Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data.

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Single nucleotide variants (SNVs) located in miRNA target sites (MTS) can disrupt the binding of targeting miRNAs. Anti-correlated miRNA-mRNA pairs between normal and tumor tissues obtained from The Cancer Genome Atlas (TCGA) can reveal important information behind these SNVs on MTS and their associated oncogenesis. In this study, using previously identified anti-correlated miRNA-mRNA pairs in 15 TCGA cancer types and publicly available variant annotation databases, namely dbNSFP (database for nonsynonymous SNPs' functional predictions) and dbMTS (database of miRNA target site SNVs), we identified multiple functional variants and their gene products that could be associated with various types of cancers. We found two genes from dbMTS and 33 from dbNSFP that passed our stringent filtering criteria (e.g., pathogenicity). Specifically, from dbMTS, we identified 23 candidate genes, two of which (BMPR1A and XIAP) were associated with diseases that increased the risk of cancer in patients. From dbNSFP, we identified 65 variants located in 33 genes that were likely pathogenic and had a potential causative relationship with cancer. This study provides a novel way of utilizing TCGA data and integrating multiple publicly available databases to explore cancer genomics.", "claims": [{"id": "claim-method", "statement": "Both tools used multivariate Cox regression to campare survival outcomes between patient groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32824926", "locator": "sections[6] \"2.4. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32824926", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes11090953", "sha256": "sha256:7948ab97464c25a7864f67460b825be31e91c686f62fca4dd1b849c6a273df04", "bytes": 27389, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes11090953", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7565843", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32824926:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5bbf8feab0afbba5eca07f9989c52c6ada1f0f4fe467887b62d55a6c0a351c5d", "bytes": 1514, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#genes-11-00953-t001", "version": null, "note": "Genes harboring 24 variants and their associated TCGA(The Cancer Genome Atlas) cancer types with disrupted miRNAs.", "structure": {"pmcid": "PMC7565843", "section_index": 8, "section_title": "3.1. Twenty four Non-Coding SNVs were Identified at Potential miRNA Target Sites", "row_count": 24, "column_count": 3}, "table": {"label": "Table 1", "caption": "Genes harboring 24 variants and their associated TCGA(The Cancer Genome Atlas) cancer types with disrupted miRNAs.", "rows": [["Gene Symbol", "Cancer Type *", "Disrupted miRNAs"], ["ACVR2B", "BRCA, HNSC, STAD", "has-miR-4670"], ["ADAM12", "THCA, BRCA, HNSC, LUAD", "has-miR-4726"], ["BMPR1A", "LUAD, KICH, KIRC", "has-miR-520f"], ["CD93", "BRCA, LIHC, LUAD, LUSC, STAD", "has-miR-1179"], ["CDS1", "BRCA, STAD, UCEC, KIRC, KIRP, LUAD", "has-miR-411"], ["CHST3", "KIRP, LUAD, STAD", "has-miR-652"], ["ELOVL4", "BRCA, UCEC, KIRC", "has-miR-185"], ["FAM20B", "KIRP, LUAD, UCEC, BRCA, STAD", "has-miR-649"], ["FLRT2", "STAD, BRCA, KIRC, LUAD", "has-miR-5688"], ["GIPC2", "LUAD, STAD", "has-miR-4765"], ["GPR143", "KIRC, KIRP, LIHC", "has-miR-520f"], ["HEMK1", "BRCA, STAD, KIRC, KIRP, LUAD", "has-miR-3911"], ["MAFB", "LUAD, PRAD, STAD, BRCA, HNSC, KICH, KIRC", "has-miR-1266"], ["PGR", "LUAD, PRAD, BRCA, KIRC", "has-miR-182"], ["PRKCA", "BRCA, KIRC, KIRP, LUAD, PRAD", "has-miR-296"], ["PTCHD1", "STAD, THCA, BRCA, HNSC", "has-miR-185"], ["SCN2B", "LUAD, PRAD, STAD, BRCA", "has-miR-141"], ["SLC30A7", "LUAD, PRAD, KICH, KIRC, KIRP, STAD, BRCA", "has-miR-152"], ["SLC39A8", "LUAD, LUSC, PRAD", "has-miR-141"], ["TLL2", "LUAD, STAD, BRCA, COAD, KIRC, KIRP", "has-miR-29a"], ["TRAM2", "LUAD, PRAD, STAD, BRCA", "has-miR-625"], ["XIAP", "BRCA, KIRP, LUAD, PRAD", "has-miR-580"], ["ZDHHC15", "STAD, BRCA, KIRC, LUAD, PRAD", "has-miR-367"]], "row_count": 24, "column_count": 3, "numeric_cells": 30, "header_rows": 1, "locator": "section[8]/table-wrap[1]#genes-11-00953-t001"}}, {"id": "asset:table:pmid:32824926:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8366f2a01ef6dce1b58fe6788413d150318972efe84fb3d7695bf967d09c5fe1", "bytes": 1156, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#genes-11-00953-t002", "version": null, "note": "Somatic SNVs located in miRNA target sites (MTS) identified by CLASH (cross-linking, ligation, and sequencing of hybrids) experiments.", "structure": {"pmcid": "PMC7565843", "section_index": 9, "section_title": "3.2. Two Hundred and Thirty Three Somatic SNVs were Identified in Experimentally Identified miRNA Target Sites", "row_count": 12, "column_count": 7}, "table": {"label": "Table 2", "caption": "Somatic SNVs located in miRNA target sites (MTS) identified by CLASH (cross-linking, ligation, and sequencing of hybrids) experiments.", "rows": [["Chromosome", "Position", "Ref. Allele", "Alt. Allele", "Gene Symbol", "MiRNA", "Cancer Classification((Tissue)(Histology))"], ["1", "154992969", "G", "C", "FLAD1", "let-7b", "(breast)(carcinoma)"], ["3", "49015647", "G", "A", "WDR6", "miR-222", "(large_intestine)(carcinoma)"], ["3", "57559757", "A", "G", "PDE12", "miR-484", "(skin)(malignant_melanoma)"], ["5", "93593940", "G", "A", "NR2F1", "miR-149", "(oesophagus)(carcinoma)"], ["5", "131204977", "A", "T", "LYRM7", "miR-30e", "(liver)(carcinoma)"], ["6", "30724942", "T", "C", "TUBB", "miR-708", "(kidney)(neoplasm)"], ["6", "43504866", "A", "T", "TJAP1", "miR-744", "(ovary)(neoplasm)"], ["7", "56063723", "T", "C", "CCT6A", "miR-3663-3p", "(ovary)(neoplasm)"], ["9", "128695535", "G", "T", "SET", "miR-185", "(ovary)(neoplasm)"], ["16", "68835430", "C", "T", "CDH1", "miR-30c", "(pancreas)(carcinoma)"], ["19", "29675270", "C", "A", "PLEKHF1", "miR-331-3p", "(liver)(carcinoma)"]], "row_count": 12, "column_count": 7, "numeric_cells": 34, "header_rows": 1, "locator": "section[9]/table-wrap[1]#genes-11-00953-t002"}}, {"id": "asset:table:pmid:32824926:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c155ee605c8b9ce8ef5b0bfb244874a74375af9ecb65ba4a554c2bceee538819", "bytes": 745, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#genes-11-00953-t003", "version": null, "note": "COSMIC results for 65 nonsynonymous variants identified from dbNSFP.", "structure": {"pmcid": "PMC7565843", "section_index": 11, "section_title": "3.4. 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