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Rombauts A, Bódalo Torruella M, Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L, Carratalà J. Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19. Biomedicines 2023; 11:biomedicines11051348. [PMID: 37239019 DOI: 10.3390/biomedicines11051348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.
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Affiliation(s)
- Alexander Rombauts
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | | | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Anna Ferrer-Salvador
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Maria Gabarrós-Subirà
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Isabel Oriol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Carlota Gudiol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Penrice-Randal R, Dong X, Shapanis AG, Gardner A, Harding N, Legebeke J, Lord J, Vallejo AF, Poole S, Brendish NJ, Hartley C, Williams AP, Wheway G, Polak ME, Strazzeri F, Schofield JPR, Skipp PJ, Hiscox JA, Clark TW, Baralle D. Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19. Front Immunol 2022; 13:988685. [PMID: 36203591 PMCID: PMC9530807 DOI: 10.3389/fimmu.2022.988685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.
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Affiliation(s)
- Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- *Correspondence: Rebekah Penrice-Randal,
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew George Shapanis
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Aaron Gardner
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
| | | | - Jelmer Legebeke
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephen Poole
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nathan J. Brendish
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Catherine Hartley
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Anthony P. Williams
- Cancer Sciences Division, Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marta E. Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Paul J. Skipp
- TopMD Precision Medicine Ltd, Southampton, United Kingdom
- Centre for Proteomic Research, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
- ASTAR Infectious Diseases Laboratories (ASTAR ID Labs), Agency for Science, Technology and Research (ASTAR) Singapore, Singapore, Singapore
| | - Tristan W. Clark
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, University of Southampton, Southampton, United Kingdom
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Colona VL, Vasiliou V, Watt J, Novelli G, Reichardt JKV. Update on human genetic susceptibility to COVID-19: susceptibility to virus and response. Hum Genomics 2021; 15:57. [PMID: 34429158 PMCID: PMC8384585 DOI: 10.1186/s40246-021-00356-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Vito Luigi Colona
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Jessica Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, Australia
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia.
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