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McLarnon T, McDaid D, Lynch SM, Cooper E, McLaughlin J, McGilligan VE, Watterson S, Shukla P, Zhang SD, Bucholc M, English A, Peace A, O’Kane M, Kelly M, Bhavsar M, Murray EK, Gibson DS, Walsh CP, Bjourson AJ, Rai TS. Potential Plasma Proteins (LGALS9, LAMP3, PRSS8 and AGRN) as Predictors of Hospitalisation Risk in COVID-19 Patients. Biomolecules 2024; 14:1163. [PMID: 39334929 PMCID: PMC11429560 DOI: 10.3390/biom14091163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/22/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Background: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has posed unprecedented challenges to healthcare systems worldwide. Here, we have identified proteomic and genetic signatures for improved prognosis which is vital for COVID-19 research. Methods: We investigated the proteomic and genomic profile of COVID-19-positive patients (n = 400 for proteomics, n = 483 for genomics), focusing on differential regulation between hospitalised and non-hospitalised COVID-19 patients. Signatures had their predictive capabilities tested using independent machine learning models such as Support Vector Machine (SVM), Random Forest (RF) and Logistic Regression (LR). Results: This study has identified 224 differentially expressed proteins involved in various inflammatory and immunological pathways in hospitalised COVID-19 patients compared to non-hospitalised COVID-19 patients. LGALS9 (p-value < 0.001), LAMP3 (p-value < 0.001), PRSS8 (p-value < 0.001) and AGRN (p-value < 0.001) were identified as the most statistically significant proteins. Several hundred rsIDs were queried across the top 10 significant signatures, identifying three significant SNPs on the FSTL3 gene showing a correlation with hospitalisation status. Conclusions: Our study has not only identified key signatures of COVID-19 patients with worsened health but has also demonstrated their predictive capabilities as potential biomarkers, which suggests a staple role in the worsened health effects caused by COVID-19.
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Affiliation(s)
- Thomas McLarnon
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Darren McDaid
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Seodhna M. Lynch
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Eamonn Cooper
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Joseph McLaughlin
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Victoria E. McGilligan
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Steven Watterson
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Priyank Shukla
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Shu-Dong Zhang
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Magda Bucholc
- School of Computing, Engineering & Intelligent Systems, Ulster University, Derry BT48 7JL, UK
| | - Andrew English
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
- School of Health and Life Sciences, Teesside University, Campus Heart, Middlesbrough TS1 3BX, UK
| | - Aaron Peace
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Derry BT47 6SB, UK
| | - Maurice O’Kane
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
- Clinical Chemistry Laboratory, Altnagelvin Hospital, Derry BT47 6SB, UK
| | - Martin Kelly
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Derry BT47 6SB, UK
| | - Manav Bhavsar
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Derry BT47 6SB, UK
| | - Elaine K. Murray
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - David S. Gibson
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Colum P. Walsh
- Biomedical Sciences Research Institute, University of Ulster, Coleraine BT52 1SA, UK
| | - Anthony J. Bjourson
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, UK
| | - Taranjit Singh Rai
- Personalised Medicine Centre, C-TRIC Building, Altnagelvin Area Hospital, School of Medicine, Ulster University, Glenshane Road, Derry-Londonderry BT47 6SB, 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: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [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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