Prognostic roles of a novel basement membranes-related gene signature in lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36845403", "kind": "science-record", "revision": 3, "content_hash": "sha256:c7aa909c8e9fa40f56947485e23717aaf2744b7a8a9d7faffabcd4092de917c8", "created_at": "2026-11-01T19:01:28Z", "updated_at": "2026-11-01T22:08:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic roles of a novel basement membranes-related gene signature in lung adenocarcinoma.", "doi": "10.3389/fgene.2023.1100560", "pmid": "36845403", "authors": ["Xingzhuang Zhu", "Xiaoyan Liu", "Xiaowen Qiu", "Zihao Niu", "Wei Dong", "Yipeng Song"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: The basement membranes (BMs) are involved in tumor progression, while few comprehensive analyses to date are performed on the role of BM-related gene signatures in lung adenocarcinoma (LUAD). Thus, we aimed to develop a novel prognostic model in LUAD based on BMs-related gene profiling. Methods: The LUAD BMs-related gene profiling and corresponding clinicopathological data were obtained from the basement membrane BASE, The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) databases. The Cox regression and least absolute shrinkage and selection operator (LASSO) methods were used to construct a BMs-based risk signature. The concordance index (C-index), receiver operating characteristic (ROC), and calibration curves were generated to evaluate the nomogram. The GSE72094 dataset was used to validate prediction of the signature. The differences in functional enrichment, immune infiltration, and drug sensitivity analyses were compared based on risk score. Results: In TCGA training cohort, 10 BMs-related genes were found, (e.g., ACAN, ADAMTS15, ADAMTS8, BCAN, etc). The signal signature based on these 10 genes was categorized into high- and low-risk groups regarding survival differences (p < 0.001). Multivariable analysis showed that the signature of combined 10 BMs-related genes was an independent prognostic predictor. Such a prognostic value of BMs-based signature in validation cohort of the GSE72094 were further verified. The GEO verification, C-index, and ROC curve showed that the nomogram had accurate prediction performance. The functional analysis suggested that BMs were mainly enriched in extracellular matrix-receptor (ECM-receptor) interaction. Moreover, the BMs-based model was correlated with immune checkpoint. Conclusion: This study identified BMs-based risk signature genes and demonstrated their ability to predict prognosis and guide personalized treatment of patients with LUAD.", "claims": [{"id": "claim-method", "statement": "The Cox regression and least absolute shrinkage and selection operator (LASSO) methods were used to construct a BMs-based risk signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36845403", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The Cox regression and least absolute shrinkage and selection operator (LASSO) methods were used to construct a BMs-based risk signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36845403", "locator": "sections[22] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A 10-gene basement membrane–related risk signature was constructed from the TCGA training cohort using Cox regression and LASSO, and the signature stratified LUAD patients by overall survival.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The LUAD patients in the low-risk group had significantly longer OS time than those in the high-risk group (p < 0.001) (Figure 2A)."}, "evidence": [{"asset": "source:pmid:36845403", "locator": "sections[11] \"Identification of a BM-related genes signature\" paragraph 5", "quote": "Finally, according to 449 LUAD cases in TCGA training cohort, the 10 BM-related risk gene signature was constructed, and the risk score was calculated based on the linear combination of gene expression levels and corresponding regression coefficients."}, {"asset": "source:pmid:36845403", "locator": "sections[12] \"Prognostic value of BM-related risk gene signature in the training cohort\" paragraph 2", "quote": "The LUAD patients in the low-risk group had significantly longer OS time than those in the high-risk group (p < 0.001) (Figure 2A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 10-gene basement membrane–related risk signature was constructed from the TCGA training cohort using Cox regression and LASSO, and the signature stratified LUAD patients by overall survival.", "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:36845403"], "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:GSE72094"], "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:GSE72094"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36845403", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2023.1100560", "sha256": 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