Identification of TP53 mutation associated-immunotype and prediction of survival in patients with hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32355765", "kind": "science-record", "revision": 7, "content_hash": "sha256:8863ac7038bc6b4dda4475c11cdf09e2ce865386f0e07fde0440e2d0d13fe748", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:01:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of TP53 mutation associated-immunotype and prediction of survival in patients with hepatocellular carcinoma.", "doi": "10.21037/atm.2020.02.98", "pmid": "32355765", "authors": ["Muqi Shi", "Yan Wang", "Weidong Tang", "Xiaohong Cui", "Han Wu", "Yijie Tang", "Peng Wang", "Wei Wu", "Haijian Zhang"], "journal": "Annals of translational medicine", "year": 2020, "abstract": "BACKGROUND: Stratification of tumors is necessary to achieve better clinical outcomes. Hepatocellular carcinoma (HCC) is commonly associated with mutation of the TP53 gene and heterogeneity in immune cell content. However, TP53 mutation-associated immunotype of HCC has not been reported yet. This study aimed to identify the TP53 mutation-associated immunotype in HCC.\nMETHODS: The mutation annotation format (MAF) document, mRNA expression data, and clinical data of HCC patients were downloaded from the publicly available The Cancer Genome Atlas (TCGA) data portal. Data from 332 HCC patients were analyzed in this study. Infiltrating immune cells were evaluated by the well-known CIBERSORT method. Additional mutation data of HCC patients were downloaded from the Catalogue of Somatic Mutations in Cancer (COSMIC) database.\nRESULTS: The TP53 gene harbored the highest frequency of mutations in HCC patients. Consequently, five lethal features, including TP53 mutations, were screened by least absolute shrinkage and selector operation (LASSO)-COX regression, according to TP53 mutations and 22 infiltrating immune cells. Two distinct subgroups of HCC were identified, namely, immunotypes A and B. Furthermore, the expression levels of co-inhibitory immune checkpoints were significantly upregulated, and the gene ontology (GO) terms or pathways to boost immune responses were found to be inhibited in the immunotype B subgroup compared to that in the immunotype A subgroup. Finally, we proved immunotype to be an independent adverse prognostic factor that contributed to improvement in the predictive accuracy of the immunotype-based model and helped in avoiding excessive medical treatment.\nCONCLUSIONS: Two distinct immunotypes of HCC, in terms of prognosis, phenotype, and function, were identified and the traditional understanding of intratumoralCD8+ T cells was subverted. Moreover, the identified immunotypes contributed to improving the predictive accuracy of the immunotype-based model and helped in avoiding excessive medical treatment in some HCC patients.", "claims": [{"id": "claim-data-access", "statement": "The mutation annotation format (MAF) document, mRNA expression data, and clinical data of HCC patients were downloaded from the publicly available TCGA data portal (up to June 13, 2018, https://tcga-data.nci.nih.gov). The MAF files were downloaded from the official website of TCGA and used to determine TMB.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32355765", "locator": "sections[4] \"Patient population\" paragraph 2", "quote": "The mutation annotation format (MAF) document, mRNA expression data, and clinical data of HCC patients were downloaded from the publicly available TCGA data portal (up to June 13, 2018, https://tcga-data.nci.nih.gov)."}, {"asset": "source:pmid:32355765", "locator": "sections[5] \"Tumor mutational burden (TMB)\" paragraph 2", "quote": "The MAF files were downloaded from the official website of TCGA and used to determine TMB."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32355765"], "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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