Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse

Frontiers in Immunology
Luiz G GardinassiSimone G Fonseca

Abstract

The current pandemic of coronavirus disease 19 (COVID-19) has affected millions of individuals and caused thousands of deaths worldwide. The pathophysiology of the disease is complex and mostly unknown. Therefore, identifying the molecular mechanisms that promote progression of the disease is critical to overcome this pandemic. To address such issues, recent studies have reported transcriptomic profiles of cells, tissues and fluids from COVID-19 patients that mainly demonstrated activation of humoral immunity, dysregulated type I and III interferon expression, intense innate immune responses and inflammatory signaling. Here, we provide novel perspectives on the pathophysiology of COVID-19 using robust functional approaches to analyze public transcriptome datasets. In addition, we compared the transcriptional signature of COVID-19 patients with individuals infected with SARS-CoV-1 and Influenza A (IAV) viruses. We identified a core transcriptional signature induced by the respiratory viruses in peripheral leukocytes, whereas the absence of significant type I interferon/antiviral responses characterized SARS-CoV-2 infection. We also identified the higher expression of genes involved in metabolic pathways including heme biosynthes...Continue Reading

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Datasets Mentioned

BETA
HRA000143
SARS-CoV-1
GSE90732
GSE147507
E-MTAB-8871
GSE1739
GSE34205
CRA002390
GSE6269

Methods Mentioned

BETA
RNA-seq
bronchoalveolar
lavage
biopsies

Software Mentioned

DESeq2
R
gplots
Cytoscape
GSEA
DESeq2 package
Gene Set Enrichment Analysis ( GSEA )
EdgeR package R
ggplot2
amap

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