A novel signature derived from metabolism-related genes GPT and SMS to predict prognosis of laryngeal squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35804447", "kind": "science-record", "revision": 4, "content_hash": "sha256:3223d26e670bd4aaa490fbd5186d5bce23c6581a41754d8ce24fbfe6ccd99ae4", "created_at": "2026-11-01T18:14:51Z", "updated_at": "2026-11-01T22:06:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel signature derived from metabolism-related genes GPT and SMS to predict prognosis of laryngeal squamous cell carcinoma.", "doi": "10.1186/s12935-022-02647-2", "pmid": "35804447", "authors": ["Yujie Shen", "Qiang Huang", "Yifan Zhang", "Chi-Yao Hsueh", "Liang Zhou"], "journal": "Cancer cell international", "year": 2022, "abstract": "BACKGROUND: A growing body of evidence has suggested the involvement of metabolism in the occurrence and development of tumors. But the link between metabolism and laryngeal squamous cell carcinoma (LSCC) has rarely been reported. This study seeks to understand and explain the role of metabolic biomarkers in predicting the prognosis of LSCC.\nMETHODS: We identified the differentially expressed metabolism-related genes (MRGs) through RNA-seq data of The Cancer Genome Atlas (TCGA) and Gene set enrichment analysis (GSEA). After the screening of protein-protein interaction (PPI), hub MRGs were analyzed by least absolute shrinkage and selection operator (LASSO) and Cox regression analyses to construct a prognostic signature. Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) was applied to verify the effectiveness of the prognostic signature in four cohorts (TCGA cohort, GSE27020 cohort, TCGA-sub1 cohort and TCGA-sub2 cohort). The expressions of the hub MRGs in LSCC cell lines and clinical samples were verified by quantitative reverse transcriptase PCR (qRT-PCR). The immunofluorescence staining of the tissue microarray (TMA) was carried out to further verify the reliability and validity of the prognostic signature. Cox regression analysis was then used to screen for independent prognostic factors of LSCC and a nomogram was constructed based on the results.\nRESULTS: Among the 180 differentially expressed MRGs, 14 prognostic MRGs were identified. A prognostic signature based on two MRGs (GPT and SMS) was then constructed and verified via internal and external validation cohorts. Compared to the adjacent normal tissues, SMS expression was higher while GPT expression was lower in LSCC tissues, indicating poorer outcomes. The prognostic signature was proven as an independent risk factor for LSCC in both internal and external validation cohorts. A nomogram based on these results was developed for clinical application.\nCONCLUSIONS: Differentially expressed MRGs were found and proven to be related to the prognosis of LSCC. We constructed a novel prognostic signature based on MRGs in LSCC for the first time and verified it via different cohorts from both databases and clinical samples. A nomogram based on this prognostic signature was developed.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analysis was performed to screen out prognostic MRGs. Least absolute shrinkage and selection operator (LASSO) analysis and multivariate Cox regression analysis were applied to construct a prognostic signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35804447", "locator": "sections[6] \"Construction and validation of a prognosis signature based on MRGs\" paragraph 2", "quote": "Univariate Cox regression analysis was performed to screen out prognostic MRGs. Least absolute shrinkage and selection operator (LASSO) analysis and multivariate Cox regression analysis were applied to construct a prognostic signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are available from the corresponding author Liang Zhou on reasonable request. The data that support the findings of this study are available at the TCGA data portal (https://tcga-data.nci.nih.gov/tcga/) and the comprehensive Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35804447", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The datasets analyzed during the current study are available from the corresponding author Liang Zhou on reasonable request. The data that support the findings of this study are available at the TCGA data portal (https://tcga-data.nci.nih.gov/tcga/) and the comprehensive Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among the 180 differentially expressed MRGs, 14 prognostic MRGs were identified, and a prognostic signature based on GPT and SMS was constructed and verified through internal and external validation cohorts.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35804447", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among the 180 differentially expressed MRGs, 14 prognostic MRGs were identified. A prognostic signature based on two MRGs (GPT and SMS) was then constructed and verified via internal and external validation cohorts."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Among the 180 differentially expressed MRGs, 14 prognostic MRGs were identified, and a prognostic signature based on GPT and SMS was constructed and verified through internal and external validation cohorts.", "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:35804447"], "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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