COVIDomics: The Proteomic and Metabolomic Signatures of COVID-19

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Mar 10

PMID 35269564

Authors

Michele Costanzo

Marianna Caterino

Roberta Fedele

Armando Cevenini

Mariarca Pontillo

Lucia Barra

Margherita Ruoppolo

Affiliations

Soon will be listed here.

Abstract

Omics-based technologies have been largely adopted during this unprecedented global COVID-19 pandemic, allowing the scientific community to perform research on a large scale to understand the pathobiology of the SARS-CoV-2 infection and its replication into human cells. The application of omics techniques has been addressed to every level of application, from the detection of mutations, methods of diagnosis or monitoring, drug target discovery, and vaccine generation, to the basic definition of the pathophysiological processes and the biochemical mechanisms behind the infection and spread of SARS-CoV-2. Thus, the term COVIDomics wants to include those efforts provided by omics-scale investigations with application to the current COVID-19 research. This review summarizes the diverse pieces of knowledge acquired with the application of COVIDomics techniques, with the main focus on proteomics and metabolomics studies, in order to capture a common signature in terms of proteins, metabolites, and pathways dysregulated in COVID-19 disease. Exploring the multiomics perspective and the concurrent data integration may provide new suitable therapeutic solutions to combat the COVID-19 pandemic.

Citing Articles

Comparative metabolomic analysis reveals shared and unique features of COVID-19 cytokine storm and surgical sepsis.

Russkikh I, Popov O, Klochkova T, Sushentseva N, Apalko S, Asinovskaya A Sci Rep. 2025; 15(1):6622.

PMID: 39994234 PMC: 11850835. DOI: 10.1038/s41598-025-90426-0.

Mapping the knowledge of omics in myocardial infarction: A scientometric analysis in R Studio, VOSviewer, Citespace, and SciMAT.

Wei X, Wang M, Yu S, Han Z, Li C, Zhong Y Medicine (Baltimore). 2025; 104(7):e41368.

PMID: 39960900 PMC: 11835070. DOI: 10.1097/MD.0000000000041368.

Recent advances in nutritional metabolism studies on SARS-CoV-2 infection.

Jiang Y, Xu L, Zheng X, Shi H Infect Med (Beijing). 2025; 4(1):100162.

PMID: 39936106 PMC: 11810712. DOI: 10.1016/j.imj.2025.100162.

Unraveling metabolic signatures in SARS-CoV-2 variant infections using multiomics analysis.

Lee S, Lee J, Lyoo K, Shin Y, Shin D, Kim J Front Immunol. 2025; 15:1473895.

PMID: 39759510 PMC: 11697598. DOI: 10.3389/fimmu.2024.1473895.

Long-term dysregulation of plasma peptidome in mild and multiple COVID-19 recovered patients revealed by a novel efficient peptidomics workflow.

Song Z, Liu C, Liu Y, Bian Z, Sun Q, He T Anal Bioanal Chem. 2024; 417(4):733-746.

PMID: 39644382 DOI: 10.1007/s00216-024-05684-0.

References

Kaur G, Ji X, Rahman I . SARS-CoV2 Infection Alters Tryptophan Catabolism and Phospholipid Metabolism. Metabolites. 2021; 11(10). PMC: 8538244. DOI: 10.3390/metabo11100659. View

Gordon D, Jang G, Bouhaddou M, Xu J, Obernier K, White K . A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020; 583(7816):459-468. PMC: 7431030. DOI: 10.1038/s41586-020-2286-9. View

Danlos F, Grajeda-Iglesias C, Durand S, Sauvat A, Roumier M, Cantin D . Metabolomic analyses of COVID-19 patients unravel stage-dependent and prognostic biomarkers. Cell Death Dis. 2021; 12(3):258. PMC: 7948172. DOI: 10.1038/s41419-021-03540-y. View

Bauer W, Weber M, Diehl-Wiesenecker E, Galtung N, Prpic M, Somasundaram R . Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection. Viruses. 2021; 13(12). PMC: 8706135. DOI: 10.3390/v13122456. View

Fraser D, Slessarev M, Martin C, Daley M, Patel M, Miller M . Metabolomics Profiling of Critically Ill Coronavirus Disease 2019 Patients: Identification of Diagnostic and Prognostic Biomarkers. Crit Care Explor. 2020; 2(10):e0272. PMC: 7587450. DOI: 10.1097/CCE.0000000000000272. View

Tanner J, Alfieri C . The Fatty Acid Lipid Metabolism Nexus in COVID-19. Viruses. 2021; 13(1). PMC: 7826519. DOI: 10.3390/v13010090. View

Zhong W, Altay O, Arif M, Edfors F, Doganay L, Mardinoglu A . Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms. EBioMedicine. 2021; 74:103723. PMC: 8626206. DOI: 10.1016/j.ebiom.2021.103723. View

Assarsson E, Lundberg M, Holmquist G, Bjorkesten J, Thorsen S, Ekman D . Homogenous 96-plex PEA immunoassay exhibiting high sensitivity, specificity, and excellent scalability. PLoS One. 2014; 9(4):e95192. PMC: 3995906. DOI: 10.1371/journal.pone.0095192. View

Wu P, Chen D, Ding W, Wu P, Hou H, Bai Y . The trans-omics landscape of COVID-19. Nat Commun. 2021; 12(1):4543. PMC: 8316550. DOI: 10.1038/s41467-021-24482-1. View

10.

Ruoppolo M, Caterino M, Albano L, Pecce R, Di Girolamo M, Crisci D . Targeted metabolomic profiling in rat tissues reveals sex differences. Sci Rep. 2018; 8(1):4663. PMC: 5856765. DOI: 10.1038/s41598-018-22869-7. View

11.

Xu Z, Shi L, Wang Y, Zhang J, Huang L, Zhang C . Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020; 8(4):420-422. PMC: 7164771. DOI: 10.1016/S2213-2600(20)30076-X. View

12.

Kong S, Hernandez-Ferrer C . Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2019; 25:587-598. PMC: 6910716. View

13.

Gasecka A, Borovac J, Guerreiro R, Giustozzi M, Parker W, Caldeira D . Thrombotic Complications in Patients with COVID-19: Pathophysiological Mechanisms, Diagnosis, and Treatment. Cardiovasc Drugs Ther. 2020; 35(2):215-229. PMC: 7569200. DOI: 10.1007/s10557-020-07084-9. View

14.

Moriarty P, Gorby L, Stroes E, Kastelein J, Davidson M, Tsimikas S . Lipoprotein(a) and Its Potential Association with Thrombosis and Inflammation in COVID-19: a Testable Hypothesis. Curr Atheroscler Rep. 2020; 22(9):48. PMC: 7381416. DOI: 10.1007/s11883-020-00867-3. View

15.

Patel H, Ashton N, Dobson R, Andersson L, Yilmaz A, Blennow K . Proteomic blood profiling in mild, severe and critical COVID-19 patients. Sci Rep. 2021; 11(1):6357. PMC: 7973581. DOI: 10.1038/s41598-021-85877-0. View

16.

Krishnan S, Nordqvist H, Ambikan A, Gupta S, Sperk M, Svensson-Akusjarvi S . Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication. Mol Cell Proteomics. 2021; 20:100159. PMC: 8490130. DOI: 10.1016/j.mcpro.2021.100159. View

17.

Bock J, Ortea I . Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response. Aging (Albany NY). 2020; 12(12):11277-11286. PMC: 7343490. DOI: 10.18632/aging.103524. View

18.

Li Y, Hou G, Zhou H, Wang Y, Tun H, Zhu A . Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery. Signal Transduct Target Ther. 2021; 6(1):155. PMC: 8047575. DOI: 10.1038/s41392-021-00508-4. View

19.

Haljasmagi L, Salumets A, Rumm A, Jurgenson M, Krassohhina E, Remm A . Longitudinal proteomic profiling reveals increased early inflammation and sustained apoptosis proteins in severe COVID-19. Sci Rep. 2020; 10(1):20533. PMC: 7689507. DOI: 10.1038/s41598-020-77525-w. View

20.

Hou X, Zhang X, Wu X, Lu M, Wang D, Xu M . Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection. Mol Cell Proteomics. 2020; 19(11):1749-1759. PMC: 7664125. DOI: 10.1074/mcp.RP120.002128. View