Identification of a necroptosis-related gene signature for making clinical predictions of the survival of patients with lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38213773", "kind": "science-record", "revision": 3, "content_hash": "sha256:f53184f9e6f67134cd9530dbe05706e0639fc852893311432a2e9be1fd790294", "created_at": "2026-11-01T19:20:07Z", "updated_at": "2026-11-01T22:11:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a necroptosis-related gene signature for making clinical predictions of the survival of patients with lung adenocarcinoma.", "doi": "10.7717/peerj.16616", "pmid": "38213773", "authors": ["Xiaoping Zhou", "Ming Zhao", "Yingzi Fan", "Ying Xu"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Lung adenocarcinoma (LUAD) is a major pathological subtype of malignant lung cancer with a poor prognosis. Necroptosis is a caspase-independent programmed cell death mode that plays a pivotal role in cancer oncogenesis and metastasis. Here, we explore the prognostic values of different necroptosis-related genes (NRGs) in LUAD.\nMethods: mRNA expression data and related clinical information for LUAD samples were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. NRGs were identified using the GeneCards database. Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model. Time-dependent receiver-operating characteristic curves and a nomogram were constructed to validate the predictive values of the prognostic signatures. A necroptosis-related protein-protein interaction network was visualised using the STRING database and Cytoscape software. Functional analyses, including Gene Ontology, Kyoto Encyclopaedia of Genes and Genomes pathway enrichment, gene set enrichment, and gene set variation analyses, were conducted to explore the underlying molecular mechanisms. Finally, the mRNA expression of the prognostic signatures in LUAD cell lines was assessed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis.\nResults: A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort. Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013). The nomogram was used to predict the prognosis of patients with LUAD. The prediction curves for 1-, 3-, and 5-year OS showed good predictive performance and the accuracy of the nomograms increased over time. RT-qPCR results demonstrated that these eight genes, especially CALM1, PRDX1, and PGLYRP1, were differentially expressed in LUAD cells.\nConclusion: We constructed a reliable eight-NRG signature that provides new insights for guiding clinical practice in the prognosis and treatment of LUAD.", "claims": [{"id": "claim-method", "statement": "Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38213773", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Least absolute shrinkage and selection operator Cox regression and multivariate Cox analysis were used to construct a prognostic risk model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original code and gene expression data of lung adenocarcinoma are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38213773", "locator": "sections[21] \"Additional Information and Declarations\" paragraph 4", "quote": "The original code and gene expression data of lung adenocarcinoma are available in the Supplemental Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort.", "kind": "quantitative", "target": {"value": 0.00013, "unit": "p-value", "tolerance": null, "source": "Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013)."}, "evidence": [{"asset": "source:pmid:38213773", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort."}, {"asset": "source:pmid:38213773", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Patients with low-risk scores had better survival outcomes than those with high-risk scores (p = 0.00013)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A prognostic model was established for eight NRGs (CALM1, DDX17, FPR1, OGT, PGLYRP1, PRDX1, TUFM, and CPSF3) based on TCGA-cohort data and validated with the GSE68465 cohort.", "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:38213773"], "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:GSE68465"], "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:GSE68465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38213773", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.16616", "sha256": "sha256:833298115c5fd20515a7a3f7f6613cf00a224be13836f6a5369854f84c9aae8c", "bytes": 37148, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.16616", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10782958", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE68465", "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=GSE68465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE68465", "version": null, "note": "The original code and gene expression data of lung adenocarcinoma are available in the Supplemental Files.", 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