Identify BCAT1 plays an oncogenic role and promotes EMT in KIRC via single cell RNA-seq and experiment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39324007", "kind": "science-record", "revision": 3, "content_hash": "sha256:be67ae59cea21bad1c5e031ce6a7e47fd43d6819fa1420d3577b5139f122f8b0", "created_at": "2026-11-01T20:29:30Z", "updated_at": "2026-11-01T22:12:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identify BCAT1 plays an oncogenic role and promotes EMT in KIRC via single cell RNA-seq and experiment.", "doi": "10.3389/fonc.2024.1446324", "pmid": "39324007", "authors": ["Shiqing Li", "Yinsheng Guo", "Guanhua Zhu", "Lu Sun", "Feng Zhou"], "journal": "Frontiers in oncology", "year": 2024, "abstract": "Background: Kidney renal clear cell carcinoma (KIRC) is a major subtype of renal cell carcinoma with poor prognosis due to its invasive and metastatic nature. Despite advances in understanding the molecular underpinnings of various cancers, the role of branched-chain amino acid transferase 1 (BCAT1) in KIRC remains underexplored. This study aims to fill this gap by investigating the oncogenic role of BCAT1 in KIRC using single-cell RNA-seq data and experimental validation.\nMethods: Single-cell transcriptomic data GSE159115 was utilized to investigate potential biomarkers in KIRC. After screening, we used BCAT1 as a target gene and investigated its function and mechanism in KIRC through databases such as TCGA-GTEx, using genome enrichment analysis (GSEA), genome variation analysis (GSVA), gene ontology (GO) and Kyoto Encyclopedia of the Genome (KEGG). BCAT1 expression was detected in clinical tissue samples using Western Blotting (WB) and immunohistochemical (IHC) staining techniques. We established cell lines stably overexpressing and knocking down BCAT1 and performed WB, qRT-PCR, cell scratch assay and transwell assay.\nResults: BCAT1 was highly expressed in KIRC and was associated with disease prognosis and TME. Patients with mutations in the BCAT1 gene had shorter overall survival (OS) and disease-free survival (DFS). patients with high BCAT1 expression had shorter OS, progression-free interval (PFI), and disease-specific survival (DSS). GSEA showed that BCAT1 was significantly enriched in epithelial mesenchymal transition (EMT). Bioinformatics analysis and WB and IHC staining showed that BCAT1 expression was higher in KIRC than in paracancerous tissues. In vitro experiments confirmed that BCAT1 in KIRC cells may promote EMT affecting its invasion, migration. We constructed a protein interaction network (PPI) to hypothesize proteins that may interact with BCAT1. Single-sample gene set enrichment analysis (ssGSEA) revealed the immune infiltration environment of BCAT1. Furthermore, hypomethylation of the BCAT1 promoter region in KIRC may contribute to disease progression by promoting BCAT1 expression.\nConclusion: BCAT1 promotes KIRC invasion and metastasis through EMT and has prognostic predictive value and potential as a biomarker. It may become a novel biomarker.", "claims": [{"id": "claim-method", "statement": "The R packages “survival” and “survminer” were used for Kaplan-Meier prognostic analysis of the high and low BCAT1 expression groups in the TCGA-KIRC dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39324007", "locator": "sections[10] \"Construction of prognostic signature\" paragraph 2", "quote": "The R packages “survival” and “survminer” were used for Kaplan-Meier prognostic analysis of the high and low BCAT1 expression groups in the TCGA-KIRC dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: GSE159115 https://pubmed.ncbi.nlm.nih.gov/34099557/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39324007", "locator": "sections[33] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: GSE159115 https://pubmed.ncbi.nlm.nih.gov/34099557/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "BCAT1 promotes KIRC invasion and metastasis through EMT and has prognostic predictive value and potential as a biomarker.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39324007", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "BCAT1 promotes KIRC invasion and metastasis through EMT and has prognostic predictive value and potential as a biomarker."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "BCAT1 promotes KIRC invasion and metastasis through EMT and has prognostic predictive value and potential as a biomarker.", "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:39324007"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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Methods: S", "thods Processing and analysis of single-cell RNA sequencing data The single-cell expression matrix of th", "detect possible batch effects in single-cell RNA sequencing (scRNA-seq) data, we performed principal com"], "order_basis": "paper_text_order:35", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ng the oncogenic role of BCAT1 in KIRC using single-cell RNA-seq data and experimental validation. Methods: S", "Methods Processing and analysis of single-cell RNA sequencing data The single-cell expression matrix of th", "9 cells. To detect possible batch effects in single-cell RNA sequencing (scRNA-seq) data, we performed principal com", "gnificant(*p < 0.05, **p < 0.01,***p<0.001). scRNA-seq and cell annotation of KIRC samples To analy"], "order_basis": "paper_text_order:483", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["as detected in clinical tissue samples using Western Blotting (WB) and immunohistochemical (IHC) staining", "levels of BCAT1 in different cell lines. (D) Western Blotting to detect the protein expression level of BC", "tage in the TCGA database. We have performed Western Blot on tumor tissue and paracancerous tissue fro"], "order_basis": "paper_text_order:985", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ssue samples using Western Blotting (WB) and immunohistochemical (IHC) staining techniques. We established ce", "stern Blotting (WB) and immunohistochemical (IHC) staining techniques. We established cell li", "on (EMT). Bioinformatics analysis and WB and IHC staining showed that BCAT1 expression was hi", "are presented in Supplementary File 1 ) (E) Immunohistochemical staining to detect the protein expression of"], "order_basis": "paper_text_order:1011", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The R packages “survival” and “survminer” were used for Kaplan-Meier prognostic analysis of the high and low BCAT1 expression groups in the TCGA-KIRC dataset."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}