A tumor microenvironment gene set-Based prognostic signature for non-small-cell lung cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36032673", "kind": "science-record", "revision": 5, "content_hash": "sha256:1da87cae3c8dd69e65f224e360173ba1619180d4d480bdb134c51cdd5cba0cc9", "created_at": "2026-11-01T18:15:11Z", "updated_at": "2026-11-01T22:49:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A tumor microenvironment gene set-Based prognostic signature for non-small-cell lung cancer.", "doi": "10.3389/fmolb.2022.849108", "pmid": "36032673", "authors": ["Yingsheng Wen", "Guangran Guo", "Longjun Yang", "Lianjuan Chen", "Dechang Zhao", "Xiaotian He", "Rusi Zhang", "Zirui Huang", "Gongming Wang", "Lanjun Zhang"], "journal": "Frontiers in molecular biosciences", "year": 2022, "abstract": "Background: The tumor microenvironment (TME) is involved in the development and progression of lung carcinomas. A deeper understanding of TME landscape would offer insight into prognostic biomarkers and potential therapeutic targets investigation. To this end, we aimed to identify the TME components of lung cancer and develop a prognostic signature to predict overall survival (OS). Methods: Expression data was retrieved from The Cancer Genome Atlas (TCGA) database and differentially expressed TME-related genes were calculated between tumor and normal tissues. Then nonnegative matrix factorization (NMF) clustering was used to identify two distinct subtypes. Results: Our analysis yielded a gene panel consisting of seven TME-related genes as candidate signature set. With this panel, our model showed that the high-risk group experienced a shorter survival time. This model was further validated by an independent cohort with data from Gene Expression Omnibus (GEO) database (GSE50081 and GSE13213). Additionally, we integrated the clinical factors and risk score to construct a nomogram for predicting prognosis. Our data suggested less immune cells infiltration but more fibroblasts were found in tumor tissues derived from patients at high-risk and those patients exhibited a worse immunotherapy response. Conclusion: The signature set proposed in this work could be an effective model for estimating OS in lung cancer patients. Hopefully analysis of the TME could have the potential to provide novel diagnostic, prognostic and therapeutic opportunities.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier analysis was used to construct a survival curve. Then, a log-rank test was applied to compare the overall survival (OS) of the two subgroups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36032673", "locator": "sections[5] \"Prognostic model construction\" paragraph 2", "quote": "Kaplan-Meier analysis was used to construct a survival curve. Then, a log-rank test was applied to compare the overall survival (OS) of the two subgroups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36032673", "locator": "sections[14] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "With this panel, our model showed that the high-risk group experienced a shorter survival time.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36032673", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "With this panel, our model showed that the high-risk group experienced a shorter survival time."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "With this panel, our model showed that the high-risk group experienced a shorter survival time.", "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:36032673"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13213"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE13213"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36032673", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmolb.2022.849108", "sha256": "sha256:c3577e3452a45e1c29227454ae999f106f3ec6510b751739ab6a38a0968a543d", "bytes": 26555, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmolb.2022.849108", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9400803", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13213", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13213", "version": null, "note": "Publicly available datasets were analyzed in this study. 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