Combined identification of ARID1A, CSMD1, and SENP3 as effective prognostic biomarkers for hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33558447", "kind": "science-record", "revision": 7, "content_hash": "sha256:74dd728a2790a953db605d2b808c5fdfaff9c93f4de877e5fb3137b6b839866f", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Combined identification of ARID1A, CSMD1, and SENP3 as effective prognostic biomarkers for hepatocellular carcinoma.", "doi": "10.18632/aging.202586", "pmid": "33558447", "authors": ["Yuanyuan Zhao", "Bo Yang", "Dong Chen", "Xiaojun Zhou", "Meixi Wang", "Jipin Jiang", "Lai Wei", "Zhishui Chen"], "journal": "Aging", "year": 2021, "abstract": "BACKGROUND: The current study aimed to understand the genetic landscape and investigate the diagnostic and prognostic biomarkers of primary hepatocellular carcinoma (HCC).\nMETHODS: A cohort of 36 Chinese HCC samples with hepatitis B virus (HBV) infection was examined by whole-exome sequencing (WES). Prognosis-related alterations were identified and further verified in the TCGA database and GSE65372 profiles in the GEO database. A Chinese replication cohort of 180 HCC samples with HBV infection was collected to evaluate the candidate genes by immunohistochemical analysis. A receiver operating characteristic (ROC) curve analysis evaluated the prognostic power of candidate genes. Finally, EdU and transwell invasion assay were performed to detect the function of candidate genes.\nRESULTS: A total of 11 novel genes showed a significant association with HCC in the discovery cohort. The data were verified using the GEO and TCGA databases, and the expression of ARID1A, CSMD1, and SENP was evaluated in the replication cohort. Furthermore, ARID1A, CSMD1, and SENP3 are effective prognostic biomarkers for HCC patients in the replication population.\nCONCLUSIONS: Molecular heterogeneity was detected in HCC patients, and ARID1A, CSMD1, and SENP3 were identified as effective HCC prognosis biomarkers. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE65372"], "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:GSE65372"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33558447", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.202586", "sha256": 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HBV-infected", "B", "21", "1", "0"], ["LAAB4BT1", "57", "male", "HCC, HBV-infected", "A", "30", "1", "0"], ["LAABBRT1", "43", "male", "HCC, HBV-infected", "NA", "144", "6", "4"], ["LAABXST1", "39", "male", "HCC, HBV-infected", "C", "78", "5", "1"], ["LAACBFT1", "59", "male", "HCC, HBV-infected", "C", "95", "6", "1"], ["LAACERT1", "47", "male", "HCC, HBV-infected", "A", "65", "8", "0"], ["LAACLYT1", "56", "male", "HCC, HBV-infected", "C", "133", "1", "1"], ["LAACQQT1", "60", "male", "HCC, HBV-infected", "NA", "462", "12", "0"], ["LAACZ6T1", "27", "male", "HCC, HBV-infected", "A", "71", "1", "0"], ["LAADHST1", "45", "male", "HCC, HBV-infected", "B", "91", "5", "0"], ["LAADHTT2", "60", "male", "HCC, HBV-infected", "B", "1", "0", "0"], ["LAADWRT1", "36", "male", "HCC, HBV-infected", "A", "69", "6", "0"], ["LAADX9T1", "34", "male", "HCC, HBV-infected", "C", "37", "4", "0"], ["LAAEBQT1", "49", "male", "HCC, HBV-infected", "B", "84", "0", "0"], ["LAAEPST1", "25", "male", "HCC, HBV-infected", "B", "31", "2", "0"], ["LAAERTT1", "36", "male", "HCC, HBV-infected", "B", "23", "2", "0"], ["LAAFWBT1", "49", "male", "HCC, HBV-infected", "B", "57", "1", "0"], ["LAL1904T", "67", "male", "HCC, HBV-infected", "NA", "148", "9", "0"], ["LBC7309T", "62", "male", "HCC, HBV-infected", "NA", "168", "15", "0"], ["LBD8969T", "49", "male", "HCC, HBV-infected", "NA", "139", "6", "0"], ["LBD9689T", "56", "male", "HCC, HBV-infected", "NA", "410", "13", "0"], ["LBE0743T", "42", "male", "HCC, HBV-infected", "A", "53", "4", "0"], ["LBE1024T", "34", "male", "HCC, HBV-infected", "NA", "21", "3", "1"], ["LBE1400T", "49", "male", "HCC, HBV-infected", "A", "56", "1", "0"], ["LBF2989T", "53", "male", "HCC, HBV-infected", "NA", "118", "15", "0"], ["LBF3617T", "54", "male", "HCC, HBV-infected", "NA", "46", "2", "1"], ["LBF4416T", "50", "male", "HCC, HBV-infected", "NA", "98", "2", "0"], ["LBG5412T", "55", "male", "HCC, HBV-infected", "NA", "49", "3", "0"], ["LBG5819T", "51", "male", "HCC, HBV-infected", 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associated with HCC prognosis in groups A and B#.", "rows": [["Gene", "Frequency in group A", "Frequency in group B", "Likelihood ratio P-value in the discovery population", "Adjusted P-value in GEO database"], ["TP53", "0.6", "0.40", ">0.05", ">0.05"], ["CTNNB1", "0.4", "0.20", "0.018*", ">0.05"], ["KMT2C", "0.3", "0", "0.03*", "0.046*"], ["ARID1A", "0.3", "0", "0.03*", "0.039*"], ["PCLO", "0.3", "0", "0.03*", ">0.05"]], "row_count": 6, "column_count": 5, "numeric_cells": 21, "header_rows": 0, "locator": "section[4]/table-wrap[1]#t2"}}, {"id": "asset:table:pmid:33558447:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7356d51ef8c1d1dcc7dcdf3959a49bf787e55c5f18f3fc5e3dde84cdc260bdd6", "bytes": 553, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t3", "version": null, "note": "New driver genes associated with early-recurrence and late-recurrence of HCC.", "structure": {"pmcid": "PMC7906131", "section_index": 5, "section_title": "New HCC driver genes identified in the discovery population", "row_count": 8, "column_count": 5}, "table": {"label": "Table 3", "caption": "New driver genes associated with early-recurrence and late-recurrence of HCC.", "rows": [["Group#", "Gene", "CHASM Score", "P-value", "FDR"], ["A", "MAP4K4", "0.738", "1.20E-03*", "0.05"], ["A", "COX5B", "0.728", "1.80E-03*", "0.1"], ["A", "ACTN3", "0.712", "2.20E-03*", "0.1"], ["A", "CFTR", "0.698", "3.80E-03*", "0.1"], ["A", "LRRC7", "0.696", "4.00E-03*", "0.1"], ["C", "PRKCG", "0.68", "1.72E-04*", "0.05"], ["C", "SENP3", "0.744", "8.00E-04*", "0.1"]], "row_count": 8, "column_count": 5, "numeric_cells": 21, "header_rows": 0, "locator": "section[5]/table-wrap[1]#t3"}}, {"id": "asset:table:pmid:33558447:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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"available", "identifier": "section[7]/table-wrap[2]#t5", "version": null, "note": "ROC curve analysis of ARID1A, CSMD1, and SENP3 expression in HCC survival prediction.", "structure": {"pmcid": "PMC7906131", "section_index": 7, "section_title": "ARID1A, CSMD1, and SENP3 are effective prognostic biomarkers for HBV-infected HCC patients in the replication population", "row_count": 4, "column_count": 7}, "table": {"label": "Table 5", "caption": "ROC curve analysis of ARID1A, CSMD1, and SENP3 expression in HCC survival prediction.", "rows": [["Parameters", "Value range", "Cutoff value", "AUC", "SE", "P-value", "95% CI"], ["ARID1A", "0–2.5", "1.5", "0.489", "0.045", "0.803", "0.402–0.576"], ["CSMD1", "0–3", "1.5", "0.573", "0.043", "0.099", "0.488–0.658"], ["SENP3", "0–2.5", "1.2", "0.609", "0.042", "0.013*", "0.526–0.692"]], "row_count": 4, "column_count": 7, "numeric_cells": 19, "header_rows": 0, "locator": "section[7]/table-wrap[2]#t5"}}, {"id": "asset:table:pmid:33558447:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e13e6e67188d305cb04a4d953f210e321b2dd4522b383a3e09d62ff5f4106639", "bytes": 1059, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[3]#t6", "version": null, "note": "Prognostic value of ARID1A, CSMD1, and SENP3 expression in HCC using the Cox regression model.", "structure": {"pmcid": "PMC7906131", "section_index": 7, "section_title": "ARID1A, CSMD1, and SENP3 are effective prognostic biomarkers for HBV-infected HCC patients in the replication population", "row_count": 8, "column_count": 5}, "table": {"label": "Table 6", "caption": "Prognostic value of ARID1A, CSMD1, and SENP3 expression in HCC using the Cox regression model.", "rows": [["Parameters", "Group 1 value", "Group 2 value", "Padj value", "HR (95% CI)"], ["ARID1A", "≤1.5", ">1.5", "0.191", "0.702 (0.413–1.194)"], ["CSMD1", "<1.5", "≥1.5", "0.125", "1.425 (0.906–2.241)"], ["SENP3", "≤1.2", ">1.2", "0.032*", "1.858 (1.054–3.272)"], ["ARID1A and CSMD1", "≤1.5 for ARID1A and ≥1.5 for CSMD1", ">1.5 for ARID1A or <1.5 for CSMD1", "0.218", "0.685 (0.375–1.251)"], ["ARID1A and SENP3", "≤1.5 for ARID1A and >1.2 for SENP3", ">1.5 for ARID1A or ≤1.2 for SENP3", "0.038*", "0.554 (0.317–0.969)"], ["CSMD1 and SENP3", "≥1.5 for CSMD1 and >1.2 for SENP3", "<1.5 for CSMD1 or ≤1.2 for SENP3", "0.006*", "0.535 (0.342–0.837)"], ["ARID1A and CSMD1 and SENP3", "≤1.5 for ARID1A and ≥1.5 for CSMD1 or >1.2 for SENP3", ">1.5 for ARID1A or <1.5 for CSMD1 or ≤1.2 for SENP3", "0.046*", "0.528 (0.282–0.989)"]], "row_count": 8, "column_count": 5, "numeric_cells": 31, "header_rows": 0, "locator": "section[7]/table-wrap[3]#t6"}}, {"id": "asset:table:pmid:33558447:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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