Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation

Abstract

Circular RNAs (circRNAs) are an integral component of the host competitive endogenous RNA (ceRNA) network. These noncoding RNAs are characterized by their unique splicing reactions to form covalently closed loop structures and play important RNA regulatory roles in cells. Recent studies showed that circRNA expressions were perturbed in viral infections and circRNAs might serve as potential antiviral targets. We investigated the host ceRNA network changes and biological relevance of circRNAs in human lung adenocarcinoma epithelial (Calu-3) cells infected with the highly pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV). A total of ≥49337 putative circRNAs were predicted. Among the 7845 genes which generated putative circRNAs, 147 (1.9%) of them each generated ≥30 putative circRNAs and were involved in various biological, cellular, and metabolic processes, including viral infections. Differential expression (DE) analysis showed that the proportion of DE circRNAs significantly (P < 0.001) increased at 24 h-post infection. These DE circRNAs were clustered into 4 groups according to their time-course expression patterns and demonstrated inter-cluster and intracluster variations in the predicted functions of their host genes. Our comprehensive circRNA-miRNA-mRNA network identified 7 key DE circRNAs involved in various biological processes upon MERS-CoV infection. Specific siRNA knockdown of two selected DE circRNAs (circFNDC3B and circCNOT1) significantly reduced MERS-CoV load and their target mRNA expression which modulates various biological pathways, including the mitogen-activated protein kinase (MAPK) and ubiquitination pathways. These results provided novel insights into the ceRNA network perturbations, biological relevance of circRNAs, and potential host-targeting antiviral strategies for MERS-CoV infection.

Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2

“…For instance, using deep sequencing of mouse lung miRNome upon SARS-CoV infection Peng and co-authors [39] showed that hsa-let-7f-5p, hsa-miR-139-3p, hsa-miR-139-5p were up-regulated directly after the infection in lung cells. A similar miRNA-seq experiment was performed on RNA isolated from Calu-3 human lung adenocarcinoma cells infected by MERS-CoV [40]. Four other miRNAs were aberrantly expressed, including down-regulated hsa-miR-98-5p as well as up-regulated hsa-miR-125a-5p, hsa-miR-125b-5p and hsa-miR-141-3p.…”

Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs

“…Differential expression analyses were performed using DESeq2 R package [ 37 ]. MiRNA profiling of Calu-3 (GSE139516) [ 38 ] and LF (GSE125183) [ 39 ] was performed as a part of independent experiments, limiting direct statistical comparisons between these cell lines. However, miRNAs that play important roles in the susceptibility or resistance to SARS-CoV-2 infection will likely display similar relative expression across cell lines (i.e., miRNAs important to viral susceptibility will likely be more highly expressed relative to other miRNAs in both Huh7 and Calu-3 and lowly expressed in A549 and LF) [ 40 ].…”

The emerging landscape of circular RNAs in immunity: breakthroughs and challenges

“…Specific siRNA knockdown of two taken DE circRNAs (circ-FNDC3B and circ-CNOT1) noticeably down-regulated MERS-CoV load and their target mRNA expression, thus modulating a wide variety of biological pathways, covering the ubiquitination and mitogen-activated protein kinase (MAPK) pathways. The mentioned results expound the potential host-targeting antiviral strategies for MERS-CoV infection, biological relevance of circRNAs, and ceRNA network perturbations [77]. Extents of circ_0004812 were enriched in chronic hepatitis B (CHB) cases and HBV-infected hepatoma cells.…”