Epigenetics of COVID-19 infected lung: systematic review and meta-analysis of gene expression data

Abstract

Objective: To investigate homogeneity and efficiency of applicating models of lung/bronchial organoids for SARS-COV2 infection research and evaluate the role of differentially expressed cytokine genes of interest.
Methods: in this systematic review and meta-analysis of Gene Expression ombious datasets, studies of lung/bronchial organoids as models of SARS-COV2 infection were evaluated. 4 datasets of GSE160435, GSE148697, GSE150819, and GSE152060 were selected for our study. DESeq / EdgeR technique was used to identify Differential Expressed Genes (DEGs).
Results: The distribution of the pooled dataset showed small variations among the 4 selected datasets. K-means cluster analysis using the KEGG Pathway database revealed activation of a cluster of genes in response to coronavirus diseases including 51 genes in the pathway of KEGG, that could verify the organoids in comparison of real COVID-19 disease specimens. proinflammatory cytokines and Granulocyte-macrophage colony-stimulating factors were selected as our genes of interest-based on the literature. We only found significant upregulation of TNF-alpha, IL23A, and IL17A genes and significant Downregulation of CSF2RB, IL20RB/A, IL24B. while downregulation of CSF2 was in controversy with reported literature.
Conclusion: Based on the data that ultimately reached the conclusion of the interferon 1 function in COVID-19 pathology, this work may confirm the models of SARS-COV-2 infection in lung organoids; nevertheless, the contradiction to real-world studies requires more research.