Comprehensive profiling and characterization of cellular microRNAs in response to coxsackievirus A10 infection in bronchial epithelial cells

Abstract

Coxsackievirus A10 (CV-A10), the causative agent of hand, foot, and mouth disease (HFMD), caused a series of outbreaks in recent years and often leads to neurological impairment, but a clear understanding of the disease pathogenesis and host response remains elusive. Cellular microRNAs (miRNAs), a large family of non-coding RNA molecules, have been reported to be key regulators in viral pathogenesis and virus-host interactions. However, the role of host cellular miRNAs defensing against CV-A10 infection is still obscure. To address this issue, we systematically analyzed miRNA expression profiles in CV-A10-infected 16HBE cells by high-throughput sequencing methods in this study. It allowed us to successfully identify 312 and 278 miRNAs with differential expression at 12 h and 24 h post-CV-A10 infection, respectively. Among these, 4 miRNAs and their target genes were analyzed by RT-qPCR, which confirmed the sequencing data. Gene target prediction and enrichment analysis revealed that the predicted targets of these miRNAs were significantly enriched in numerous cellular processes, especially in regulation of basic physical process, host immune response and neurological impairment. And the integrated network was built to further indicate the regulatory roles of miRNAs in host-CV-A10 interactions. Consequently, our findings could provide a beneficial basis for further studies on the regulatory roles of miRNAs relevant to the host immune responses and neuropathogenesis caused by CV-A10 infection.

Keywords: Bioinformatics analysis; Coxsackievirus A10 (CV-A10); Hand, foot, and mouth disease (HFMD); High-throughput sequencing; MicroRNAs (miRNAs).

Fig. 1

Distribution of small RNAs among different categories: infected and uninfected CV-A10 groups

Fig. 2

The miRNA signatures of CV-A10 infection. A Distribution of miRNA expression values in Control, CV-A10-12 h and CV-A10-24 h groups. B Bar graph showing the number of differentially expressed miRNAs in different groups. C Venn diagram displaying the overlapped miRNAs during the process of CV-A10 infection. D Distribution patterns across different samples based on common differentially expressed miRNAs analyzing by hierarchical clustering in HUVEC cells following CV-A10 infection

Fig. 3

Trend analysis of differentially expressed miRNAs in response to CV-A10 infection over time

Fig. 4

Functional enrichment analysis of target genes of persistent up-regulated miRNAs. A GO terms for BP of target genes. B GO terms for MF of target genes. C GO terms for CC of target genes. D KEGG Pathway annotations for target genes

Fig. 5

Functional enrichment analysis of target genes of persistent down-regulated miRNAs. A GO terms for BP of target genes. B GO terms for MF of target genes. C GO terms for CC of target genes. D KEGG Pathway annotations for target genes

Fig. 6

Complex network construction. A Venn plot indicating the target genes obtained from the analysis of BP-related genes and Pathway-related genes mediated by up-regulated miRNAs. B The co-expression network for the predicted target genes potentially involved in cells-pathogen interaction. C Regulatory network linking miRNAs to their putative target genes

Fig. 7

A Venn plot indicating the target genes obtained from the analysis of BP-related genes and Pathway-related genes mediated by down-regulated miRNAs. B The co-expression network for the predicted target genes potentially involved in cells-pathogen interaction. C Regulatory network linking miRNAs to their putative target genes

Fig. 8

RT-qPCR data showing validation of the sequencing results for differentially regulated miRNAs. A and their relevant target genes B in HUVEC cells infected with CV-A10