Genome-wide profiling of the PIWI-interacting RNA-mRNA regulatory networks in epithelial ovarian cancers

PLoS One. 2018 Jan 10;13(1):e0190485. doi: 10.1371/journal.pone.0190485. eCollection 2018.

Abstract

PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing. We detected 219, 256 and 234 piRNAs in normal ovary, endometrioid and serous ovarian cancer samples respectively. We observed piRNAs are encoded from various genomic regions, among which introns harbor the majority of them. Surprisingly, piRNAs originated from different genomic contexts showed the varied level of conservations across vertebrates. The functional analysis of predicted targets of differentially expressed piRNAs revealed these could modulate key processes and pathways involved in ovarian oncogenesis. Our study provides the first comprehensive piRNA landscape in these samples and a useful resource for further functional studies to decipher new mechanistic views of piRNA-mediated gene regulatory networks affecting ovarian oncogenesis. The RNA-seq data is submitted to GEO database (GSE83794).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carcinoma, Ovarian Epithelial
  • Female
  • Gene Expression Profiling*
  • Gene Regulatory Networks*
  • Humans
  • Neoplasms, Glandular and Epithelial / genetics*
  • Ovarian Neoplasms / genetics*
  • RNA, Messenger / genetics*
  • RNA, Small Interfering / genetics*

Substances

  • RNA, Messenger
  • RNA, Small Interfering

Grants and funding

This work was supported by Department of Science and Technology, Govt. of India (SR/WOS-A/LS-311/2013) awarded to G.S. and Department of Biotechnology, Govt. of India (BT/PR6772/GBD/27/468/2012) awarded to B.M.