Transcription Factor Driven Gene Regulation in COVID-19 Patients

Abstract

SARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcription factors can play in driving differential regulation in patients affected by COVID-19 is a focal point to unveil virus infection. In this regard, we have identified 19 transcription factors which are predicted to target human proteins interacting with Spike glycoprotein of SARS-CoV-2. Transcriptomics RNA-Seq data derived from 13 human organs are used to analyse expression correlation between identified transcription factors and related target genes in both COVID-19 patients and healthy individuals. This resulted in the identification of transcription factors showing the most relevant impact in terms of most evident differential correlation between COVID-19 patients and healthy individuals. This analysis has also identified five organs such as the blood, heart, lung, nasopharynx and respiratory tract in which a major effect of differential regulation mediated by transcription factors is observed. These organs are also known to be affected by COVID-19, thereby providing consistency to our analysis. Furthermore, 31 key human genes differentially regulated by the transcription factors in the five organs are identified and the corresponding KEGG pathways and GO enrichment are also reported. Finally, the drugs targeting those 31 genes are also put forth. This in silico study explores the effects of transcription factors on human genes interacting with Spike glycoprotein of SARS-CoV-2 and intends to provide new insights to inhibit the virus infection.

scSniper: Single-cell Deep Neural Network-based Identification of Prominent Biomarkers

“…Notably, the figure showcases an increase in ribosome related genes in expression from classical monocytes derived from diseased patients compared to the healthy control. The importance of RPS14 as a transcription factor for COVID-19 has been supported by its listing as a predicted marker in [29]. Other genes like RPS19, RPL26, and RPS7 have also been flagged as differentially expressed genes in COVID-19 by [30].…”

Long COVID: Molecular Mechanisms and Detection Techniques

“…A major unknown is the organ and tissue distribution of the TFs associated with COVID-19. An interesting discovery is the identification of a list of 19 TFs regulating the expression of a network of 31 gene products directly interacting with the Spike protein of COVID-19, especially in the blood, heart, lung, nasopharynx, and respiratory tract [ 51 ]. Several TFs in the list belonged to the Krüppel-like factor family (KLF), which raises the prospect of redundant or overlapping regulation.…”