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

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29320577", "kind": "science-record", "revision": 9, "content_hash": "sha256:1e91a8b2c1208c87e3f26c0928aa3643a90fc66bcc49082fec20026f6572fe26", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T22:43:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genome-wide profiling of the PIWI-interacting RNA-mRNA regulatory networks in epithelial ovarian cancers.", "doi": "10.1371/journal.pone.0190485", "pmid": "29320577", "authors": ["Garima Singh", "Jyoti Roy", "Pratiti Rout", "Bibekanand Mallick"], "journal": "PloS one", "year": 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).", "claims": [{"id": "claim-method", "statement": "The differential expression analysis of the small RNAs was performed using DESeq of Bioconductor [28] to obtain a set of piRNAs significantly up- or down-regulated in each of the two EOCa types with respect to normal ovary as a control.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29320577", "locator": "sections[10] \"Identification of differentially expressed piRNAs\" paragraph 2", "quote": "The differential expression analysis of the small RNAs was performed using DESeq of Bioconductor [28] to obtain a set of piRNAs significantly up- or down-regulated in each of the two EOCa types with respect to normal ovary as a control."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA-seq data is submitted to GEO database (GSE83794).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29320577", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The RNA-seq data is submitted to GEO database (GSE83794)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used DESeq with a fold-change threshold of ≥1.5 and p-value ≤0.05 to identify differentially expressed piRNAs in ENOCa and SOCa relative to normal ovary; the underlying RNA-seq data were submitted to GEO under accession GSE83794. The headline result was the identification of 219, 256, and 234 piRNAs in normal ovary, endometrioid ovarian cancer, and serous ovarian cancer samples, respectively.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29320577"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The RNA-seq data is submitted to GEO database (GSE83794)", "r subtypes, serous and endometrioid by small RNA sequencing. We detected 219, 256 and 234 piRNAs in norm", "d western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prev"], "order_basis": "paper_text_order:597", "id": "assay:2"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["opsy. The samples were stored at -80°C until next-generation sequencing, and other experiments were performed. 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