Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34820170", "kind": "science-record", "revision": 4, "content_hash": "sha256:d6f17ab2c42bb8e88a3ad8ab15b3cbf72ccd16108951275db6396d40090c4ed1", "created_at": "2026-11-01T17:36:31Z", "updated_at": "2026-11-01T22:05:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of keygenes, miRNAs and miRNA-mRNA regulatory pathways for chemotherapy resistance in ovarian cancer.", "doi": "10.7717/peerj.12353", "pmid": "34820170", "authors": ["Wenwen Wang", "Wenwen Zhang", "Yuanjing Hu"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Chemotherapy resistance, especially platinum resistance, is the main cause of poor prognosis of ovarian cancer. It is of great urgency to find molecular markers and mechanism related to platinum resistance in ovarian cancer.\nMETHODS: One mRNA dataset (GSE28739) and one miRNA dataset (GSE25202) were acquired from Gene Expression Omnibus (GEO) database. The GEO2R tool was used to screen out differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) between platinum-resistant and platinum-sensitive ovarian cancer patients. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed using the DAVID to present the most visibly enriched pathways. Protein-protein interaction (PPI) of these DEGs was constructed based on the information of the STRING database. Hub genes related to platinum resistance were visualized by Cytoscape software. Then, we chose seven interested hub genes to further validate using qRT-PCR in A2780 ovarian cancer cell lines. And, at last, the TF-miRNA-target genes regulatory network was predicted and constructed using miRNet software.\nRESULTS: A total of 63 upregulated DEGs, 124 downregulated DEGs, four upregulated miRNAs and six downregulated miRNAs were identified. From the PPI network, the top 10 hub genes were identified, which were associated with platinum resistance. Our further qRT-PCR showed that seven hub genes (BUB1, KIF2C, NUP43, NDC80, NUF2, CCNB2 and CENPN) were differentially expressed in platinum-resistant ovarian cancer cells. Furthermore, the upstream transcription factors (TF) for upregulated DE-miRNAs were SMAD4, NFKB1, SMAD3, TP53 and HNF4A. Three overlapping downstream target genes (KIF2C, STAT3 and BUB1) were identified by miRNet, which was regulated by hsa-miR-494.\nCONCLUSIONS: The TF-miRNA-mRNA regulatory pairs, that is TF (SMAD4, NFKB1 and SMAD3)-miR-494-target genes (KIF2C, STAT3 and BUB1), were established. In conclusion, the present study is of great significance to find the key genes of platinum resistance in ovarian cancer. Further study is needed to identify the mechanism of these genes in ovarian cancer.", "claims": [{"id": "claim-method", "statement": "GEO online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used. Genes that met the criteria (adjusted p value < 0.05 and |log2Fold Change| ≥ 0.5) were considered as DEGs. Adjusted p value < 0.05 and |log2Fold Change| ≥ 1.5 were set as the thresholds for identifying DE-miRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34820170", "locator": "sections[4] \"Identification of DEGs and DE-miRNAs\" paragraph 2", "quote": "GEO online analysis tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used. Genes that met the criteria (adjusted p value < 0.05 and |log2Fold Change| ≥ 0.5) were considered as DEGs. Adjusted p value < 0.05 and |log2Fold Change| ≥ 1.5 were set as the thresholds for identifying DE-miRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data are available as Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34820170", "locator": "sections[29] \"Data Availability\" paragraph 2", "quote": "The raw data are available as Supplemental Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of GSE28739 and GSE25202 identified 187 DEGs and 10 DE-miRNAs between platinum-resistant and platinum-sensitive ovarian cancer samples.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Based on GEO2R analysis, a total of 187 DEGs (63 upregulated genes and 124 downregulated genes) were identified based on the criteria of adjusted p value < 0.05 and |log2Fold Change| ≥ 0.5."}, "evidence": [{"asset": "source:pmid:34820170", "locator": "sections[14] \"Identification of DEGs and DE-miRNAs\" paragraph 2", "quote": "Based on GEO2R analysis, a total of 187 DEGs (63 upregulated genes and 124 downregulated genes) were identified based on the criteria of adjusted p value < 0.05 and |log2Fold Change| ≥ 0.5."}, {"asset": "source:pmid:34820170", "locator": "sections[14] \"Identification of DEGs and DE-miRNAs\" paragraph 2", "quote": "In miRNA datasets GES25202, a total of 10 DE-miRNAs (four upregulated miRNAs and six downregulated miRNAs) were detected, which was shown in Table 3."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of GSE28739 and GSE25202 identified 187 DEGs and 10 DE-miRNAs between platinum-resistant and platinum-sensitive ovarian cancer samples.", "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:34820170"], "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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