Dataset Information

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

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).

SUBMITTER: Singh G

PROVIDER: S-EPMC5761873 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Singh Garima G Roy Jyoti J Rout Pratiti P Mallick Bibekanand B

PloS one 20180110 1

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 ...[more]

PMID: 29320577

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Project description:Purpose: The aim of this study is to identify known and novel small RNAs (Piwi-interacting RNAs and microRNAs) in normal ovary and epithelial ovarian malignancies by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways of the two most frequently observed and highly lethal subtypes of epithelial ovarian cancers, endometrioid ovarian cancer (ENOCa) and serous ovarian cancer (SOCa). The study has been performed in normal ovarian tissues as well as malignant tissues of these cancer subtypes. Methods: 1 µg of total RNA was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. Small RNA sequencing was carried out by Genotypic Technology, Bangalore, India on Illumina Next-Seq 500 platform. Library preparation was done by performing 3' and 5' adapter ligation followed by reverse transcription of cDNA and amplification of the library. The construct of the library was fractionated to select 16-40 nucleotide insert of small RNAs using PAGE. The quality check of the library was done in Agilent Technologies 2100 Bioanalyzer using a DNA-specific chip, such as High Sensitivity DNA. The sequence reads that passed through Quality Check by FastQC and aligned to the human genome (hg19) were further analysed using in-house pipelines and set of known and novel piRNAs and miRNAs were identified. The sets of known piRNAs and miRNAs identified were assessed for their involvement in neoplastic processes of ovarian cancer subtypes by performing target analysis and GO enrichment studies. Results: Using an in-house prediction pipeline, we mapped about 10-15 million sequence reads per sample to the human genome (hg19) and detected 256, 234 and 219 annotated piRNAs in ENOCa, SOCa, and normal ovary respectively; whereas the average number of known miRNAs present in each sample was estimated to be 480. The annotated piRNAs obtained from each sample exhibited varied length distribution between 26-32 nts. Conclusions: For the first time, our study reported the presence of piRNAs in ENOCa, SOCa and normal ovarian tissue from the next-gen sequencing of small RNAs of 16-40 nts length. The extensive catalogue of human EOCa small RNAs (both piRNAs and miRNAs) detected in this study provides a useful resource to dissect complex neoplastic events that are possibly mediated by these ncRNAs, especially by piRNAs. Moreover, these piRNAs could be used as probable small RNA biomarkers for the EOCa.

Dataset Information

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

Publications

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

Similar Datasets

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