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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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Yoshiji S, Butler-Laporte G, Lu T, Willett JDS, Su CY, Nakanishi T, Morrison DR, Chen Y, Liang K, Hultström M, Ilboudo Y, Afrasiabi Z, Lan S, Duggan N, DeLuca C, Vaezi M, Tselios C, Xue X, Bouab M, Shi F, Laurent L, Münter HM, Afilalo M, Afilalo J, Mooser V, Timpson NJ, Zeberg H, Zhou S, Forgetta V, Farjoun Y, Richards JB. Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity. Nat Metab 2023; 5:248-264. [PMID: 36805566 PMCID: PMC9940690 DOI: 10.1038/s42255-023-00742-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/10/2023] [Indexed: 02/22/2023]
Abstract
Obesity is a major risk factor for Coronavirus disease (COVID-19) severity; however, the mechanisms underlying this relationship are not fully understood. As obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index using Mendelian randomization. This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using Mendelian randomization. We found that an s.d. increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71, P = 1.63 × 10-10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing, NPNT was expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.
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Grants
- C18281/A29019 Cancer Research UK
- 365825 CIHR
- 409511 CIHR
- 100558 CIHR
- 169303 CIHR
- The Richards research group is supported by the Canadian Institutes of Health Research (CIHR: 365825, 409511, 100558, 169303), the McGill Interdisciplinary Initiative in Infection and Immunity (MI4), the Lady Davis Institute of the Jewish General Hospital, the Jewish General Hospital Foundation, the Canadian Foundation for Innovation, the NIH Foundation, Cancer Research UK, Genome Québec, the Public Health Agency of Canada, McGill University, Cancer Research UK [grant number C18281/A29019] and the Fonds de Recherche Québec Santé (FRQS). J.B.R. is supported by an FRQS Mérite Clinical Research Scholarship. Support from Calcul Québec and Compute Canada is acknowledged. TwinsUK is funded by the Welcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. S.Y. is supported by the Japan Society for the Promotion of Science. T.L. has been supported by a Vanier Canada Graduate Scholarship, an FRQS doctoral training fellowship, and a McGill University Faculty of Medicine Studentship. These funding agencies mentioned above had no role in the design, implementation, or interpretation of this study.
- MEXT | Japan Society for the Promotion of Science (JSPS)
- Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)
- Fonds de Recherche du Québec-Société et Culture (FRQSC)
- Cancer Research UK (CRUK)
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Affiliation(s)
- Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Julian Daniel Sunday Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Computer Science, McGill University, Montréal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - David R Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Kevin Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Michael Hultström
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, 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
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Shanshan Lan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Mitra Vaezi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Fangyi Shi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | | | - Marc Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Jonathan Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Division of Cardiology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | | | - Hugo Zeberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada.
- 5 Prime Sciences, Montréal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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3
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Butler-Laporte G, Gonzalez-Kozlova E, Su CY, Zhou S, Nakanishi T, Brunet-Ratnasingham E, Morrison D, Laurent L, Aflalo J, Aflalo 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 M, Langenberg C, Forgetta V, Mooser V, Marron T, Beckmann ND, Kenigsberg E, Charney AW, Kim-Schulze S, Merad M, Kaufmann DE, Gnjatic S, Richards JB. Correction: The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 2022; 19:40. [PMID: 36376796 PMCID: PMC9663286 DOI: 10.1186/s12014-022-09378-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Computer Science, McGill University, Montreal, QC, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, Kyoto, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | | | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Jonathan Aflalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marc Aflalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Danielle Henry
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, 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, Jewish General Hospital, McGill University, Montreal, QC, 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, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Nardin Rezk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Louis Petitjean
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Charlotte Guzman
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Branka Vulesevic
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Olumide Adeleye
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Tala Abdullah
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Noor Almamlouk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Yara Moussa
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, 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, Jewish General Hospital, McGill University, Montreal, QC, 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
- SomaLogic Inc, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas Marron
- 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
- Early Phase Trials Unit, 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
| | - Ephraim Kenigsberg
- Genetics and Genomic Sciences, 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
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, 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
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, 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.
- 5 Prime Sciences, Montreal, QC, Canada.
- McGill University, King's College London (Honorary), Jewish General Hospital, Pavilion H-4133755 Côte-Ste-Catherine, Montreal, QC, H3T 1E2, Canada.
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Butler-Laporte G, Gonzalez-Kozlova E, Su CY, Zhou S, Nakanishi T, Brunet-Ratnasingham E, Morrison D, 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 M, Langenberg C, Forgetta V, Mooser V, Marron T, Beckmann N, Kenigsberg E, Charney AW, Kim-Schulze S, Merad M, Kaufmann DE, Gnjatic S, Richards JB. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 2022; 19:34. [PMID: 36171541 PMCID: PMC9516500 DOI: 10.1186/s12014-022-09371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/15/2021] [Accepted: 08/21/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions. METHODS We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support. RESULTS 580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex. CONCLUSIONS Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.
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Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | | | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, 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
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, KyotoKyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | | | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Jonathan Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Marc Afilalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Danielle Henry
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, 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, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Nardin Rezk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Louis Petitjean
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Charlotte Guzman
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Branka Vulesevic
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Olumide Adeleye
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Tala Abdullah
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Noor Almamlouk
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Yara Moussa
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montréal, Québec, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montréal, Québec, 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, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | | | | | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- SomaLogic Inc, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Thomas Marron
- 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
- Early Phase Trials Unit, Mount Sinai Hospital, New York, NY, USA
| | - Noam Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- Genetics and Genomic Sciences, 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
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Precision Immunology Institute, 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, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada.
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.
- Department of Twin Research, King's College London, London, UK.
- 5 Prime Sciences, Montreal, Québec, Canada.
- McGill University, King's College London (Honorary), Jewish General Hospital, Pavilion H-4133755 Côte-Ste-Catherine, Montréal, Québec, H3T 1E2, Canada.
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5
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Theurich G, DeLuca C, Campbell T, Liu F, Saint K, Vertenstein M, Chen J, Oehmke R, Doyle J, Whitcomb T, Wallcraft A, Iredell M, Black T, da Silva AM, Clune T, Ferraro R, Li P, Kelley M, Aleinov I, Balaji V, Zadeh N, Jacob R, Kirtman B, Giraldo F, McCarren D, Sandgathe S, Peckham S, Dunlap R. THE EARTH SYSTEM PREDICTION SUITE: Toward a Coordinated U.S. Modeling Capability. Bull Am Meteorol Soc 2016; 97:1229-1247. [PMID: 29568125 PMCID: PMC5859946 DOI: 10.1175/bams-d-14-00164.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users. The ESPS represents a culmination of efforts to create a common Earth system model architecture, and the advent of increasingly coordinated model development activities in the U.S. ESPS component interfaces are based on the Earth System Modeling Framework (ESMF), community-developed software for building and coupling models, and the National Unified Operational Prediction Capability (NUOPC) Layer, a set of ESMF-based component templates and interoperability conventions. This shared infrastructure simplifies the process of model coupling by guaranteeing that components conform to a set of technical and semantic behaviors. The ESPS encourages distributed, multi-agency development of coupled modeling systems, controlled experimentation and testing, and exploration of novel model configurations, such as those motivated by research involving managed and interactive ensembles. ESPS codes include the Navy Global Environmental Model (NavGEM), HYbrid Coordinate Ocean Model (HYCOM), and Coupled Ocean Atmosphere Mesoscale Prediction System (COAMPS®); the NOAA Environmental Modeling System (NEMS) and the Modular Ocean Model (MOM); the Community Earth System Model (CESM); and the NASA ModelE climate model and GEOS-5 atmospheric general circulation model.
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Affiliation(s)
| | - C DeLuca
- Earth System Research Laboratory, NOAA-CIRES, Boulder, CO
| | | | - F Liu
- Cherokee Services Group, Fort Collins, CO
| | - K Saint
- Cherokee Services Group, Fort Collins, CO
| | - M Vertenstein
- National Center for Atmospheric Research, Boulder, CO
| | - J Chen
- Science Applications International Corporation, McLean, VA
| | - R Oehmke
- Earth System Research Laboratory, NOAA-CIRES, Boulder, CO
| | - J Doyle
- Naval Research Laboratory, Monterey, CA
| | | | | | - M Iredell
- NOAA NCEP Environmental Modeling Center, College Park, MD
| | - T Black
- NOAA NCEP Environmental Modeling Center, College Park, MD
| | | | - T Clune
- NASA Goddard Space Flight Center, Greenbelt, MD
| | - R Ferraro
- NASA Jet Propulsion Laboratory, Pasadena, CA
| | - P Li
- NASA Jet Propulsion Laboratory, Pasadena, CA
| | - M Kelley
- NASA Goddard Institute for Space Studies, New York, NY
| | - I Aleinov
- NASA Goddard Institute for Space Studies, New York, NY
| | - V Balaji
- Geophysical Fluid Dynamics Laboratory and Princeton University, Princeton, NJ
| | - N Zadeh
- Geophysical Fluid Dynamics Laboratory and Princeton University, Princeton, NJ
| | - R Jacob
- Argonne National Laboratory, Lemont, IL
| | | | - F Giraldo
- Naval Postgraduate School, Monterey, CA
| | - D McCarren
- Navy at Commander, Naval Meteorology and Oceanography, Silver Spring, MD
| | - S Sandgathe
- University of Washington Applied Physics Laboratory, Seattle, WA
| | | | - R Dunlap
- Earth System Research Laboratory, NOAA-CIRES, Boulder, CO
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7
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Abstract
Virus infection of target cells can result in different biological outcomes: lytic infection, cellular transformation, or cell death by apoptosis. Cells respond to virus infection by the activation of specific transcription factors involved in cytokine gene regulation and cell growth control. The ubiquitously expressed interferon regulatory factor 3 (IRF-3) transcription factor is directly activated following virus infection through posttranslational modification. Phosphorylation of specific C-terminal serine residues results in IRF-3 dimerization, nuclear translocation, and activation of DNA-binding and transactivation potential. Once activated, IRF-3 transcriptionally up regulates alpha/beta interferon genes, the chemokine RANTES, and potentially other genes that inhibit viral infection. We previously generated constitutively active [IRF-3(5D)] and dominant negative (IRF-3 DeltaN) forms of IRF-3 that control target gene expression. In an effort to characterize the growth regulatory properties of IRF-3, we observed that IRF-3 is a mediator of paramyxovirus-induced apoptosis. Expression of the constitutively active form of IRF-3 is toxic, preventing the establishment of stably transfected cells. By using a tetracycline-inducible system, we show that induction of IRF-3(5D) alone is sufficient to induce apoptosis in human embryonic kidney 293 and human Jurkat T cells as measured by DNA laddering, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay, and analysis of DNA content by flow cytometry. Wild-type IRF-3 expression augments paramyxovirus-induced apoptosis, while expression of IRF-3 DeltaN blocks virus-induced apoptosis. In addition, we demonstrate an important role of caspases 8, 9, and 3 in IRF-3-induced apoptosis. These results suggest that IRF-3, in addition to potently activating cytokine genes, regulates apoptotic signalling following virus infection.
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Affiliation(s)
- C Heylbroeck
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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Abstract
The purpose of this study was to investigate the effects of apolipoprotein (apo) E genotype on plasma apo E levels as well as serum total, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglyceride, and glucose values in 734 middle-aged and elderly, female and male subjects. Apo E allele frequencies were similar to those reported in other Caucasian populations. After adjustment for medications, alcohol use, smoking, age, and body mass index, apo E genotype was noted to have significant effects on apo E, total cholesterol, LDL cholesterol, and glucose levels in females, and on apo E, LDL cholesterol, and HDL cholesterol levels, as well as the total cholesterol (TC)/HDL cholesterol ratio in males. Female and male subjects with the apo E4 allele had significantly (P<0.05) lower plasma apo E (25 and 15%) and higher LDL cholesterol levels (5 and 2%), while those with the apo E2 allele had significantly (P<0.05) higher apo E (32 and 27%) and lower LDL cholesterol levels (10 and 10%) than the apo E3/3 group. Moreover, female apo E4 carriers had significantly (P<0.05) lower glucose values (11%) than the apo E3/3 group. These data are consistent with the concept that, in addition to the well known effects of apo E genotype on LDL-C values, this locus plays a very significant role in modulating plasma apo E levels.
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Affiliation(s)
- I A Larson
- Division of Nutritional Science, Justus Liebig University, Giessen, Germany
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9
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Abstract
Interferons are a large family of multifunctional secreted proteins involved in antiviral defense, cell growth regulation and immune activation. Viral infection induces transcription of multiple IFN genes, a response that is in part mediated by the interferon regulatory factors (IRFs). The initially characterized members IRF-1 and IRF-2 are now part of a growing family of transcriptional regulators that has expanded to nine members. The functions of the IRFs have also expanded to include distinct roles in biological processes such as pathogen response, cytokine signaling, cell growth regulation and hematopoietic development. The aim of this review is to provide an update on the novel discoveries in the area of IRF transcription factors and the important roles of the new generation of IRFs--particularly IRF-3, IRF-4 and IRF-7.
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Affiliation(s)
- Y Mamane
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
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10
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Abstract
HIV infection leads to the progressive loss of CD4+ T cells and the near complete destruction of the immune system in the majority of infected individuals. High levels of viral gene expression and replication result in part from the activation of NF-kappaB transcription factors, which in addition to orchestrating the host inflammatory response also activate the HIV-1 long terminal repeat. NF-kappaB induces the expression of numerous cytokine, chemokine, growth factor and immunoregulatory genes, many of which promote HIV-1 replication. Thus, NF-kappaB activation represents a double edged sword in HIV-1 infected cells, since stimuli that induce an NF-kappaB mediated immune response will also lead to enhanced HIV-1 transcription. NF-kappaB has also been implicated in apoptotic signaling, protecting cells from programmed cell death under most circumstances and accelerating apoptosis in others. Therefore, activation of NF-kappaB can impact upon HIV-1 replication and pathogenesis at many levels, making the relationship between HIV-1 expression and NF-kappaB activation multi-faceted. This review will attempt to analyse the many faces and functions of NF-kappaB in the HIV-1 lifecycle.
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Affiliation(s)
- C DeLuca
- Lady Davis Institute for Medical Research, Department of Microbiology, McGill AIDS Center, McGill University, Montreal, Canada
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11
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Seman LJ, DeLuca C, Jenner JL, Cupples LA, McNamara JR, Wilson PW, Castelli WP, Ordovas JM, Schaefer EJ. Lipoprotein(a)-cholesterol and coronary heart disease in the Framingham Heart Study. Clin Chem 1999; 45:1039-46. [PMID: 10388480] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
BACKGROUND Increased plasma lipoprotein(a) [Lp(a)] concentrations have been reported to be an independent risk factor for coronary heart disease (CHD) in some prospective studies, but not in others. These inconsistencies may relate to a lack of standardization and the failure of some immunoassays to measure all apolipoprotein(a) isoforms equally. METHODS We measured plasma Lp(a)-cholesterol [Lp(a)-C] in a Caucasian population of offspring and spouses of the Framingham Heart Study participants, using a lectin-based assay (LipoproTM). We compared the prevalence of increased Lp(a)-C to the presence of sinking pre-beta-lipoprotein (SPB). We also related Lp(a)-C concentrations to the prevalence of CHD risk in the entire population. RESULTS The mean (+/- SD) Lp(a)-C concentration in the Framingham population (n = 3121) was 0.186 +/- 0.160 mmol/L, with no significant gender or age differences. The mean Lp(a)-C concentrations in the absence or presence of SPB were 0.158 +/- 0. 132 mmol/L and 0.453 +/- 0.220 mmol/L, respectively (P <0.0001). The mean Lp(a)-C concentration in men with CHD (n = 156) was 0.241 +/- 0. 204 mmol/L, which was significantly (P <0.001) higher, by 34%, than in controls. The odds ratio for CHD risk in men with Lp(a)-C >/=0. 259 mmol/L (>/=10 mg/dL), after adjusting for age, HDL-cholesterol, LDL-cholesterol, smoking, diabetes, blood pressure, and body mass index, was 2.293 (confidence interval, 1.55-3.94; P <0.0005). Lp(a)-C values correlated highly with a Lp(a)-mass immunoassay [ApotekTM Lp(a); r = 0.832; P <0.0001; n = 1000]. CONCLUSIONS An increased Lp(a)-C value >/=0.259 mmol/L (>/=10 mg/dL) is an independent CHD risk factor in men with a relative risk of more than 2, but was inconclusive in women. Lp(a)-C measurements offer an alternative to Lp(a)-mass immunoassays and can be performed on automated analyzers.
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Affiliation(s)
- L J Seman
- Division of Endocrinology, Diabetes, Metabolism and Molecular Medicine, New England Medical Center and Tufts University School of Medicine, 750 Washington St., Boston, MA 02111, USA
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12
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DeLuca C, Petropoulos L, Zmeureanu D, Hiscott J. Nuclear IkappaBbeta maintains persistent NF-kappaB activation in HIV-1-infected myeloid cells. J Biol Chem 1999; 274:13010-6. [PMID: 10224051 DOI: 10.1074/jbc.274.19.13010] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Monocytic cells exhibit constitutive NF-kappaB activation upon infection with human immunodeficiency virus-1 (HIV-1). Because IkappaBbeta has been implicated in maintaining NF-kappaB.DNA binding, we sought to investigate whether IkappaBbeta was involved in maintaining persistent NF-kappaB activation in HIV-1-infected monocytic cell lines. IkappaBbeta was present in the nucleus of HIV-1-infected cells and participated in the ternary complex formation with NF-kappaB and DNA. In contrast to uninfected cells, the addition of recombinant glutathione S-transferase-IkappaBalpha protein to preformed NF-kappaB.DNA complexes from HIV-1-infected cell extracts did not completely dissociate the complexes, suggesting that IkappaBbeta may protect NF-kappaB complexes from IkappaBalpha-mediated dissociation. Immunodepletion of IkappaBbeta resulted in an NF-kappaB.DNA binding complex that was sensitive to IkappaBalpha-mediated dissociation, thus demonstrating the protective role of IkappaBbeta. In addition, co-transfection studies with an NF-kappaB-dependent reporter construct demonstrated that IkappaBbeta co-expression partially alleviated inhibition of NF-kappaB-mediated gene expression by IkappaBalpha, implying that IkappaBbeta can maintain transcriptionally active NF-kappaB.DNA complexes. Furthermore, constitutive phosphorylation of IkappaBalpha was observed. Immunoprecipitation of the IkappaB kinase (IKK) complex followed by in vitro analysis of kinase activity demonstrated that IKK was constitutively activated in HIV-1-infected myeloid cells. Thus, virus-induced constitutive IKK activation, coupled with the maintenance of a ternary NF-kappaB.DNA complex by IkappaBbeta, maintains persistent NF-kappaB activity in HIV-1-infected myeloid cells.
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Affiliation(s)
- C DeLuca
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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Abstract
HIV-1 infection of primary monocytic cells and myeloid cell lines results in sustained NF-kappaB activation. Recently, NF-kappaB induction has been shown to play a role in protecting cells from programmed cell death. In the present study, we sought to investigate whether constitutive NF-kappaB activity in chronically HIV-1-infected promonocytic U937 (U9-IIIB) and myeloblastic PLB-985 (PLB-IIIB) cells affects apoptotic signaling. TNFalpha and cycloheximide caused infected cells to undergo apoptosis more rapidly than parental U937 and PLB-985 cells. Inhibition of TNFalpha-induced NF-kappaB activation using the antioxidant N-acetylcysteine (NAC) resulted in increased apoptosis in both U937 and U9-IIIB cells, while preactivation of NF-kappaB with the non-apoptotic inducer IL-1beta caused a relative decrease in apoptosis. Inhibition of constitutive NF-kappaB activity in U9-IIIB and PLB-IIIB cells also induced apoptosis, suggesting that NF-kappaB protects cells from a persistent apoptotic signal. TNFalpha plus NAC treatment resulted in a marked decrease in Bcl-2 protein levels in HIV-1-infected cells, coupled with an increase in Bax protein compared to uninfected cells, suggesting that the difference in susceptibility to TNFalpha-induced apoptosis may relate to the differences in relative levels of Bcl-2 and Bax. The protective role of NF-kappaB in blocking TNFalpha- and HIV-1-induced apoptosis was supported by studies in Jurkat T cells engineered to express IkappaB alpha repressor mutants (TD-IkappaB) under the control of a tetracycline-responsive promoter. Cells underwent apoptosis in response to TNFalpha only when NF-kappaB activation was inhibited by TD-IkappaB expression. As was observed for the U9-IIIB cells, TNFalpha treatment also induced a marked decrease in Bcl-2 protein levels in TD-IkappaB expressing cells. These experiments demonstrate that apoptotic signaling is perturbed in HIV-1-infected U9-IIIB cells and indicate that NF-kappaB activation may play an additional protective role against HIV-1-induced apoptosis in myeloid cells.
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Affiliation(s)
- C DeLuca
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Department of Medicine, McGill University, Montreal, Quebec, Canada
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Kwon H, Pelletier N, DeLuca C, Genin P, Cisternas S, Lin R, Wainberg MA, Hiscott J. Inducible expression of IkappaBalpha repressor mutants interferes with NF-kappaB activity and HIV-1 replication in Jurkat T cells. J Biol Chem 1998; 273:7431-40. [PMID: 9516441 DOI: 10.1074/jbc.273.13.7431] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus (HIV-1) utilizes the NF-kappaB/Rel proteins to regulate transcription through NF-kappaB binding sites in the HIV-1 long terminal repeat (LTR). Normally, NF-kappaB is retained in the cytoplasm by inhibitory IkappaB proteins; after stimulation by multiple activators including viruses, IkappaBalpha is phosphorylated and degraded, resulting in NF-kappaB release. In the present study, we examined the effect of tetracycline-inducible expression of transdominant repressors of IkappaBalpha (TD-IkappaBalpha) on HIV-1 multiplication using stably selected Jurkat T cells. TD-IkappaBalpha was inducibly expressed as early as 3 h after doxycycline addition and dramatically reduced both NF-kappaB DNA binding activity and LTR-directed gene activity. Interestingly, induced TD-IkappaBalpha expression also decreased endogenous IkappaBalpha expression to undetectable levels by 24 h after induction, demonstrating that TD-IkappaBalpha repressed endogenous NF-kappaB-dependent gene transcription. TD-IkappaBalpha expression also sensitized Jurkat cells to tumor necrosis factor-induced apoptosis. De novo HIV-1 infection of Jurkat cells was dramatically altered by TD-IkappaBalpha induction, resulting in inhibition of HIV-1 multiplication, as measured by p24 antigen, reverse transcriptase, and viral RNA. Given the multiple functions of the NF-kappaB/IkappaB pathway, TD-IkappaBalpha expression may interfere with HIV-1 multiplication at several levels: LTR-mediated transcription, Rev-mediated export of viral RNA, inhibition of HIV-1-induced pro-inflammatory cytokines, and increased sensitivity of HIV-1-infected cells to apoptosis.
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Affiliation(s)
- H Kwon
- Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec H3T 1E2, Canada
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Hiscott J, Beauparlant P, Crepieux P, DeLuca C, Kwon H, Lin R, Petropoulos L. Cellular and viral protein interactions regulating I kappa B alpha activity during human retrovirus infection. J Leukoc Biol 1997; 62:82-92. [PMID: 9225998 DOI: 10.1002/jlb.62.1.82] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
NF-kappa B/Rel transcription factors participate in the activation of numerous genes involved in immune regulation/inflammation including cytokines, cell surface receptors, adhesion molecules, and acute phase proteins. NF-kappa B activity is controlled by inhibitory proteins, I kappa Bs, that maintain the DNA-binding forms of NF-kappa B in an inactive state in the cytoplasm. Many viruses, including the human retroviruses HIV-1 and HTLV-1, also utilize the NF-kappa B/I kappa B pathway to their transcriptional advantage during viral infection. Our recent studies have focused on the I kappa B alpha inhibitor and have characterized several protein interactions that modulate the functional activity of I kappa B alpha during human retrovirus infection. In this article, we summarise recent studies demonstrating that (1) chronic HIV-1 infection of human myelomonoblastic PLB-985 cells leads to constitutive NF-kappa B activity, activated in part due to enhanced I kappa B alpha turnover and increased NF-kappa B/Rel production; (2) HTLV-1 Tax protein physically associates with the I kappa B alpha protein in vivo and in vitro and also mediates a 20- to 40-fold stimulation of NF-kappa B DNA binding activity mediated via an enhancement of NF-kappa B dimer formation; (3) casein kinase II phosphorylates I kappa B alpha at multiple sites in the C-terminal PEST domains and regulates I kappa B alpha function; (4) transdominant forms of I kappa B alpha, mutated in critical Ser or Thr residues required for inducer-mediated (S32A,S36A) and/or constitutive phosphorylation block HIV LTR trans-activation and also effectively inhibit HIV-1 multiplication in a single cycle infection model; and (5) the amino-terminal 55aa of I kappa B alpha (NIK) interacts with the human homologue of dynein light chain 1, a small 9-kDa human homologue of the dynein light chain protein involved in microtubule and cytoskeletal dynamics. Together, our results highlight a number of intriguing molecular interactions between I kappa B alpha and cellular or viral proteins that modulate transcription factor activity and nuclear-cytoplasmic flow of host proteins.
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Affiliation(s)
- J Hiscott
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montreal, Quebec, Canada
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Wong E, DeLuca C, Boily C, Charleson S, Cromlish W, Denis D, Kargman S, Kennedy BP, Ouellet M, Skorey K, O'Neill GP, Vickers PJ, Riendeau D. Characterization of autocrine inducible prostaglandin H synthase-2 (PGHS-2) in human osteosarcoma cells. Inflamm Res 1997; 46:51-9. [PMID: 9085144 DOI: 10.1007/s000110050063] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The human osteosarcoma 143.98.2 cell line was found to express high levels of prostaglandin synthase-2 (PGHS-2) without detectable levels of prostaglandin synthase-1 (PGHS-1) as measured by reverse transcriptase-polymerase chain reaction (RT-PCR) and immunoblot analysis. Maximal levels of PGHS-2 induction were attained when the cells were grown beyond confluence. The osteosarcoma cells also secrete IL-1 alpha, IL-1 beta and TNF alpha in the culture medium. PGHS-2 expression was inducible by the exogenous addition of these cytokines as well as conditioned media from auto-induced cultures and inhibitable by treatment with dexamethasone. In contrast, undifferentiated U937 cells selectively express PGHS-1 as analyzed by RT-PCR and Western blotting. The effects of non-steroidal anti-inflammatory drugs (NSAIDs) on the cellular PGE2 production mediated by each isoform of human PGHS were determined using osteosarcoma and undifferentiated U937 cells. When cells were preincubated with inhibitors to allow time-dependent inhibition prior to arachidonic acid stimulation, NS-398, CGP 28238, L-745,337, SC-58125 all behaved as potent (IC50 = 1-30 nM) and selective inhibitors of PGHS-2, in contrast to indomethacin, flurbiprofen or diclofenac which are potent inhibitors of enzymes. DuP-697 and sulindac sulfide were also potent inhibitors of PGHS-2 but both compounds inhibited cellular PGHS-1 activity at higher doses (IC50 = 0.2-0.4 microM). Time-dependent inhibition of PGE2 production in osteosarcoma cells was observed for indomethacin, diclofenac and etodolac. The synthesis of PGE2 by U937 cells was strongly dependent on exogenous arachidonic acid (100-fold stimulation) whereas confluent osteosarcoma cells also produced PGE2 without exogenous stimulus (7-fold stimulation by arachidonic acid). Osteosarcoma cells grown beyond confluence released more PGE2 from endogenous substrate than arachidonic acid stimulated undifferentiated U937 cells. These results indicate that osteosarcoma cells selectively express PGHS-2 with an autocrine regulation and effective utilization of endogenous arachidonic acid for PGE2 synthesis.
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Affiliation(s)
- E Wong
- Department of Biochemistry and Molecular Biology, Merck Frosst Centre for Therapeutic Research, Pointe-Claire-Dorval, Quebec, Canada
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DeLuca C, Roulston A, Koromilas A, Wainberg MA, Hiscott J. Chronic human immunodeficiency virus type 1 infection of myeloid cells disrupts the autoregulatory control of the NF-kappaB/Rel pathway via enhanced IkappaBalpha degradation. J Virol 1996; 70:5183-93. [PMID: 8764027 PMCID: PMC190474 DOI: 10.1128/jvi.70.8.5183-5193.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Productive human immunodeficiency virus type 1 (HIV-1) infection causes sustained NF-kappaB DNA-binding activity in chronically infected monocytic cells. A direct temporal correlation exists between HIV infection and the appearance of NF-kappaB DNA-binding activity in myelomonoblastic PLB-985 cells. To examine the molecular basis of constitutive NF-kappaB DNA-binding activity in HIV1 -infected cells, we analyzed the phosphorylation and turnover of IkappaBalpha protein, the activity of the double-stranded RNA-dependent protein kinase (PKR) and the intracellular levels of NF-kappaB subunits in the PLB-985 and U937 myeloid cell models. HIV-1 infection resulted in constitutive, low-level expression of type 1 interferon (IFN) at the mRNA level. Constitutive PKR activity was also detected in HIV-1-infected cells as a result of low-level IFN production, since the addition of anti-IFN-alpha/beta antibody to the cells decreased PKR expression. Furthermore, the analysis of IkappaBalpha turnover demonstrated an increased degradation of IkappaBalpha in HIV-1-infected cells that may account for the constitutive DNA binding activity. A dramatic increase in the intracellular levels of NF-kappaB subunits c-Rel and NF-kappaB2 p100 and a moderate increase in NF-kappaB2 p52 and RelA(p65) were detected in HIV-1-infected cells, whereas NF-kappaB1 p105/p50 levels were not altered relative to the levels in uninfected cells. We suggest that HIV-1 infection of myeloid cells induces IFN production and PKR activity, which in turn contribute to enhanced IkappaBalpha phosphorylation and subsequent degradation. Nuclear translocation of NF-kappaB subunits may ultimately increase the intracellular pool of NF-kappaB/IkappaBalpha by an autoregulatory mechanism. Enhanced turnover of IkappaBalpha and the accumulation of NF-kappaB/Rel proteins may contribute to the chronically activated state of HIV-1-infected cells.
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Affiliation(s)
- C DeLuca
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
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DeNardin E, DeLuca C, Levine MJ, Genco RJ. Antibodies directed to the chemotactic factor receptor detect differences between chemotactically normal and defective neutrophils from LJP patients. J Periodontol 1990; 61:609-17. [PMID: 2231227 DOI: 10.1902/jop.1990.61.10.609] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [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] [Indexed: 12/30/2022]
Abstract
Localized juvenile periodontitis (LJP) is a progressively destructive infection of the supporting tissues of the teeth, primarily affecting adolescents. In this disease, patients' polymorphonuclear leukocytes (PMN) exhibit decreased chemotaxis (CTX) and decreased binding of the chemotactic peptide N-formyl-l-methionyl-l-leucyl-l-phenyl-alanine (FMLP) to specific receptors on the PMN surface. Since the FMLP receptor is involved in the activation of the PMN, and its subsequent response to chemotactic stimuli, a decrease in the chemotactic peptide receptor, as seen in LJP patients, is suspected to be a predisposing factor for this disease. To define differences in the FMLP receptor between CTX defective LJP patients and CTX normal donors, a battery of monoclonal antibodies reactive against the FMLP receptor was prepared. The FMLP receptor was affinity-purified, and was found to be comprised of two components, one of 68 kDa, and the other of 94 kDa. Only the 68 kDa component specifically bound a radioiodinated FMLP analogue in a photoaffinity experiment. Seven monoclonal antibodies were selected on the basis of their reactivity with the 68 kDa receptor component, and of these, 5 showed reduced binding against PMN from CTX defective LJP donors when compared to their reactivity against PMN from CTX normal subjects. Two of the 7 anti-68 kDa antibodies reacted with PMN from both sets of subjects at a comparable extent. Furthermore, the presence of 20 nmol of FMLP inhibited the binding of 5 of the anti-receptor antibodies to whole PMN, including one that showed no difference in binding between CTX normal and defective PMN, and 4 of the 5 that did show such difference.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- E DeNardin
- Department of Oral Biology, State University of New York, School of Dental Medicine, Buffalo
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Abstract
Monoclonal antibody prepared against highly purified rat liver G6PD was used to probe the mode of regulation of this enzyme in a mammalian model system. Material cross-reacting with antibody against liver G6PD was found in similar amounts in extracts of two genetically related rat hepatoma cell lines, only one of which exhibits detectable enzymatic activity when both are cultured under identical conditions in vitro. The data suggest a post-translational event is necessary for the expression of catalytic activity for G6PD in this model system.
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Zambon JJ, DeLuca C, Slots J, Genco RJ. Studies of leukotoxin from Actinobacillus actinomycetemcomitans using the promyelocytic HL-60 cell line. Infect Immun 1983; 40:205-12. [PMID: 6572616 PMCID: PMC264837 DOI: 10.1128/iai.40.1.205-212.1983] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The promyelocytic HL-60 cell line was examined for susceptibility to leukotoxin from Actinobacillus actinomycetemcomitans. Strains of A. actinomycetemcomitans which caused lysis of human peripheral blood polymorphonuclear leukocytes also lysed HL-60 cells as determined by release of intracellular lactate dehydrogenase. The killing of HL-60 cells by A. actinomycetemcomitans was dose dependent and temperature dependent, reached maximal levels after 45 min of incubation, and was inhibited by rabbit antisera to A. actinomycetemcomitans. Of 100 oral isolates of A. actinomycetemcomitans from 55 subjects, 16% from 11 healthy subjects, 43% from 13 adult periodontitis patients, 75% from 4 insulin-dependent diabetics, 66% from 2 generalized juvenile periodontitis patients, and 55% from 25 localized juvenile periodontitis patients produced leukotoxin. The same subject could harbor both leukotoxin-producing and -nonproducing isolates. The significantly higher proportion of leukotoxin-producing isolates in the disease groups compared with the healthy group is consistent with the hypothesis that leukotoxin from A. actinomycetemcomitans is an important virulence factor in the pathogenesis of certain forms of periodontal disease.
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Gold RM, Sawchenko PE, DeLuca C, Alexander J, Eng R. Vagal mediation of hypothalamic obesity but not of supermarket dietary obesity. Am J Physiol 1980; 238:R447-53. [PMID: 7377384 DOI: 10.1152/ajpregu.1980.238.5.r447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In two independent experiments, complete subdiaphragmatic vagotomy did not prevent the development of the obesity that results from the addition of highly palatable foods to the diet of rats. The vagotomized animals exhibited only a 1-day delay in the onset of overeating, and this only when first exposed to the tasty diet. In independent tests of the functional completeness of the vagotomies, the vagotomized animals failed to overeat or gain excessive weight on a standard laboratory diet following bilaterally parasagittal hypothalamic knife cuts. Thus, hypothalamic knife-cut obesity requires the integrity of the vagus for its full expression, whereas dietary obesity does not.
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DeLuca C, Brown JA, Shows TB. Lysosomal arylsulfatase deficiencies in humans: chromosome assignments for arylsulfatase A and B. Proc Natl Acad Sci U S A 1979; 76:1957-61. [PMID: 36611 PMCID: PMC383512 DOI: 10.1073/pnas.76.4.1957] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genetics of human lysosomal arylsulfatases A and B (aryl-sulfate sulfohydrolase, EC 3.1.6.1), associated with childhood disease, has been studied with human-rodent somatic cell hybrids. Deficiency of arylsulfatase A (ARS(A)) in humans results in a progressive neurodegenerative disease, metachromatic leukodystrophy. Deficiency of arylsulfatase B (ARS(B)) is associated with skeletal and growth malformations, termed the Maroteaux-Lamy syndrome. Simultaneous deficiency of both enzymes is associated with the multiple sulfatase deficiency disease, suggesting a common relationship for ARS(A) and ARS(B). The genetic and structural relationships of human ARS(A) and ARS(B) have been determined by the use of human-Chinese hamster somatic cell hybrids. Independent enzyme segregation in cell hybrids demonstrated different chromosome assignments for the structural genes, ARS(A) and ARS(B), coding for the two lysosomal enzymes. ARS(A) activity showed concordant segregation with mitochondrial aconitase encoded by a gene assigned to chromosome 22. ARS(B) segregated with beta-hexosaminidase B encoded by a gene assigned to chromosome 5. These assignments were confirmed by chromosome analyses. The subunit structures of ARS(A) and ARS(B) were determined by their electrophoretic patterns in cell hybrids; a dimeric structure was demonstrated for ARS(A) and a monomeric structure for ARS(B). Although the multiple sulfatase deficiency disorder suggests a shared relationship between ARS(A) and ARS(B), independent segregation of these enzymes in cell hybrids did not support a common polypeptide subunit or structural gene assignment. The evidence demonstrates the assignment of ARS(A) to chromosome 22 and ARS(B) to chromosome 5. A third gene that affects ARS(A) and ARS(B) activity is suggested by the multiple sulfatase deficiency disorder.
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Abstract
Infusion can be maintained at a constant rate over an extended period of time in vivo by the use of an implanted diffusion chamber. Plasma 59Fe was maintained at a constant level for 10 days when infused from a s.c. implant. Injected isotope was cleared exponentially with a half-clearance time of about 8 h.
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DeLuca C, Massaro EJ, Cohen MM. Biochemical and cytogenetic characterization of rat hepatoma cell lines in vitro. Cancer Res 1972; 32:2435-40. [PMID: 4404256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Gioeli RP, DeLuca C. Modification of the use of the pipette filler for reducing the hazards of contamination. Appl Microbiol 1971; 22:946-7. [PMID: 5132100 PMCID: PMC376456 DOI: 10.1128/am.22.5.946-947.1971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
An adaptation is described which makes the common propipette readily acceptable for repetitive use. The application of pressure from an appropriate gas to permit rapid delivery of fluids and a method by which the propipette may be used comfortably in one hand make this tool amenable to routine use in a practical attempt to reduce the risks of contamination to both the operator and his cultures.
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