Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33987034", "kind": "science-record", "revision": 6, "content_hash": "sha256:33cadef5eade402448352a7f646e6c7d7ec465d07d07a50d4dd4a737a5f175be", "created_at": "2026-11-01T15:41:35Z", "updated_at": "2026-11-01T21:25:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer.", "doi": "10.7717/peerj.11377", "pmid": "33987034", "authors": ["Chongyang Ren", "Xiaojiang Tang", "Haitao Lan"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq.\nMETHODS: We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset.\nRESULTS: We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis.", "claims": [{"id": "claim-method", "statement": "Survival analysis was performed in R Studio with the survminer package via the Cox proportional hazards regression model and visualized by survival package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33987034", "locator": "sections[5] \"Correlation and survival analysis\" paragraph 3", "quote": "Survival analysis was performed in R Studio with the survminer package via the Cox proportional hazards regression model and visualized by survival package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nData is available at NCBI GEO: GSE20685 and at Xena.\nLink to Xena: https://xenabrowser.net/datapages/?dataset=TCGA.BRCA.sampleMap%2FHiSeqV2host=https%3A%2F%2Ftcga.xenahubs.netremoveHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33987034", "locator": "sections[29] \"Data Availability Statement\" paragraphs 1-4", "quote": "The following information was supplied regarding data availability:\nData is available at NCBI GEO: GSE20685 and at Xena.\nLink to Xena: https://xenabrowser.net/datapages/?dataset=TCGA.BRCA.sampleMap%2FHiSeqV2host=https%3A%2F%2Ftcga.xenahubs.netremoveHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33987034"], "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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"taxon": "Homo sapiens", "title": "Microarray-based molecular subtyping of breast cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33987034:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e342b821265d9042e4e3acaff0536aff9d3c533cdf03e7f32769f479ee02740d", "bytes": 524, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#table-1", "version": null, "note": "Hazard ratio and P value of each group.", "structure": {"pmcid": "PMC8103922", "section_index": 15, "section_title": "Survival and protein-protein interaction network analysis", "row_count": 5, "column_count": 6}, "table": {"label": "Table 1", "caption": "Hazard ratio and P value of each group.", "rows": [["Data source", 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