Construction and experimental verification of a novel nine-glycosylation-related gene prognostic risk model for clear cell renal carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39524749", "kind": "science-record", "revision": 4, "content_hash": "sha256:bff6213e55dce35943cef182c0d7f6eb5d5814e910715e07d3bb1247a7fbca16", "created_at": "2026-11-01T20:29:47Z", "updated_at": "2026-11-01T22:55:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and experimental verification of a novel nine-glycosylation-related gene prognostic risk model for clear cell renal carcinoma.", "doi": "10.1016/j.heliyon.2024.e39258", "pmid": "39524749", "authors": ["Wanlei Sun", "Long Guo", "Jianqing Ye", "Min Zhou", "Cong Shu", "Xin Ying", "Hongliang Liu", "Fei Liu"], "journal": "Heliyon", "year": 2024, "abstract": "Objective: Patients with clear cell renal carcinoma (ccRCC) typically have poor prognosis. Glycosylation modification plays an important role in ccRCC. This study aimed to develop a novel signature for predicting ccRCC prognosis based on glycosylation-related genes (GRGs).\nMethods: Differentially expressed GRGs (DE_GRGs) were identified using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus and used for constructing the risk model. The function of key genes was validated.\nResults: Twenty-two DE_GRGs were intersected between GSE53757 and TCGA. Patients with ccRCC were divided into two clusters based on the expression profile of these DE_GRGs. Significant differences in the infiltration of 10 immune cell types were observed between two subclusters. Subsequently, the prognostic signatures of nine DE_GRGs (CHST9, COLGALT1, FUT3, FUT6, HS3ST2, POMGNT2, ST8SIA4, UGT3A1, and UGT8) were established. Patients in the high-risk group showed a poorer prognosis relative to the low-risk group. According to univariate and multivariate Cox regression analyses, the risk score, stage, and grade could be independent prognostic factors. A nomogram incorporating information on gender, age, risk group, TNM stage, and clinical stage showed accurate prediction in the survival probability. Except for CHST9, HS3ST2, and ST8SIA4, expression patterns of the remaining 6 DE_GRGs in Caki-1 and 786-O cells were confirmed by quantitative real-time PCR. FUT6 overexpression resulted in the inhibition of proliferation, migration, and invasion of ccRCC cells.\nConclusion: This study established a nine-DE_GRG-based prognostic signature, which independently predicted ccRCC prognosis. This finding emphasizes that GRGs are stratification factors for the precise prognosis of ccRCC.", "claims": [{"id": "claim-method", "statement": "Based on these 256 GRGs, differentially expressed GRGs (DE_GRGs) were identified in TCGA and GSE53757 datasets using limma package (version 3.56.2) with a screening threshold of logFC ≥1 and false discovery rate (FDR) < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39524749", "locator": "sections[4] \"Data collection and processing\" paragraph 2", "quote": "Based on these 256 GRGs, differentially expressed GRGs (DE_GRGs) were identified in TCGA and GSE53757 datasets using limma package (version 3.56.2) with a screening threshold of logFC ≥1 and false discovery rate (FDR) < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39524749", "locator": "sections[26] \"Data availability\" paragraph 2", "quote": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Twenty-two DE_GRGs were intersected between GSE53757 and TCGA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39524749", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Twenty-two DE_GRGs were intersected between GSE53757 and TCGA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Twenty-two DE_GRGs were intersected between GSE53757 and TCGA.", "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:39524749"], "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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FUT6 overexpression resulted in the inhibit"], "order_basis": "paper_text_order:1534", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["high- and low-risk groups. Cell culture and transfection Human renal cortex proximal tubule epithelia", "onstructed into the pcDNA3.1 vector and then transfected into Caki-1 and 786-O cells using Lipofectam"], "order_basis": "paper_text_order:3698", "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": ["40) were acquired from iCell. 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