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Review
. 2021 Dec 7;19(1):501.
doi: 10.1186/s12967-021-03168-8.

Multi-omics approach to COVID-19: a domain-based literature review

Chiara Montaldo #  1 , Francesco Messina #  1 , Isabella Abbate  1 , Manuela Antonioli  1 , Veronica Bordoni  1 , Alessandra Aiello  1 , Fabiola Ciccosanti  1 , Francesca Colavita  1 , Chiara Farroni  1 , Saeid Najafi Fard  1 , Emanuela Giombini  1 , Delia Goletti  1 , Giulia Matusali  1 , Gabriella Rozera  1 , Martina Rueca  1 , Alessandra Sacchi  1 , Mauro Piacentini  1   2 , Chiara Agrati  1 , Gian Maria Fimia  1   3 , Maria Rosaria Capobianchi  4 , Francesco Nicola Lauria  1 , Giuseppe Ippolito  1
Affiliations
Review

Multi-omics approach to COVID-19: a domain-based literature review

Chiara Montaldo et al. J Transl Med. .

Abstract

Background: Omics data, driven by rapid advances in laboratory techniques, have been generated very quickly during the COVID-19 pandemic. Our aim is to use omics data to highlight the involvement of specific pathways, as well as that of cell types and organs, in the pathophysiology of COVID-19, and to highlight their links with clinical phenotypes of SARS-CoV-2 infection.

Methods: The analysis was based on the domain model, where for domain it is intended a conceptual repository, useful to summarize multiple biological pathways involved at different levels. The relevant domains considered in the analysis were: virus, pathways and phenotypes. An interdisciplinary expert working group was defined for each domain, to carry out an independent literature scoping review.

Results: The analysis revealed that dysregulated pathways of innate immune responses, (i.e., complement activation, inflammatory responses, neutrophil activation and degranulation, platelet degranulation) can affect COVID-19 progression and outcomes. These results are consistent with several clinical studies.

Conclusions: Multi-omics approach may help to further investigate unknown aspects of the disease. However, the disease mechanisms are too complex to be explained by a single molecular signature and it is necessary to consider an integrated approach to identify hallmarks of severity.

Keywords: COVID-19; Conceptual domain; Host signatures; Omics; Pathways; Phenotypes; SARS-CoV-2.

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Conflict of interest statement

The authors declare no competing interests. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Fig. 1
Fig. 1
Schematic diagram of conceptual domains, subdomains, and omics data, distributed on scale gradient. The definition of COVID-19 phenotypes is the WHO one [9]
Fig. 2
Fig. 2
Article selection flowchart
Fig. 3
Fig. 3
Omics contribution in understanding COVID-19 pathogenesis. Omics data analyzed, organized by omics technique, tissue and pathways comparing COVID-19 to healthy donors or severe versus mild outcomes. Red lines represent upregulated pathways, blue lines represent downregulated processes. A black line is used when the same pathway has been described as both up- and down-regulated
See this image and copyright information in PMC

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