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Khoramjoo M, Srinivasan K, Wang K, Wishart D, Prasad V, Oudit GY. Protocol to identify biomarkers in patients with post-COVID condition using multi-omics and machine learning analysis of human plasma. STAR Protoc 2024; 5:103041. [PMID: 38678567 PMCID: PMC11068918 DOI: 10.1016/j.xpro.2024.103041] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/03/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Here, we present a workflow for analyzing multi-omics data of plasma samples in patients with post-COVID condition (PCC). Applicable to various diseases, we outline steps for data preprocessing and integrating diverse assay datasets. Then, we detail statistical analysis to unveil plasma profile changes and identify biomarker-clinical variable associations. The last two steps discuss machine learning techniques for unsupervised clustering of patients based on their inherent molecular similarities and feature selection to identify predictive biomarkers. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Mobin Khoramjoo
- Department of Physiology, University of Alberta, Edmonton, AB T6G 2H7, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Karthik Srinivasan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Kaiming Wang
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2S2, Canada; Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada
| | - David Wishart
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vinay Prasad
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Gavin Y Oudit
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2S2, Canada; Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada.
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Wang K, Khoramjoo M, Srinivasan K, Gordon PMK, Mandal R, Jackson D, Sligl W, Grant MB, Penninger JM, Borchers CH, Wishart DS, Prasad V, Oudit GY. Sequential multi-omics analysis identifies clinical phenotypes and predictive biomarkers for long COVID. Cell Rep Med 2023; 4:101254. [PMID: 37890487 PMCID: PMC10694626 DOI: 10.1016/j.xcrm.2023.101254] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/25/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023]
Abstract
The post-acute sequelae of COVID-19 (PASC), also known as long COVID, is often associated with debilitating symptoms and adverse multisystem consequences. We obtain plasma samples from 117 individuals during and 6 months following their acute phase of infection to comprehensively profile and assess changes in cytokines, proteome, and metabolome. Network analysis reveals sustained inflammatory response, platelet degranulation, and cellular activation during convalescence accompanied by dysregulation in arginine biosynthesis, methionine metabolism, taurine metabolism, and tricarboxylic acid (TCA) cycle processes. Furthermore, we develop a prognostic model composed of 20 molecules involved in regulating T cell exhaustion and energy metabolism that can reliably predict adverse clinical outcomes following discharge from acute infection with 83% accuracy and an area under the curve (AUC) of 0.96. Our study reveals pertinent biological processes during convalescence that differ from acute infection, and it supports the development of specific therapies and biomarkers for patients suffering from long COVID.
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Affiliation(s)
- Kaiming Wang
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mobin Khoramjoo
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Department of Physiology, University of Alberta, Edmonton, AB, Canada
| | - Karthik Srinivasan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Paul M K Gordon
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rupasri Mandal
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, Canada
| | - Dana Jackson
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada
| | - Wendy Sligl
- Department of Critical Care Medicine, University of Alberta, Edmonton, AB, Canada; Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Maria B Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Josef M Penninger
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada; Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - David S Wishart
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB, Canada
| | - Vinay Prasad
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Department of Physiology, University of Alberta, Edmonton, AB, Canada.
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