Identification of an immune subtype-related prognostic signature of clear cell renal cell carcinoma based on single-cell sequencing analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37035172", "kind": "science-record", "revision": 3, "content_hash": "sha256:5bcb7f71c751c011bc7fdf5c24df7a3b63ca27013ed97757b04e4e03f61e59cb", "created_at": "2026-11-01T19:01:41Z", "updated_at": "2026-11-01T22:09:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of an immune subtype-related prognostic signature of clear cell renal cell carcinoma based on single-cell sequencing analysis.", "doi": "10.3389/fonc.2023.1067987", "pmid": "37035172", "authors": ["Zongyao Fan", "Hewei Xu", "Qingyu Ge", "Weilong Li", "Junjie Zhang", "Yannan Pu", "Zhengsen Chen", "Sicong Zhang", "Jun Xue", "Baixin Shen", "Liucheng Ding", "Zhongqing Wei"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Background: There is growing evidence that immune cells are strongly associated with the prognosis and treatment of clear cell renal cell carcinoma (ccRCC). Our aim is to construct an immune subtype-related model to predict the prognosis of ccRCC patients and to provide guidance for finding appropriate treatment strategies.\nMethods: Based on single-cell analysis of the GSE152938 dataset from the GEO database, we defined the immune subtype-related genes in ccRCC. Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database. Then, we carried out a series of evaluation analyses around the model. Finally, we proved the role of VMP1 in ccRCC by cellular assays.\nResult: Initially, based on TCGA ccRCC patient data and GEO ccRCC single-cell data, we successfully constructed a prognostic model consisting of five genes. Survival analysis showed that the higher the risk score, the worse the prognosis. We also found that the model had high predictive accuracy for patient prognosis through ROC analysis. In addition, we found that patients in the high-risk group had stronger immune cell infiltration and higher levels of immune checkpoint gene expression. Finally, cellular experiments demonstrated that when the VMP1 gene was knocked down, 786-O cells showed reduced proliferation, migration, and invasion ability and increased levels of apoptosis.\nConclusion: Our study can provide a reference for the diagnosis and treatment of patients with ccRCC.", "claims": [{"id": "claim-method", "statement": "Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37035172", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37035172", "locator": "sections[29] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material. 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Cell culture and transfection CcRCC cell-lines 786-O was purchased from th", "rchased from RiboBio (Guangzhou, China), and transfected with Lipofectamine 2000 reagent (Invitrogen,", "USA) supplemented with 10% FBS (Gibco, USA). siRNA VMP1 and siRNA negative control were purchas", "ed with 10% FBS (Gibco, USA). siRNA VMP1 and siRNA negative control were purchased from RiboBio"], "order_basis": "paper_text_order:2123", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["lection Cell Bank (Shanghai, China) and were cultured in RPMI-1640 medium (Gibco, USA) supplemented w"], "order_basis": "paper_text_order:2284", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}