Comprehensive analysis of the circRNA expression profile and circRNA-miRNA-mRNA network in the pathogenesis of EV-A71 infection

Hu, Yuanliang; Xu, Yanyan; Duan, Xiaoli; Rui-bing, Wang; Li, Rufang; You, Long; Liu, Longding; Zhang, Yunhui

doi:10.1016/j.virusres.2021.198502

Cited by 10 publications

(11 citation statements)

References 43 publications

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“…Enrichment analysis showed that enriched GO-BP terms mainly focused on the “metabolic process” and “protein modification,” which was largely consistent with EV71 or CV-A16 virus infection. However, enrichment analysis of SH-SY5Y cells infected with EV71 or CA-16 indicated association with the “gonadotropin-releasing hormone receptor pathway,” “Wnt signaling pathway,” “angiogenesis,” and “p53 pathway”, which were not present in our analysis with CVB5 infection [ 24 , 25 ]. In our study, host genes that correspond to the differentially expressed circRNAs were mainly involved in “ubiquitin mediated proteolysis”, “tight junction,” and the regulation of other signaling pathways, such as the MAPK pathway.…”

Section: Discussionmentioning

confidence: 94%

Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5

Yang

Shi

et al. 2022

International Journal of Genomics

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Coxsackievirus B5 (CVB5) is the causative agent of hand, foot, and mouth disease (HFMD) that can cause neurological complications and fatalities. Circular RNA (circRNA) has been shown to play an important role in regulating pathogenic processes. However, the functions of circRNA in response to CVB5 infection remain unclear. In our research, RNA-seq was employed to analyze the expression profiles of circRNAs in SH-SY5Y cells with or without CVB5 infection. Out of 5,665 circRNAs identified to be expressed in SH-SY5Y cells, 163 circRNAs were found to be differentially expressed significantly. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the differentially expressed circRNAs were mainly involved in ubiquitin-mediated proteolysis and signaling pathways during CVB5 infection. Additionally, RT-qPCR was used to validate the RNA-seq data, and a circRNA–miRNA–mRNA interaction network was constructed based on two circRNAs, such as hsa_circ_0008378 and novel_circ_0014617, which were associated with the regulation of innate immune response in host cells. Additionally, we confirmed the two circRANs up-regulated the key factors in the IFN-I signaling pathway, hampering viral replication. Our data provide a new perspective that facilitates further understanding of the virus-host mechanism.

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Section: Discussionmentioning

confidence: 94%

Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5

Yang

Shi

et al. 2022

International Journal of Genomics

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“…Integrative analysis performed by Lu and coauthors revealed regulatory activities of circRNAs and their particular interaction with other RNAs via circRNA-miRNA-mRNA regulatory axis during Hantavirus infection [ 91 ]. In addition various recent study showed that circRNAs have been shown to bind to miRNAs and serve as natural miRNA sponges, influencing the activities of associated miRNAs and the gene expressions controlled by miRNAs [ 92 ]. Prioritized circRNAs includes hsa_circ_0080942 and hsa_circ_0080135.…”

Section: Discussionmentioning

confidence: 99%

Mapping CircRNA–miRNA–mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection

et al. 2023

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Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection.

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“…Also, the ceRNA network involves lncRNAs that act as sponges for miRNAs to regulate mRNA expression. The MALAT1/miR-194-5p/DUSP1 ceRNA regulatory axis during EV71 infection was involved in cell apoptosis, but no association was found with autophagy in that study [ 80 ]. During CV-A16 infection, the three key circRNA-associated ceRNA networks pointed out to the immune system and inflammation mediated by the chemokine and cytokine signaling pathway, including hsa_circ_0004447/hsa-miR-942-5p/MMP2, hsa_circ_0078617/hsa-miR-6780b-5p/ MMP2, and hsa_circ_0078617/hsa-miR-5196-5p/MMP2 [ 79 ].…”

Section: The Network Of Ncrna Profile In Hfmd Virus Infectionmentioning

confidence: 97%

“…About all, 1769 and 1192 circRNAs were differentially expressed in the CVA16-12 h and CVA16-24 h groups. In EV71-infected cells, 10,405 and 4710 circRNAs were detected at 12 h and 24 h post-infection, of which 1851 and 951 circRNAs were differentially expressed in the EV71-12 h and EV71-24 h groups [ 79 , 80 ]. Our group identified the expression profile of circRNAs after CVB5 infection of RD cells [ 81 ].…”

Section: Cellular Circrna Profile In Hfmd Virus Infectionmentioning

confidence: 99%

Roles of Non-Coding RNAs in Virus-Host Interaction About Pathogenesis of Hand-Foot-Mouth Disease

Chen

et al. 2022

Curr Microbiol

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Noncoding RNAs (ncRNAs) represent the largest and main transcriptome products and play various roles in the biological activity of cells and pathological processes. Accumulating evidence shows that microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) are important ncRNAs that play vital regulatory roles during viral infection. Hand-foot-mouth disease (HFMD) virus causes hand-foot-mouth disease, and is also associated with various serious complications and high mortality. However, there is currently no effective treatment. In this review, we focus on advances in the understanding of the modulatory role of ncRNAs during HFMD virus infection. Specifically, we discuss the generation, classification, and regulatory mechanisms of miRNA, lncRNA, and circRNA in the interaction between virus and host, with a particular focus on their influence with viral replication and infection. Analysis of these underlying mechanisms can help provide a foundation for the development of ncRNA-based antiviral therapies.

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Comprehensive analysis of the circRNA expression profile and circRNA-miRNA-mRNA network in the pathogenesis of EV-A71 infection

Cited by 10 publications

References 43 publications

Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5

Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5

Mapping CircRNA–miRNA–mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection

Roles of Non-Coding RNAs in Virus-Host Interaction About Pathogenesis of Hand-Foot-Mouth Disease

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