The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39063083", "kind": "science-record", "revision": 2, "content_hash": "sha256:b0ab3fcdeeed9e7401b4f5eee2be703e0338d670742eb1f7cca1ae7fa01704e1", "created_at": "2026-11-01T20:29:08Z", "updated_at": "2026-11-01T21:33:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors.", "doi": "10.3390/ijms25147841", "pmid": "39063083", "authors": ["Kacper Maciejewski", "Marek Giers", "Urszula Oleksiewicz", "Patrycja Czerwinska"], "journal": "International journal of molecular sciences", "year": 2024, "abstract": "Dysregulation of histone deacetylases (HDACs) is closely associated with cancer development and progression. Here, we comprehensively analyzed the association between all HDAC family members and several clinicopathological and molecular traits of solid tumors across 22 distinct tumor types, focusing primarily on cancer stemness and immunity. To this end, we used publicly available TCGA data and several bioinformatic tools (i.e., GEPIA2, TISIDB, GSCA, Enrichr, GSEA). Our analyses revealed that class I and class II HDAC proteins are associated with distinct cancer phenotypes. The transcriptomic profiling indicated that class I HDAC members, including HDAC2, are positively associated with cancer stemness, while class IIA HDAC proteins, represented by HDAC7, show a negative correlation to cancer stem cell-like phenotypes in solid tumors. In contrast to tumors with high amounts of HDAC7 proteins, the transcriptome signatures of HDAC2-overexpressing cancers are significantly enriched with biological terms previously determined as stemness-associated genes. Moreover, high HDAC2-expressing tumors are depleted with immune-related processes, and HDAC2 expression correlates with tumor immunosuppressive microenvironments. On the contrary, HDAC7 upregulation is significantly associated with enhanced immune responses, followed by enriched infiltration of CD4+ and CD8+ T cells. This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors.", "claims": [{"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the TCGA and Prognoscan repositories—TCGA: BLCA, BRCA, CESC, ESCA, GBM, HNSC, KIRC, KIRC, LIHC, LUAD, LUSC, OV, PAAD, PRAD, SARC, SKCM, STAD, TGCT, THCA, UCEC datasets (Firehose Legacy) from the cBioportal, https://www.cbioportal.org/ (accessed on 15 October 2023); and GDC PANCAN dataset from the USCS Xena Browser, https://xena.ucsc.edu/ (accessed on 22 October 2023); Prognoscan: all available datasets at http://dna00.bio.kyutech.ac.jp/PrognoScan/ (accessed on 8 May 2024).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39063083", "locator": "sections[25] \"Data Availability Statement\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the TCGA and Prognoscan repositories—TCGA: BLCA, BRCA, CESC, ESCA, GBM, HNSC, KIRC, KIRC, LIHC, LUAD, LUSC, OV, PAAD, PRAD, SARC, SKCM, STAD, TGCT, THCA, UCEC datasets (Firehose Legacy) from the cBioportal, https://www.cbioportal.org/ (accessed on 15 October 2023); and GDC PANCAN dataset from the USCS Xena Browser, https://xena.ucsc.edu/ (accessed on 22 October 2023); Prognoscan: all available datasets at http://dna00.bio.kyutech.ac.jp/PrognoScan/ (accessed on 8 May 2024)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39063083", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "This is the first comprehensive report demonstrating robust and versatile associations between specific HDAC family members, cancer dedifferentiation, and anti-tumor immune statuses in solid tumors.", "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:39063083"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["Melanoma-PRJEB23709", "STAD-PRJEB25780", "Melanoma-GSE100797", "RCC-GSE67501"], "resolved_accessions": [], "statements": ["The datasets supporting the conclusions of this article are available in the TCGA and Prognoscan repositories—TCGA: BLCA, BRCA, CESC, ESCA, GBM, HNSC, KIRC, KIRC, LIHC, LUAD, LUSC, OV, PAAD, PRAD, SARC, SKCM, STAD, TGCT, THCA, UCEC datasets (Firehose Legacy) from the cBioportal, https://www.cbioportal.org/ (accessed on 15 October 2023); and GDC PANCAN dataset from the USCS Xena Browser, https://xena.ucsc.edu/ (accessed on 22 October 2023); Prognoscan: all available datasets at http://dna00.bio.kyutech.ac.jp/PrognoScan/ (accessed on 8 May 2024)."], "basis": "The paper names Melanoma-PRJEB23709, STAD-PRJEB25780, Melanoma-GSE100797, RCC-GSE67501, but the accession does not resolve in the repository (no reason recorded, no reason recorded, no reason recorded, no reason recorded), so the data cannot be reached from here. 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