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pmid:33330025
CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer.
Yutao Wang · Kexin Yan · Jiaxing Lin · Yang Liu · Jianfeng Wang · Xuejie Li · Xinxin Li · Zhixiong Hua · Zhenhua Zheng · Jianxiu Shi · Siqing Sun · Jianbin Bi
Frontiers in oncology · 2020 doi:10.3389/fonc.2020.553399
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Experiment
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Execution
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33330025", "kind": "science-record", "revision": 7, "content_hash": "sha256:63388493418c41227c5ecc47835239908b896e765ee4e30913a41e2eb706835d", "created_at": "2026-11-01T15:41:19Z", "updated_at": "2026-11-01T22:02:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer.", "doi": "10.3389/fonc.2020.553399", "pmid": "33330025", "authors": ["Yutao Wang", "Kexin Yan", "Jiaxing Lin", "Yang Liu", "Jianfeng Wang", "Xuejie Li", "Xinxin Li", "Zhixiong Hua", "Zhenhua Zheng", "Jianxiu Shi", "Siqing Sun", "Jianbin Bi"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "PURPOSE: To identify immune-related co-expressed genes that promote CD8+ T cell infiltration in bladder cancer, and to explore the interactions among relevant genes in the tumor microenvironment.\nMETHOD: We obtained bladder cancer gene matrix and clinical information data from TCGA, GSE32894 and GSE48075. The \"estimate\" package was used to calculate tumor purity and immune score. The CIBERSORT algorithm was used to assess CD8+ T cell proportions. Weighted gene co-expression network analysis was used to identify the co-expression modules with CD8+ T cell proportions and bladder tumor purity. Subsequently, we performed correlation analysis among angiogenesis factors, angiogenesis inhibitors, immune inflammatory responses, and CD8+ T cell related genes in tumor microenvironment.\nRESULTS: A CD8+ T cell related co-expression network was identified. Eight co-expressed genes (PSMB8, PSMB9, PSMB10, PSME2, TAP1, IRF1, FBOX6, ETV7) were identified as CD8+ T cell-related genes that promoted infiltration of CD8+ T cells, and were enriched in the MHC class I tumor antigen presentation process. The proteins level encoded by these genes (PSMB10, PSMB9, PSMB8, TAP1, IRF1, and FBXO6) were lower in the high clinical grade patients, which suggested the clinical phenotype correlation both in mRNA and protein levels. These factors negatively correlated with angiogenesis factors and positively correlated with angiogenesis inhibitors. PD-1 and PD-L1 positively correlated with these genes which suggested PD-1 expression level positively correlated with the biological process composed by these co-expression genes. In the high expression group of these genes, inflammation and immune response were more intense, and the tumor purity was lower, suggesting that these genes were immune protective factors that improved the prognosis in patients with bladder cancer.\nCONCLUSION: These co-expressed genes promote high levels of infiltration of CD8+ T cells in an immunoproteasome process involved in MHC class I molecules. The mechanism might provide new pathways for treatment of patients who are insensitive to PD-1 immunotherapy due to low degrees of CD8+ T cell infiltration.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33330025", "locator": "sections[11] \"Statistical Analysis\" paragraph 2", "quote": "Kaplan–Meier survival analysis was applied to generate overall survival curves and the log-rank test was used to calculate the significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE32894", "GSE48075"], "resolved_accessions": ["GSE32894", "GSE48075"], "statements": ["Publicly available datasets were analyzed in this study. This data can be found here: The datasets TCGA-BLCA for this study can be found in the [The Cancer Genome Atlas] [http://cancergenome.nih.gov/)].The datasets GSE32894 and GSE48075 for this study can be found in the [GEO] [http://www.ncbi.nlm.nih.gov/geo/]."], "basis": "The paper names GSE32894, GSE48075 in GEO and the accession resolves in the repository. 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