Three-gene risk model in papillary renal cell carcinoma: a robust likelihood-based survival analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33154194", "kind": "science-record", "revision": 7, "content_hash": "sha256:e5c0e91d54eab4875f7518dd08424e91c1b584e4e2ac68e86bad027a9ddd165b", "created_at": "2026-11-01T15:41:15Z", "updated_at": "2026-11-01T21:24:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Three-gene risk model in papillary renal cell carcinoma: a robust likelihood-based survival analysis.", "doi": "10.18632/aging.104001", "pmid": "33154194", "authors": ["Yutao Wang", "Kexin Yan", "Jiaxing Lin", "Jianfeng Wang", "Zhenhua Zheng", "Xinxin Li", "Zhixiong Hua", "Yuepeng Bu", "Jianxiu Shi", "Siqing Sun", "Xuejie Li", "Yang Liu", "Jianbin Bi"], "journal": "Aging", "year": 2020, "abstract": "BACKGROUND: Papillary renal cell carcinoma (PRCC) accounts for 15% of all renal cell carcinomas. The molecular mechanisms of renal papillary cell carcinoma remain unclear, and treatments for advanced disease are limited.\nRESULT: We built the computing model as follows: Risk score = 1.806 * TPX2 - 0.355 * TXNRD2 - 0.805 * SLC6A20. The 3-year AUC of overall survival was 0.917 in the training set (147 PRCC samples) and 0.760 in the test set (142 PRCC samples). Based on the robust model, M2 macrophages showed positive correlation with risk score, while M1 macrophages were the opposite. PRCC patients with low risk score showed higher tumor mutation burden. TPX2 is a risk factor, and co-expression factors were enriched in cell proliferation and cancer-related pathways. Finally, the proliferation and invasion of PRCC cell line were decreased in the TPX2 reduced group, and the differential expression was identified. TPX2 is a potential risk biomarker which involved in cell proliferation in PRCC.\nCONCLUSION: We conducted a study to develop a three gene model for predicting prognosis in patients with papillary renal cell carcinoma. Our findings may provide candidate biomarkers for prognosis that have important implications for understanding the therapeutic targets of papillary renal cell carcinoma.\nMETHOD: Gene expression matrix and clinical data were obtained from TCGA (The Cancer Genome Atlas), GSE26574, GSE2048, and GSE7023. Prognostic factors were identified using \"survival\" and \"rbsurv\" packages, and a risk score was constructed using Multivariate Cox regression analysis. The co-expression networks of the factors in model were constructed using the \"WGCNA\" package. The co-expression genes of factors were enriched and displayed the biological process. Based on this robust risk model, immune cells infiltration proportions and tumor mutation burdens were compared between risk groups. Subsequently, using the PRCC cell line, the role of TPX2 was determined by Cell proliferation assay, 5-Ethynyl-20-deoxyuridine assay and Transwell assay.", "claims": [{"id": "claim-method", "statement": "The expression matrix and clinical information of renal papillary cell carcinoma were obtained from TCGA (http://cancergenome.nih.gov/). We obtained the expression matrix and platform comment information of GSE26574 [27], GSE7023 [28], GSE 2748 [29] from the GEO Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). The “Survival” package [30] was used to obtain prognostic factors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33154194", "locator": "sections[14] \"Data acquisition and processing\" paragraph 2", "quote": "The expression matrix and clinical information of renal papillary cell carcinoma were obtained from TCGA (http://cancergenome.nih.gov/)."}, {"asset": "source:pmid:33154194", "locator": "sections[14] \"Data acquisition and processing\" paragraph 2", "quote": "We obtained the expression matrix and platform comment information of GSE26574 [27], GSE7023 [28], GSE 2748 [29] from the GEO Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:33154194", "locator": "sections[15] \"Prognostic factors selection\" paragraph 2", "quote": "The “Survival” package [30] was used to obtain prognostic factors."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression matrix and clinical information of renal papillary cell carcinoma were obtained from TCGA (http://cancergenome.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33154194", "locator": "sections[14] \"Data acquisition and processing\" paragraph 2", "quote": "The expression matrix and clinical information of renal papillary cell carcinoma were obtained from TCGA (http://cancergenome.nih.gov/)."}], "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:33154194"], "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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