Establishment of a Lymph Node Metastasis-Associated Prognostic Signature for Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36793937", "kind": "science-record", "revision": 2, "content_hash": "sha256:67bd161b0e740658ab06ced2595151a492b3213f1e6765db1e9fbfba7a6c76a8", "created_at": "2026-11-01T19:01:23Z", "updated_at": "2026-11-01T21:30:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a Lymph Node Metastasis-Associated Prognostic Signature for Lung Adenocarcinoma.", "doi": "10.1155/2023/6585109", "pmid": "36793937", "authors": ["Jiao Yu", "Gang Li", "Yingxuan Tian", "Shufen Huo"], "journal": "Genetics research", "year": 2023, "abstract": "Background: Lung adenocarcinoma (LUAD) is the most common histological subtype of non-small cell lung cancer (NSCLC) with a low 5-year survival rate, which may be associated with the presence of metastatic tumors at the time of diagnosis, especially lymph node metastasis (LNM). This study aimed to construct a LNM-related gene signature for predicting the prognosis of patients with LUAD.\nMethods: RNA sequencing data and clinical information of LUAD patients were extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Samples were divided into metastasis (M) and nonmetastasis (NM) groups based on LNM status. Differentially expressed genes (DEGs) between M and NM groups were screened, and then WGCNA was applied to identify key genes. Furthermore, univariate Cox and LASSO regression analyses were conducted to construct a risk score model, and the predictive performance of model was validated by GSE68465, GSE42127, and GSE50081. The protein and mRNA expression level of LNM-associated genes were detected by human protein atlas (HPA) and GSE68465.\nResults: A prognostic model based on eight LNM-related genes (ANGPTL4, BARX2, GPR98, KRT6A, PTPRH, RGS20, TCN1, and TNS4) was developed. Patients in the high-risk group had poorer overall survival than those in the low-risk group, and validation analysis showed that this model had potential predictive value for patients with LUAD. HPA analysis supported the upregulation of ANGPTL4, KRT6A, BARX2, RGS20 and the downregulation of GPR98 in LUAD compared with normal tissues.\nConclusion: Our results indicated that the eight LNM-related genes signature had potential value in the prognosis of patients with LUAD, which may have important practical implications.", "claims": [{"id": "claim-method", "statement": "Based on the mRNA expression levels of the overlapping genes, univariate Cox regression analysis was performed by using the survival package (Version 2.41-1; https://bioconductor.org/packages/survivalr/) to screen prognosis-related genes, with p value < 0.05 as cutoff value. Then, optimal gene signature was obtained via LASSO analysis using Lars package (Version 1.2; https://cran.r-project.org/web/packages/lars/index.html).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36793937", "locator": "sections[6] \"2.4. Establishment of a Prognostic Model\" paragraph 2", "quote": "Based on the mRNA expression levels of the overlapping genes, univariate Cox regression analysis was performed by using the survival package (Version 2.41-1; https://bioconductor.org/packages/survivalr/) to screen prognosis-related genes, with p value < 0.05 as cutoff value. Then, optimal gene signature was obtained via LASSO analysis using Lars package (Version 1.2; https://cran.r-project.org/web/packages/lars/index.html)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets 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:36793937", "locator": "sections[29] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A prognostic model based on eight LNM-related genes (ANGPTL4, BARX2, GPR98, KRT6A, PTPRH, RGS20, TCN1, and TNS4) was developed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36793937", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A prognostic model based on eight LNM-related genes (ANGPTL4, BARX2, GPR98, KRT6A, PTPRH, RGS20, TCN1, and TNS4) was developed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A prognostic model based on eight LNM-related genes (ANGPTL4, BARX2, GPR98, KRT6A, PTPRH, RGS20, TCN1, and TNS4) was developed.", "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:36793937"], "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:GSE42127"], "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:GSE42127"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36793937", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2023/6585109", "sha256": 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