Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes

Abstract

In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission. To further understand the molecular mechanisms underlying the associations of HPV infection with genital diseases, we developed a systematic method for viral miRNA identification and viral miRNA-mediated regulatory network construction based on genome-wide sequence analysis. The complete genomes of certain high-risk HPV subtypes were used to predict putative viral pre-miRNAs by bioinformatics approaches. In addition, small RNA libraries in human cervical lesions from existing publications were collected to validate the predicted HPV pre-miRNAs. For the construction of virally encoded miRNA-mediated regulatory network of HPV infection, cervical squamous epithelial carcinoma gene expression data were extracted from the RNA sequencing platform in The Cancer Genome Atlas; the differentially expressed genes were used to identify the putative targets of viral miRNAs. Predicted cellular target genes of HPV-encoded miRNAs provide an overview of these viral miRNA's putative functions. Finally, a large-scale genome analysis was carried out to examine the phylogenetic relationship and structural evolution among genital HPV types that have the potential to cause genital cancer. In this study, we discovered putative HPV-encoded miRNAs, which were validated against the small RNA libraries in human cervical lesions. Furthermore, as indicated by their biological functions, host genes targeted by HPV-encoded miRNAs may play significant roles in virus infection and carcinogenesis. These viral miRNAs pose as promising candidates for the development of antiviral drugs. More importantly, the identified subtype-specific miRNAs have the potential to be used as biomarkers for HPV subtype determination.

Viral miRNAs as Active Players and Participants in Tumorigenesis

“…Interestingly, HPV41-miRNAs and FcPV1-miRNAs are involved in the control of HPV life cycle [83]. In other recent studies, Weng et al showed that HPV-miRNAs differ in their number depending on the HPV species [15], and Virtanem et al revealed that miRNAs belonging to HPV-16 species such as miR-H1, miR-H3, miR-H5, and miR-H6 were found in tumor samples [84]. Qian et al recognized nine putative HPV-encoded miRNAs, (HPV6-mir-H1, HPV16-mir-H1, HPV16-mir-H2, HPV16-mir-H3, HPV16-mir-H5, HPV16-mir-H6, HPV38-mir-H1, HPV45-mir-H1, and HPV68-mir-H1) through tissue sequencing of human cervical lesion and cell lines.…”

“…The characterization of the complete genomes of HPV subtypes by bioinformatics methods also allows the prediction of potential v-miRNAs and their target genes, providing a fundamental tool for understanding the role of HPV-encoded miRNAs in the carcinogenesis process of HPV-associated cancers [15]. Further studies are needed to discover new HPV-encoded miRNAs and their implications for both virus infection and carcinogenesis.…”

“…Considering that the survival ability of a virus depends on its capacity to escape host immunosurveillance [14], viruses encode multiple miRNAs that show immunomodulatory functions involved in the regulation of critical innate and adaptive immune mechanisms used by the host to defend himself [14]. Moreover, it has been described that v-miRNAs allow viruses to enter the latent phase of their life cycle and become undetected by the host's immune system, with this being a further risk factor for cancer development [15]. Here we have examined the current knowledge of miRNAs encoded by six oncoviruses, Epstein-Barr virus (EBV), Kaposi's Sarcoma Herpesvirus/Human Herpesvirus-8 (KSHV/HHV8), Human Papillomavirus (HPV), Hepatitis C Virus (HCV), Hepatitis B Virus (HBV) and Merkel Cell Polyomavirus (MCPyV) (Figure 1), and the virally influenced cellular pathways (Table 1) and their relationships with the immune system.…”

Improvement in RNA quantity and quality in cervico-vaginal cytology

“…Previous studies have demonstrated the important role of long non-coding RNAs, circular RNAs, microRNAs and mRNAs in cervical cancer development and progression [2][3][4]. High-quality RNA is a pre-requisite for gene expression studies.…”

The Role of miRNAs in Virus-Mediated Oncogenesis

“…Several years later, the same group performed the analysis of the reported miRNAs in cervical samples by quantitative RT–PCR, and they detected low levels of expression of these miRNAs in all cases [ 198 ]. Finally, Weng et al [ 199 ] have developed a systematic method for viral miRNA identification and regulatory network construction based on genome-wide sequence analysis, and have predicted other putative miRNAs by bioinformatics approaches. The target genes of these predicted miRNAs play roles in virus infection and carcinogenesis and might be possible targets for antiviral drugs.…”