Single-cell combined bioinformatics analysis: construction of immune cluster and risk prognostic model in kidney renal clear cells based on CD8+ T cell-associated genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38291496", "kind": "science-record", "revision": 2, "content_hash": "sha256:d7c8456d3857baaa5f9047b5dcbf3858472e1ee078569465e264a7d242013000", "created_at": "2026-11-01T19:20:13Z", "updated_at": "2026-11-01T21:32:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell combined bioinformatics analysis: construction of immune cluster and risk prognostic model in kidney renal clear cells based on CD8+ T cell-associated genes.", "doi": "10.1186/s40001-024-01689-8", "pmid": "38291496", "authors": ["Haifeng Gao", "Hang Sun", "Aifeng He", "Hui Liu", "Zihang Zhang", "Dongling Li", "Weipu Mao", "Jinke Qian"], "journal": "European journal of medical research", "year": 2024, "abstract": "BACKGROUND: Kidney cancer is an immunogenic solid tumor, characterized by high tumor burden and infiltration of CD8+ T cells. Although immunotherapy targeting the PD1/CTLA-4 axis has demonstrated excellent clinical efficacy, clinical outcomes in most patients are poor.\nMETHODS: We used the RNA sequencing data from the GEO database for KIRC GSE121636 and normal kidney tissue GSE131685, and performed single-cell analysis for cluster identification, pathway enrichment, and CD8+ T cell-associated gene identification. Subsequently, the significance of different CD8+ T-cell associated gene subtypes was elucidated by consensus clustering, pathway analysis, mutated gene analysis, and KIRC immune microenvironment analysis in the TCGA-KIRC disease cohort. Single gene analysis identified LAG3 as the most critical CD8+ T-cell-associated gene and its function was verified by cell phenotype and immunohistochemistry in KIRC.\nRESULTS: In the present study, CD8+ T-cell associated genes in KIRC were screened, including GZMK, CD27, CCL4L2, FXYD2, LAG3, RGS1, CST7, DUSP4, CD8A, and TRBV20-1 and an immunological risk prognostic model was constructed (risk score = - 0.291858656434841*GZMK - 0.192758342489394*FXYD2 + 0.625023643446193*LAG3 + 0.161324477181591*RGS1 - 0.380169045328895*DUSP4 - 0.107221347575037*TRBV20-1). LAG3 was identified and proved as the most critical CD8+ T cell-associated gene in KIRC.\nCONCLUSION: We proposed and constructed an immunological risk prognostic model for CD8+ T cell-associated genes and identified LAG3 as a pivotal gene for KIRC progression and CD8+ T-cell infiltration. The model comprehensively explained the immune microenvironment and provided novel immune-related therapeutic targets and biomarkers in KIRC.", "claims": [{"id": "claim-method", "statement": "The “Survival R package” was used to analyze differential expression, overall survival (OS), disease-specific survival, and progression-free survival of CD8+ T cell-associated genes based on single-cell sequencing and assays.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38291496", "locator": "sections[4] \"Differential expression and survival prognosis analysis\" paragraph 2", "quote": "The “Survival R package” was used to analyze differential expression, overall survival (OS), disease-specific survival, and progression-free survival of CD8+ T cell-associated genes based on single-cell sequencing and assays."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Renal epithelial cells (HK-2) and renal cancer cell lines (ACHN and 786-O) were obtained from the surgical laboratory of Zhongda Hospital, Southeast University, and were provided by Dr. Weipu Mao.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38291496", "locator": "sections[34] \"notes\" paragraph 1", "quote": "Renal epithelial cells (HK-2) and renal cancer cell lines (ACHN and 786-O) were obtained from the surgical laboratory of Zhongda Hospital, Southeast University, and were provided by Dr. Weipu Mao."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Single gene analysis identified LAG3 as the most critical CD8+ T-cell-associated gene and its function was verified by cell phenotype and immunohistochemistry in KIRC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38291496", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Single gene analysis identified LAG3 as the most critical CD8+ T-cell-associated gene and its function was verified by cell phenotype and immunohistochemistry in KIRC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Single gene analysis identified LAG3 as the most critical CD8+ T-cell-associated gene and its function was verified by cell phenotype and immunohistochemistry in KIRC.", "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:38291496"], "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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