Transcriptome analysis following enterovirus 71 and coxsackievirus A16 infection in respiratory epithelial cells

Abstract

Enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) are the major pathogens responsible for hand, foot and mouth disease (HFMD), but the mechanism by which these viruses cause disease remains unclear. In this study, we used transcriptome sequencing technology to investigate changes in the transcriptome profiles after infection with EV-A71 and CV-A16 in human bronchial epithelial (16HBE) cells. Using systematic bioinformatics analysis, we then searched for useful clues regarding the pathogenesis of HFMD. As a result, a total of 111 common differentially expressed genes were present in both EV-A71-and CV-A16-infected cells. A trend analysis of these 111 genes showed that 91 of them displayed the same trend in EV-A71 and CV-A16 infection, including 49 upregulated genes and 42 downregulated genes. These 91 genes were further used to conduct GO, pathway, and coexpression network analysis. It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. Finally, we randomly selected 10 differentially expressed genes for qRT-PCR to validate the transcriptome sequencing data. The experimental qRT-PCR results were roughly in agreement with the results of transcriptome sequencing. Collectively, our results provide clues to the mechanism of pathogenesis of HFMD induced by EV-A71 and CV-A16.

HMGB1 is involved in viral replication and the inflammatory response in coxsackievirus A16-infected 16HBE cells via proteomic analysis and identification

“…In the past decade, transcriptomics has been used to analyze the interactions between viruses and host cells [ 8 ]. We also performed an in-depth analysis of the changes in transcriptomics in respiratory epithelial cells following EV-A71 and CV-A16 infections, which also provided useful clues regarding the pathogenesis of HFMD [ 9 ]. However, the identification of changes in the transcriptome can only represent the transcriptional level, and the genes that are changed at the transcriptional level cannot directly reflect the situation of their protein levels, while the proteins are what truly works in the body, and the differential protein expression can better reflect the physiological changes of host cells induced by virus infection [ 10 , 11 ].…”

Transcriptome sequencing analysis of echovirus 30 infection reveals its potential pathogenesis

“…RNA sequencing (RNA-Seq) is widely used to investigate the differences in gene expressions at genome-wide levels ( Stark et al, 2019 ; Zhang et al, 2021 ). Many studies have analyzed the transcriptome expression profiles of microbial infections, which provide clues regarding pathogenic mechanisms ( Poma et al, 2020 ; Song et al, 2020 ; Li et al, 2021 ). At present, most of the data associated with RNA-Seq of EVs are about enterovirus 71 (EV-A71) and coxsackievirus A16 (CVA16) ( Song et al, 2020 ).…”

“…Many studies have analyzed the transcriptome expression profiles of microbial infections, which provide clues regarding pathogenic mechanisms ( Poma et al, 2020 ; Song et al, 2020 ; Li et al, 2021 ). At present, most of the data associated with RNA-Seq of EVs are about enterovirus 71 (EV-A71) and coxsackievirus A16 (CVA16) ( Song et al, 2020 ). In contrast, RNA-Seq data about E30, which is a virulent EV, are lacking, and hence, there is an urgent need to further supplement the RNA-Seq analysis.…”