Identification of a novel immunogenic death-associated model for predicting the immune microenvironment in lung adenocarcinoma from single-cell and Bulk transcriptomes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39247599", "kind": "science-record", "revision": 3, "content_hash": "sha256:e816cfef1c6a4ebaf4fee262d627e5cf971c6cee6042989d97a53858d9bce0d7", "created_at": "2026-11-01T20:29:23Z", "updated_at": "2026-11-01T22:12:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a novel immunogenic death-associated model for predicting the immune microenvironment in lung adenocarcinoma from single-cell and Bulk transcriptomes.", "doi": "10.7150/jca.98659", "pmid": "39247599", "authors": ["Xinyu Pan", "Huili Chen", "Linxiang Zhang", "Yiluo Xie", "Kai Zhang", "Chaoqun Lian", "Xiaojing Wang"], "journal": "Journal of Cancer", "year": 2024, "abstract": "Background: Studies on immunogenic death (ICD) in lung adenocarcinoma are limited, and this study aimed to determine the function of ICD in LUAD and to construct a novel ICD-based prognostic model to improve immune efficacy in lung adenocarcinoma patients. Methods: The data for lung adenocarcinoma were obtained from the Cancer Genome Atlas (TCGA) database and the National Center for Biotechnology Information (GEO). The single-cell data were obtained from Bischoff P et al. To identify subpopulations, we performed descending clustering using TSNE. We collected sets of genes related to immunogenic death from the literature and identified ICD-related genes through gene set analysis of variance (GSVA) and weighted gene correlation network analysis (WGCNA). Lung adenocarcinoma patients were classified into two types using consistency clustering. The difference between the two types was analyzed to obtain differential genes. An immunogenic death model (ICDRS) was established using LASSO-Cox analysis and compared with lung adenocarcinoma models of other individuals. External validation was performed in the GSE31210 and GSE50081 cohorts. The efficacy of immunotherapy was assessed using the TIDE algorithm and the IMvigor210, GSE78220, and TCIA cohorts. Furthermore, differences in mutational profiles and immune microenvironment between different risk groups were investigated. Subsequently, ROC diagnostic curves and KM survival curves were used to screen ICDRS key regulatory genes. Finally, RT-qPCR was used to verify the differential expression of these genes. Results: Eight ICD genes were found to be highly predictive of LUAD prognosis and significantly correlated with it. Multivariate analysis showed that patients in the low-risk group had a higher overall survival rate than those in the high-risk group, indicating that the model was an independent predictor of LUAD. Additionally, ICDRS demonstrated better predictive ability compared to 11 previously published models. Furthermore, significant differences in biological function and immune cell infiltration were observed in the tumor microenvironment between the high-risk and low-risk groups. It is noteworthy that immunotherapy was also significant in both groups. These findings suggest that the model has good predictive efficacy. Conclusions: The ICD model demonstrated good predictive performance, revealing the tumor microenvironment and providing a new method for evaluating the efficacy of pre-immunization. This offers a new strategy for future treatment of lung adenocarcinoma.", "claims": [{"id": "claim-method", "statement": "An immunogenic death model (ICDRS) was established using LASSO-Cox analysis and compared with lung adenocarcinoma models of other individuals.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39247599", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "An immunogenic death model (ICDRS) was established using LASSO-Cox analysis and compared with lung adenocarcinoma models of other individuals."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets provided in this study can be found in online repositories. The name and login number of the repository can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39247599", "locator": "sections[27] \"ack\" paragraph 1", "quote": "The datasets provided in this study can be found in online repositories. The name and login number of the repository can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "An eight-gene immunogenic death-related risk score (ICDRS) was found to be highly predictive of LUAD prognosis and significantly correlated with it.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39247599", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eight ICD genes were found to be highly predictive of LUAD prognosis and significantly correlated with it."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "An eight-gene immunogenic death-related risk score (ICDRS) was found to be highly predictive of LUAD prognosis and significantly correlated with it.", "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:39247599"], "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. 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