Construction of a Novel Damage-Associated Molecular-Pattern-Related Signature to Assess Lung Adenocarcinoma's Prognosis and Immune Landscape.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38254708", "kind": "science-record", "revision": 3, "content_hash": "sha256:8b8f43a900f8290d888dcfcf853fb65d6d99623c2904b7dcf09527d7f0bcd867", "created_at": "2026-11-01T19:20:10Z", "updated_at": "2026-11-01T22:11:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of a Novel Damage-Associated Molecular-Pattern-Related Signature to Assess Lung Adenocarcinoma's Prognosis and Immune Landscape.", "doi": "10.3390/biom14010108", "pmid": "38254708", "authors": ["Xinyue Liu", "Shuxi Yao", "Yanqi Feng", "Piao Li", "Yiming Li", "Shu Xia"], "journal": "Biomolecules", "year": 2024, "abstract": "Immunogenic death (ICD) stimulates adaptive immunity and affects immunotherapeutic efficacy, an important part of which is damage-associated molecular patterns (DAMPs). However, the function of these DAMPs for lung adenocarcinoma (LUAD) remains obscure. We initially found differentially expressed genes (DEGs) with prognostic significance related to DAMPs with the TCGA database and then used the least absolute shrinkage and selection operator (LASSO) regression to create a risk signature strongly correlated with overall survival (OS) with eight DEGs. Validation was performed externally using the external data set GSE68465. Lower-risk LUAD patients were found to be more chemotherapy-resistant and enriched for more immune-related pathways than those with higher risk scores, and patients with different risks showed different levels of immune cell infiltration. PANX1, a crucial gene closely associated with lung adenocarcinoma, was identified using the weighted correlation network analysis (WGCNA), and experiments revealed that PANX1 promotes the proliferation as well as invasion of LUAD cells. Furthermore, PANX1 was found to be positively correlated with CD274, CD276, and M2 macrophage markers. We developed and validated an entirely new gene signature related to DAMPs that may be useful for LUAD patient prognosis, immune microenvironment, and chemotherapeutic drug sensitivity prediction. The results may also guide clinical immunotherapy and chemotherapy approaches for LUAD patients.", "claims": [{"id": "claim-method", "statement": "The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was used to identify the genes and regression coefficients with the greatest predictive power after screening for prognostic DEGs with univariate Cox analysis and, finally, to build a risk signature on the most promising 8 genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38254708", "locator": "sections[5] \"2.3. Assessment of a Risk Signature Based on DAMP-Associated Genes\" paragraph 2", "quote": "The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was used to identify the genes and regression coefficients with the greatest predictive power after screening for prognostic DEGs with univariate Cox analysis and, finally, to build a risk signature on the most promising 8 genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study can be found online as described above. The TCGA database is located at https://portal.gdc.cancer.gov, accessed on 3 December 2022, accession number: TCGA-LUAD; the GEO database is located at https://www.ncbi.nlm.nih.gov/gds, accessed on 3 December 2022, accession number: GSE68465.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38254708", "locator": "sections[39] \"Data Availability Statement\" paragraph 2", "quote": "The datasets used in this study can be found online as described above. The TCGA database is located at https://portal.gdc.cancer.gov, accessed on 3 December 2022, accession number: TCGA-LUAD; the GEO database is located at https://www.ncbi.nlm.nih.gov/gds, accessed on 3 December 2022, accession number: GSE68465."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study developed and validated an eight-gene DAMP-related risk signature for assessing prognosis, immune microenvironment, and chemotherapeutic drug sensitivity in lung adenocarcinoma patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38254708", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We developed and validated an entirely new gene signature related to DAMPs that may be useful for LUAD patient prognosis, immune microenvironment, and chemotherapeutic drug sensitivity prediction."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study developed and validated an eight-gene DAMP-related risk signature for assessing prognosis, immune microenvironment, and chemotherapeutic drug sensitivity in lung adenocarcinoma patients.", "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:38254708"], "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:38254708", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biom14010108", "sha256": "sha256:f583cf91986ad4dfdc31fdaf3924723b1212dbae917ec9fcabf89e5dfc6bf8bd", "bytes": 58405, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biom14010108", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10813434", "source": "europe_pmc_fulltext", "coverage": "whole_body", "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 datasets used in this study can be found online as described above. 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