51
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Medini H, Zirman A, Mishmar D. Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring toward glycolysis. iScience 2021; 24:103471. [PMID: 34812416 PMCID: PMC8599136 DOI: 10.1016/j.isci.2021.103471] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/15/2021] [Accepted: 11/14/2021] [Indexed: 01/06/2023] Open
Abstract
Mitochondria are pivotal for bioenergetics, as well as in cellular response to viral infections. Nevertheless, their role in COVID-19 was largely overlooked. Here, we analyzed available bulk RNA-seq datasets from COVID-19 patients and corresponding healthy controls (three blood datasets, N = 48 healthy, 119 patients; two respiratory tract datasets, N = 157 healthy, 524 patients). We found significantly reduced mtDNA gene expression in blood, but not in respiratory tract samples from patients. Next, analysis of eight single-cells RNA-seq datasets from peripheral blood mononuclear cells, nasopharyngeal samples, and Bronchoalveolar lavage fluid (N = 1,192,243 cells), revealed significantly reduced mtDNA gene expression especially in immune system cells from patients. This is associated with elevated expression of nuclear DNA-encoded OXPHOS subunits, suggesting compromised mitochondrial-nuclear co-regulation. This, together with elevated expression of ROS-response genes and glycolysis enzymes in patients, suggest rewiring toward glycolysis, thus generating beneficial conditions for SARS-CoV-2 replication. Our findings underline the centrality of mitochondrial dysfunction in COVID-19. mtDNA gene expression is downregulated in COVID-19 blood, but not in respiratory tract Decreased mtDNA gene expression disrupts mito-nuclear coordination mtDNA is downregulated and rewired toward glycolysis especially in immune system cells Mitochondrial dysfunction is central to the etiology of COVID19
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Affiliation(s)
- Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Building 40, Room 009, Beer-Sheva 84105, Israel
| | - Amit Zirman
- Department of Life Sciences, Ben-Gurion University of the Negev, Building 40, Room 009, Beer-Sheva 84105, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Building 40, Room 009, Beer-Sheva 84105, Israel
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52
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Almansa R, Herrero-Rodríguez C, Martínez-Huélamo M, Vicente-Andres MDP, Nieto-Barbero JA, Martín-Ballesteros M, Rodilla-Carvajal MDM, de la Fuente A, Ortega A, Alonso-Ramos MJ, Wacker J, Liesenfeld O, Sweeney TE, Bermejo-Martin JF, García-Ortiz L. A host transcriptomic signature for identification of respiratory viral infections in the community. Eur J Clin Invest 2021; 51:e13626. [PMID: 34120332 DOI: 10.1111/eci.13626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Fever-7 is a test evaluating host mRNA expression levels of IFI27, JUP, LAX, HK3, TNIP1, GPAA1 and CTSB in blood able to detect viral infections. This test has been validated mostly in hospital settings. Here we have evaluated Fever-7 to identify the presence of respiratory viral infections in a Community Health Center. METHODS A prospective study was conducted in the "Servicio de Urgencias de Atención Primaria" in Salamanca, Spain. Patients with clinical signs of respiratory infection and at least one point in the National Early Warning Score were recruited. Fever-7 mRNAs were profiled on a Nanostring nCounter® SPRINT instrument from blood collected upon patient enrolment. Viral diagnosis was performed on nasopharyngeal aspirates (NPAs) using the Biofire-RP2 panel. RESULTS A respiratory virus was detected in the NPAs of 66 of the 100 patients enrolled. Median National Early Warning Score was 7 in the group with no virus detected and 6.5 in the group with a respiratory viral infection (P > .05). The Fever-7 score yielded an overall AUC of 0.81 to predict a positive viral syndromic test. The optimal operating point for the Fever-7 score yielded a sensitivity of 82% with a specificity of 71%. Multivariate analysis showed that Fever-7 was a robust marker of viral infection independently of age, sex, major comorbidities and disease severity at presentation (OR [CI95%], 3.73 [2.14-6.51], P < .001). CONCLUSIONS Fever-7 is a promising host immune mRNA signature for the early identification of a respiratory viral infection in the community.
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Affiliation(s)
- Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Herrero-Rodríguez
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain.,Unidad de Investigación en Atención Primaria de Salamanca (APISAL), Instituto de investigación Biomédica de Salamanca (IBSAL), Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Misericordia Martínez-Huélamo
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Maria Del Pilar Vicente-Andres
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Jose Angel Nieto-Barbero
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Miryam Martín-Ballesteros
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Maria Del Mar Rodilla-Carvajal
- Servicio de Urgencias de Atención Primaria de Salamanca (SUAP). Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Maria Jesus Alonso-Ramos
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain
| | | | | | | | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud, Salamanca, Spain.,Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis García-Ortiz
- Unidad de Investigación en Atención Primaria de Salamanca (APISAL), Instituto de investigación Biomédica de Salamanca (IBSAL), Gerencia de Atención Primaria de Salamanca, Gerencia Regional de salud de Castilla y León (SACyL), Salamanca, Spain.,Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, Spain
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53
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Sakaram S, Hasin-Brumshtein Y, Khatri P, He YD, Sweeney TE. A Multi-mRNA Prognostic Signature for Anti-TNFα Therapy Response in Patients with Inflammatory Bowel Disease. Diagnostics (Basel) 2021; 11:1902. [PMID: 34679598 PMCID: PMC8534494 DOI: 10.3390/diagnostics11101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Anti-TNF-alpha (anti-TNFα) therapies have transformed the care and management of inflammatory bowel disease (IBD). However, they are expensive and ineffective in greater than 50% of patients, and they increase the risk of infections, liver issues, arthritis, and lymphoma. With 1.6 million Americans suffering from IBD and global prevalence on the rise, there is a critical unmet need in the use of anti-TNFα therapies: a test for the likelihood of therapy response. Here, as a proof-of-concept, we present a multi-mRNA signature for predicting response to anti-TNFα treatment to improve the efficacy and cost-to-benefit ratio of these biologics. METHODS We surveyed public data repositories and curated four transcriptomic datasets (n = 136) from colonic and ileal mucosal biopsies of IBD patients (pretreatment) who were subjected to anti-TNFα therapy and subsequently adjudicated for response. We applied a multicohort analysis with a leave-one-study-out (LOSO) approach, MetaIntegrator, to identify significant differentially expressed (DE) genes between responders and non-responders and then used a greedy forward search to identify a parsimonious gene signature. We then calculated an anti-TNFα response (ATR) score based on this parsimonious gene signature to predict responder status and assessed discriminatory performance via an area-under-receiver operating-characteristic curve (AUROC). RESULTS We identified 324 significant DE genes between responders and non-responders. The greedy forward search yielded seven genes that robustly distinguish anti-TNFα responders from non-responders, with an AUROC of 0.88 (95% CI: 0.70-1). The Youden index yielded a mean sensitivity of 91%, mean specificity of 76%, and mean accuracy of 86%. CONCLUSIONS Our findings suggest that there is a robust transcriptomic signature for predicting anti-TNFα response in mucosal biopsies from IBD patients prior to treatment initiation. This seven-gene signature should be further investigated for its potential to be translated into a predictive test for clinical use.
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Affiliation(s)
- Suraj Sakaram
- Inflammatix, Inc., 863 Mitten Rd., Suite 104, Burlingame, CA 94010, USA; (S.S.); (Y.H.-B.)
| | | | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA 94305, USA;
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yudong D. He
- Inflammatix, Inc., 863 Mitten Rd., Suite 104, Burlingame, CA 94010, USA; (S.S.); (Y.H.-B.)
| | - Timothy E. Sweeney
- Inflammatix, Inc., 863 Mitten Rd., Suite 104, Burlingame, CA 94010, USA; (S.S.); (Y.H.-B.)
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54
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Zhang W, Zhang Y, Min Z, Mo J, Ju Z, Guan W, Zeng B, Liu Y, Chen J, Zhang Q, Li H, Zeng C, Wei Y, Chan GCF. COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. Nucleic Acids Res 2021; 50:D747-D757. [PMID: 34554255 PMCID: PMC8728200 DOI: 10.1093/nar/gkab850] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/26/2022] Open
Abstract
Many open access transcriptomic data of coronavirus disease 2019 (COVID-19) were generated, they have great heterogeneity and are difficult to analyze. To utilize these invaluable data for better understanding of COVID-19, additional software should be developed. Especially for researchers without bioinformatic skills, a user-friendly platform is mandatory. We developed the COVID19db platform (http://hpcc.siat.ac.cn/covid19db & http://www.biomedical-web.com/covid19db) that provides 39 930 drug–target–pathway interactions and 95 COVID-19 related datasets, which include transcriptomes of 4127 human samples across 13 body sites associated with the exposure of 33 microbes and 33 drugs/agents. To facilitate data application, each dataset was standardized and annotated with rich clinical information. The platform further provides 14 different analytical applications to analyze various mechanisms underlying COVID-19. Moreover, the 14 applications enable researchers to customize grouping and setting for different analyses and allow them to perform analyses using their own data. Furthermore, a Drug Discovery tool is designed to identify potential drugs and targets at whole transcriptomic scale. For proof of concept, we used COVID19db and identified multiple potential drugs and targets for COVID-19. In summary, COVID19db provides user-friendly web interfaces to freely analyze, download data, and submit new data for further integration, it can accelerate the identification of effective strategies against COVID-19.
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Affiliation(s)
- Wenliang Zhang
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China
| | - Yan Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China
| | - Zhuochao Min
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jing Mo
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China
| | - Zhen Ju
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Wen Guan
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Binghui Zeng
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China.,Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yang Liu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China
| | - Jianliang Chen
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China
| | - Qianshen Zhang
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China
| | - Hanguang Li
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China
| | - Chunxia Zeng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Godfrey Chi-Fung Chan
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong 518053, China.,Department of Pediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong 999077, China
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55
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Giannattasio A, Maglione M, D'Anna C, Muzzica S, Angrisani F, Acierno S, Perrella A, Tipo V. Silent RSV in infants with SARS-CoV-2 infection: A case series. Pediatr Pulmonol 2021; 56:3044-3046. [PMID: 34033702 PMCID: PMC8242430 DOI: 10.1002/ppul.25465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 02/05/2023]
Affiliation(s)
- Antonietta Giannattasio
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Marco Maglione
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Carolina D'Anna
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Stefania Muzzica
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Francesca Angrisani
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Sabrina Acierno
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Alessandro Perrella
- Cardarelli Hospital, Infectious Disease-Health Policy Direction, Naples, Italy
| | - Vincenzo Tipo
- Pediatric Emergency and Short Stay Unit, Santobono-Pausilipon Children's Hospital, Naples, Italy
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56
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Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9998697. [PMID: 34457122 PMCID: PMC8397550 DOI: 10.1155/2021/9998697] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022]
Abstract
The pandemic of the coronavirus disease 2019 (COVID-19) has posed huge threats to healthcare systems and the global economy. However, the host response towards COVID-19 on the molecular and cellular levels still lacks full understanding and effective therapies are in urgent need. Here, we integrate three datasets, GSE152641, GSE161777, and GSE157103. Compared to healthy people, 314 differentially expressed genes were identified, which were mostly involved in neutrophil degranulation and cell division. The protein-protein network was established and two significant subsets were filtered by MCODE: ssGSEA and CIBERSORT, which comprehensively revealed the alternation of immune cell abundance. Weighted gene coexpression network analysis (WGCNA) as well as GO and KEGG analyses unveiled the role of neutrophils and T cells during the progress of the disease. Based on the hospital-free days after 45 days of follow-up and statistical methods such as nonnegative matrix factorization (NMF), submap, and linear correlation analysis, 31 genes were regarded as the signature of the peripheral blood of COVID-19. Various immune cells were identified to be related to the prognosis of the patients. Drugs were predicted for the genes in the signature by DGIdb. Overall, our study comprehensively revealed the relationship between the inflammatory response and the disease course, which provided strategies for the treatment of COVID-19.
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57
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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] [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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58
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Meng F, Siu GKH, Mok BWY, Sun J, Fung KSC, Lam JYW, Wong NK, Gedefaw L, Luo S, Lee TMH, Yip SP, Huang CL. Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells. Cells 2021; 10:1762. [PMID: 34359932 PMCID: PMC8307234 DOI: 10.3390/cells10071762] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression that may be used to identify the pathological pathways influenced by disease and cellular interactions. Viral miRNAs (v-miRNAs) encoded by both DNA and RNA viruses induce immune dysregulation, virus production, and disease pathogenesis. Given the absence of effective treatment and the prevalence of highly infective SARS-CoV-2 strains, improved understanding of viral-associated miRNAs could provide novel mechanistic insights into the pathogenesis of COVID-19. In this study, SARS-CoV-2 v-miRNAs were identified by deep sequencing in infected Calu-3 and Vero E6 cell lines. Among the ~0.1% small RNA sequences mapped to the SARS-CoV-2 genome, the top ten SARS-CoV-2 v-miRNAs (including three encoded by the N gene; v-miRNA-N) were selected. After initial screening of conserved v-miRNA-N-28612, which was identified in both SARS-CoV and SARS-CoV-2, its expression was shown to be positively associated with viral load in COVID-19 patients. Further in silico analysis and synthetic-mimic transfection of validated SARS-CoV-2 v-miRNAs revealed novel functional targets and associations with mechanisms of cellular metabolism and biosynthesis. Our findings support the development of v-miRNA-based biomarkers and therapeutic strategies based on improved understanding of the pathophysiology of COVID-19.
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Affiliation(s)
- Fei Meng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Bobo Wing-Yee Mok
- Department of Microbiology, The University of Hong Kong, Hong Kong, China;
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Jiahong Sun
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong, China;
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China;
| | - Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Thomas M. H. Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China;
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
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59
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A single transcript for the prognosis of disease severity in COVID-19 patients. Sci Rep 2021; 11:12174. [PMID: 34108608 PMCID: PMC8190311 DOI: 10.1038/s41598-021-91754-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
With many countries strapped for medical resources due to the COVID-19 pandemic, it is highly desirable to allocate the precious resources to those who need them the most. Several markers have been found to be associated with the disease severity in COVID-19 patients. However, the established markers only display modest prognostic power individually and better markers are urgently needed. The aim of this study is to investigate the potential of S100A12, a prominent marker gene for bacterial infection, in the prognosis of disease severity in COVID-19 patients. To ensure the robustness of the association, a total of 1695 samples from 14 independent transcriptome datasets on sepsis, influenza infection and COVID-19 infection were examined. First, it was demonstrated that S100A12 was a marker for sepsis and severity of sepsis. Then, S100A12 was found to be a marker for severe influenza infection, and there was an upward trend of S100A12 expression as the severity level of influenza infection increased. As for COVID-19 infection, it was found that S100A12 expression was elevated in patients with severe and critical COVID-19 infection. More importantly, S100A12 expression at hospital admission was robustly correlated with future quantitative indexes of disease severity and outcome in COVID-19 patients, superior to established prognostic markers including CRP, PCT, d-dimer, ferritin, LDH and fibrinogen. Thus, S100A12 is a valuable novel prognostic marker for COVID-19 severity and deserves more attention.
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60
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Zheng H, Rao AM, Dermadi D, Toh J, Murphy Jones L, Donato M, Liu Y, Su Y, Dai CL, Kornilov SA, Karagiannis M, Marantos T, Hasin-Brumshtein Y, He YD, Giamarellos-Bourboulis EJ, Heath JR, Khatri P. Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses. Immunity 2021; 54:753-768.e5. [PMID: 33765435 PMCID: PMC7988739 DOI: 10.1016/j.immuni.2021.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
Viral infections induce a conserved host response distinct from bacterial infections. We hypothesized that the conserved response is associated with disease severity and is distinct between patients with different outcomes. To test this, we integrated 4,780 blood transcriptome profiles from patients aged 0 to 90 years infected with one of 16 viruses, including SARS-CoV-2, Ebola, chikungunya, and influenza, across 34 cohorts from 18 countries, and single-cell RNA sequencing profiles of 702,970 immune cells from 289 samples across three cohorts. Severe viral infection was associated with increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells. We identified protective and detrimental gene modules that defined distinct trajectories associated with mild versus severe outcomes. The interferon response was decoupled from the protective host response in patients with severe outcomes. These findings were consistent, irrespective of age and virus, and provide insights to accelerate the development of diagnostics and host-directed therapies to improve global pandemic preparedness.
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Affiliation(s)
- Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Aditya M Rao
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Jiaying Toh
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Immunology program, Stanford University, CA 94305, USA
| | - Lara Murphy Jones
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA; Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Stanford University, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA
| | - Yiran Liu
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Cancer Biology program, Stanford University, CA 94305, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Cheng L Dai
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Minas Karagiannis
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | - Theodoros Marantos
- 4(th) Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
| | | | | | | | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, CA 94305, USA.
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61
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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62
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Pang Z, Zhou G, Chong J, Xia J. Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets. Metabolites 2021; 11:44. [PMID: 33435351 PMCID: PMC7827862 DOI: 10.3390/metabo11010044] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 has spread across the world since 2019, causing a global pandemic. The pathogenesis of the viral infection and the associated clinical presentations depend primarily on host factors such as age and immunity, rather than the viral load or its genetic variations. A growing number of omics studies have been conducted to characterize the host immune and metabolic responses underlying the disease progression. Meta-analyses of these datasets have great potential to identify robust molecular signatures to inform clinical care and to facilitate therapeutics development. In this study, we performed a comprehensive meta-analysis of publicly available global metabolomics datasets obtained from three countries (United States, China and Brazil). To overcome high heterogeneity inherent in these datasets, we have (a) implemented a computational pipeline to perform consistent raw spectra processing; (b) conducted meta-analyses at pathway levels instead of individual feature levels; and (c) performed visual data mining on consistent patterns of change between disease severities for individual studies. Our analyses have yielded several key metabolic signatures characterizing disease progression and clinical outcomes. Their biological interpretations were discussed within the context of the current literature. To the best of our knowledge, this is the first comprehensive meta-analysis of global metabolomics datasets of COVID-19.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (G.Z.); (J.C.)
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (G.Z.); (J.C.)
| | - Jasmine Chong
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (G.Z.); (J.C.)
| | - Jianguo Xia
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada; (Z.P.); (G.Z.); (J.C.)
- Department of Animal Science, McGill University, 21111 Lakeshore Road, Ste Anne de Bellevue, QC H9X 3V9, Canada
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63
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Suárez-Fariñas M, Tokuyama M, Wei G, Huang R, Livanos A, Jha D, Levescot A, Irizar H, Kosoy R, Cording S, Wang W, Losic B, Ungaro RC, Di’Narzo A, Martinez-Delgado G, Suprun M, Corley MJ, Stojmirovic A, Houten SM, Peters L, Curran M, Brodmerkel C, Perrigoue J, Friedman JR, Hao K, Schadt EE, Zhu J, Ko HM, Cho J, Dubinsky MC, Sands BE, Ndhlovu L, Cerf-Bensusan N, Kasarskis A, Colombel JF, Harpaz N, Argmann C, Mehandru S. Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2-related Disease. Gastroenterology 2021; 160:287-301.e20. [PMID: 32980345 PMCID: PMC7516468 DOI: 10.1053/j.gastro.2020.09.029] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication within enterocytes. METHODS Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation, and IBD treatment. RESULTS A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and nonbiologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. In addition, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. CONCLUSIONS These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19. Preprint doi: https://doi.org/10.1101/2020.05.21.109124.
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Affiliation(s)
- Mayte Suárez-Fariñas
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Minami Tokuyama
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gabrielle Wei
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Alexandra Livanos
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anais Levescot
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Haritz Irizar
- University College London, Department Mental Health Sciences Unit, London, UK
| | - Roman Kosoy
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sascha Cording
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Wenhui Wang
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bojan Losic
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C. Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Antonio Di’Narzo
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Maria Suprun
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Sander M. Houten
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lauren Peters
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | | | - Ke Hao
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E. Schadt
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huaibin M. Ko
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy Cho
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce E. Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lishomwa Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, New York City, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York.
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