference as a kmer comparison problem. First, genomes (or contigs) are deconstructed into kmers. Then, native genome-wide distributions of interpulse durations (IPDs) for kmers are compared with corresponding whole genome amplified (WGA, modification free) IPD distributions using log likelihood ratios. Finally, kmers are ranked and greedily selected by iteratively correcting for sequences within a particular kmer's neighborhood. Conclusions Our method can detect multiple types of modifications, even at very low-coverage and in the presence of mixed genomes. Additionally, we are able to predict modified motifs when genomes with "neighbor" modified motifs exist within the sample. Lastly, we show that these motifs can provide an alternative source of information by which to cluster metagenomics contigs and that iterative refinement on these clustered contigs can further improve both sensitivity and specificity of motif detection. Availability https://github.com/alibashir/EMMCKmer
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Zufferey F, Sherr EH, Beckmann ND, Hanson E, Maillard AM, Hippolyte L, Macé A, Ferrari C, Kutalik Z, Andrieux J, Aylward E, Barker M, Bernier R, Bouquillon S, Conus P, Delobel B, Faucett WA, Goin-Kochel RP, Grant E, Harewood L, Hunter JV, Lebon S, Ledbetter DH, Martin CL, Männik K, Martinet D, Mukherjee P, Ramocki MB, Spence SJ, Steinman KJ, Tjernagel J, Spiro JE, Reymond A, Beckmann JS, Chung WK, Jacquemont S. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders. J Med Genet 2013; 49:660-8. [PMID: 23054248 PMCID: PMC3494011 DOI: 10.1136/jmedgenet-2012-101203] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background The recurrent ∼600 kb 16p11.2 BP4-BP5 deletion is among the most frequent known genetic aetiologies of autism spectrum disorder (ASD) and related neurodevelopmental disorders. Objective To define the medical, neuropsychological, and behavioural phenotypes in carriers of this deletion. Methods We collected clinical data on 285 deletion carriers and performed detailed evaluations on 72 carriers and 68 intrafamilial non-carrier controls. Results When compared to intrafamilial controls, full scale intelligence quotient (FSIQ) is two standard deviations lower in carriers, and there is no difference between carriers referred for neurodevelopmental disorders and carriers identified through cascade family testing. Verbal IQ (mean 74) is lower than non-verbal IQ (mean 83) and a majority of carriers require speech therapy. Over 80% of individuals exhibit psychiatric disorders including ASD, which is present in 15% of the paediatric carriers. Increase in head circumference (HC) during infancy is similar to the HC and brain growth patterns observed in idiopathic ASD. Obesity, a major comorbidity present in 50% of the carriers by the age of 7 years, does not correlate with FSIQ or any behavioural trait. Seizures are present in 24% of carriers and occur independently of other symptoms. Malformations are infrequently found, confirming only a few of the previously reported associations. Conclusions The 16p11.2 deletion impacts in a quantitative and independent manner FSIQ, behaviour and body mass index, possibly through direct influences on neural circuitry. Although non-specific, these features are clinically significant and reproducible. Lastly, this study demonstrates the necessity of studying large patient cohorts ascertained through multiple methods to characterise the clinical consequences of rare variants involved in common diseases.
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Affiliation(s)
- Flore Zufferey
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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38
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Kollerits B, Coassin S, Beckmann ND, Teumer A, Kiechl S, Döring A, Kavousi M, Hunt SC, Lamina C, Paulweber B, Kutalik Z, Nauck M, van Duijn CM, Heid IM, Willeit J, Brandstätter A, Adams TD, Mooser V, Aulchenko YS, Völzke H, Kronenberg F. Genetic evidence for a role of adiponutrin in the metabolism of apolipoprotein B-containing lipoproteins. Hum Mol Genet 2009; 18:4669-76. [PMID: 19729411 DOI: 10.1093/hmg/ddp424] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adiponutrin (PNPLA3) is a predominantly liver-expressed transmembrane protein with phospholipase activity that is regulated by fasting and feeding. Recent genome-wide association studies identified PNPLA3 to be associated with hepatic fat content and liver function, thus pointing to a possible involvement in the hepatic lipoprotein metabolism. The aim of this study was to examine the association between two common variants in the adiponutrin gene and parameters of lipoprotein metabolism in 23,274 participants from eight independent West-Eurasian study populations including six population-based studies [Bruneck (n = 800), KORA S3/F3 (n = 1644), KORA S4/F4 (n = 1814), CoLaus (n = 5435), SHIP (n = 4012), Rotterdam (n = 5967)], the SAPHIR Study as a healthy working population (n = 1738) and the Utah Obesity Case-Control Study including a group of 1037 severely obese individuals (average BMI 46 kg/m2) and 827 controls from the same geographical region of Utah. We observed a strong additive association of a common non-synonymous variant within adiponutrin (rs738409) with age-, gender-, and alanine-aminotransferase-adjusted lipoprotein concentrations: each copy of the minor allele decreased levels of total cholesterol on average by 2.43 mg/dl (P = 8.87 x 10(-7)), non-HDL cholesterol levels by 2.35 mg/dl (P = 2.27 x 10(-6)) and LDL cholesterol levels by 1.48 mg/dl (P = 7.99 x 10(-4)). These associations remained significant after correction for multiple testing. We did not observe clear evidence for associations with HDL cholesterol or triglyceride concentrations. In conclusion, our study suggests that adiponutrin is involved in the metabolism of apoB-containing lipoproteins.
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Affiliation(s)
- Barbara Kollerits
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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Yuan X, Waterworth D, Perry JRB, Lim N, Song K, Chambers JC, Zhang W, Vollenweider P, Stirnadel H, Johnson T, Bergmann S, Beckmann ND, Li Y, Ferrucci L, Melzer D, Hernandez D, Singleton A, Scott J, Elliott P, Waeber G, Cardon L, Frayling TM, Kooner JS, Mooser V. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Am J Hum Genet 2008. [PMID: 18940312 DOI: 10.1016/j.ajhg.2008.09.012.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Plasma liver-enzyme tests are widely used in the clinic for the diagnosis of liver diseases and for monitoring the response to drug treatment. There is considerable evidence that human genetic variation influences plasma levels of liver enzymes. However, such genetic variation has not been systematically assessed. In the present study, we performed a genome-wide association study of plasma liver-enzyme levels in three populations (total n = 7715) with replication in three additional cohorts (total n = 4704). We identified two loci influencing plasma levels of alanine-aminotransferase (ALT) (CPN1-ERLIN1-CHUK on chromosome 10 and PNPLA3-SAMM50 on chromosome 22), one locus influencing gamma-glutamyl transferase (GGT) levels (HNF1A on chromosome 12), and three loci for alkaline phosphatase (ALP) levels (ALPL on chromosome 1, GPLD1 on chromosome 6, and JMJD1C-REEP3 on chromosome 10). In addition, we confirmed the associations between the GGT1 locus and GGT levels and between the ABO locus and ALP levels. None of the ALP-associated SNPs were associated with other liver tests, suggesting intestine and/or bone specificity. The mechanisms underlying the associations may involve cis- or trans-transcriptional effects (some of the identified variants were associated with mRNA transcription in human liver or lymphoblastoid cells), dysfunction of the encoded proteins (caused by missense variations at the functional domains), or other unknown pathways. These findings may help in the interpretation of liver-enzyme tests and provide candidate genes for liver diseases of viral, metabolic, autoimmune, or toxic origin. The specific associations with ALP levels may point to genes for bone or intestinal diseases.
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Affiliation(s)
- Xin Yuan
- Genetics Division, GlaxoSmithKline, King of Prussia, PA 19406, USA
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Yuan X, Waterworth D, Perry JRB, Lim N, Song K, Chambers JC, Zhang W, Vollenweider P, Stirnadel H, Johnson T, Bergmann S, Beckmann ND, Li Y, Ferrucci L, Melzer D, Hernandez D, Singleton A, Scott J, Elliott P, Waeber G, Cardon L, Frayling TM, Kooner JS, Mooser V. Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Am J Hum Genet 2008; 83:520-8. [PMID: 18940312 DOI: 10.1016/j.ajhg.2008.09.012] [Citation(s) in RCA: 350] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Revised: 09/16/2008] [Accepted: 09/16/2008] [Indexed: 12/13/2022] Open
Abstract
Plasma liver-enzyme tests are widely used in the clinic for the diagnosis of liver diseases and for monitoring the response to drug treatment. There is considerable evidence that human genetic variation influences plasma levels of liver enzymes. However, such genetic variation has not been systematically assessed. In the present study, we performed a genome-wide association study of plasma liver-enzyme levels in three populations (total n = 7715) with replication in three additional cohorts (total n = 4704). We identified two loci influencing plasma levels of alanine-aminotransferase (ALT) (CPN1-ERLIN1-CHUK on chromosome 10 and PNPLA3-SAMM50 on chromosome 22), one locus influencing gamma-glutamyl transferase (GGT) levels (HNF1A on chromosome 12), and three loci for alkaline phosphatase (ALP) levels (ALPL on chromosome 1, GPLD1 on chromosome 6, and JMJD1C-REEP3 on chromosome 10). In addition, we confirmed the associations between the GGT1 locus and GGT levels and between the ABO locus and ALP levels. None of the ALP-associated SNPs were associated with other liver tests, suggesting intestine and/or bone specificity. The mechanisms underlying the associations may involve cis- or trans-transcriptional effects (some of the identified variants were associated with mRNA transcription in human liver or lymphoblastoid cells), dysfunction of the encoded proteins (caused by missense variations at the functional domains), or other unknown pathways. These findings may help in the interpretation of liver-enzyme tests and provide candidate genes for liver diseases of viral, metabolic, autoimmune, or toxic origin. The specific associations with ALP levels may point to genes for bone or intestinal diseases.
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Affiliation(s)
- Xin Yuan
- Genetics Division, GlaxoSmithKline, King of Prussia, PA 19406, USA
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