International Journal of Molecular Sciences

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Dear Colleagues,

Functional genomics can be a preferable tool to study expression changes induced by viral infections, such as COVID-19, as the changes tend to be dynamic or multilevel, as well as irreducibly complex. The corollary of the complexity is that there is no simple reductionist explanation of how an animal cell reacts to a pathogen, either in the early or late stages of an infection. Rather, a genome of the infected cell can move as a whole to a new transcriptomic state. If this hypothesis is generally true, science can benefit from microarray profiling of gene expression patterns during infections.

In the planned Special Issue of the International Journal of Molecular Sciences, I would like to invite the submission of further genomic studies of responses to common pathogens. Transcriptomic or statistical studies are of most interest (genomic studies are also of interest if they are correlated with host responses to an infection).

Dr. Łukasz Huminiecki
Guest Editor

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Keywords

functional genomics
microarrays
RNAseq
bioinformatics
SARS-CoV-2
COVID-19
viral infection

Published Papers (1 paper)

Review

34 pages, 3292 KiB

Open AccessReview

Bulk and Single-Cell RNA Sequencing Elucidate the Etiology of Severe COVID-19

by Łukasz Huminiecki

Int. J. Mol. Sci. 2024, 25(6), 3280; https://doi.org/10.3390/ijms25063280 - 14 Mar 2024

Viewed by 1174

Abstract

Coronavirus disease 2019 (COVID-19) is a type of pneumonia caused by the SARS-CoV-2 coronavirus. It can cause acute pulmonary and systemic inflammation, which can lead to death in severely ill patients. This study explores the potential reasons behind severe COVID-19 and its similarities to systemic autoimmune diseases. This study reviewed unbiased high-throughput gene expression datasets, including next-generation and single-cell RNA sequencing. A total of 27 studies and eight meta-analyses were reviewed. The studies indicated that severe COVID-19 is associated with the upregulation of genes involved in pro-inflammatory, interferon, and cytokine/chemokine pathways. Additionally, changes were observed in the proportions of immune cell types in the blood and tissues, along with degenerative alterations in lung epithelial cells. Genomic evidence also supports the association of severe COVID-19 with various inflammatory syndromes, such as neuronal COVID-19, acute respiratory distress syndrome, vascular inflammation, and multisystem inflammatory syndrome. In conclusion, this study suggests that gene expression profiling plays a significant role in elucidating the etiology of severe COVID-19. Full article

(This article belongs to the Special Issue Genomic Studies Related to SARS-CoV-2 and Other Common Pathogens)

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