Prognostic correlation between specialized capillary endothelial cells and lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38533005", "kind": "science-record", "revision": 3, "content_hash": "sha256:e5bcb92bd77c92b27df4242f9396950e555294c4f8aea2dc41ca23aab2012a1e", "created_at": "2026-11-01T19:20:28Z", "updated_at": "2026-11-01T22:11:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic correlation between specialized capillary endothelial cells and lung adenocarcinoma.", "doi": "10.1016/j.heliyon.2024.e28236", "pmid": "38533005", "authors": ["Rongchang Zhao", "Yan Ding", "Rongbo Han", "Rongjie Ding", "Jun Liu", "Chunrong Zhu", "Dan Ding", "Minhui Bao"], "journal": "Heliyon", "year": 2024, "abstract": "Background: In-depth analysis of the functional changes occurring in endothelial cells (ECs) involved in capillary formation can help to elucidate the mechanism of tumour vascular growth.\nMethods: Appropriate datasets were retrieved from the GEO database to obtain single-cell data on LUAD samples and adjacent normal tissue samples. ECs were selected by an automatic annotation program in R and further subdivided based on reported EC marker genes. Functional changes in different types of capillary ECs were then visualized, and the concrete expression was classified by genetic data in the TCGA. Finally, a prognostic model was constructed to predict immunoinfiltration status, survival and drug therapy effects.\nResults: The LUAD data contained in the GSE183219 dataset were suitable for our analysis. After dimensionality reduction analysis and cell annotation, EC general capillary and EC aerocyte subsets as capillary specialized phenotypes showed a series of functional changes in tumour samples, with a total of 108 genes found to undergo functional changes. Use of CellPhoneDB revealed a close interaction of activity between ECs. After integration of TCGA, GSE68465 and GSE11969 datasets, the genes obtained were analysed by cluster analysis and risk model construction, identifying 8 genes. Drug sensitivity, immune cell and molecular differences can be accurately predicted.\nConclusions: EC general capillary and EC aerocyte subsets are recognized capillary ECs in the tumour microenvironment, and the functional changes between them are relevant to the prognosis and treatment of LUAD patients and have the potential to be used in target therapy.", "claims": [{"id": "claim-method", "statement": "Univariate Cox analysis was performed for the DEGs, followed by least absolute shrinkage and selection operator (LASSO) regression analysis to screen for suitable genes for the construction of prognostic models.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38533005", "locator": "sections[9] \"Construction and evaluation of the prognostic model\" paragraph 2", "quote": "Univariate Cox analysis was performed for the DEGs, followed by least absolute shrinkage and selection operator (LASSO) regression analysis to screen for suitable genes for the construction of prognostic models."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The code is provided in the Supplementary code Material. Source data are provided with this paper. All other datasets generated and analysed in the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38533005", "locator": "sections[23] \"Data availability\" paragraph 2", "quote": "The code is provided in the Supplementary code Material. Source data are provided with this paper. All other datasets generated and analysed in the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The eight-gene prognostic model achieved AUC values of 0.729, 0.723, and 0691 for predicting survival at 1, 3, and 5 years, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38533005", "locator": "sections[18] \"Applicability and accuracy of the prognostic model\" paragraph 2", "quote": "According to the prognostic model, the area under the curve (AUC) for survival at 1, 3, and 5 years was 0.729, 0.723, and 0691, respectively (Fig. 10A), with better survival in the training cohort (0.752, 0.767, and 0.766, respectively) (Fig. 10B) and slightly worse survival in the test cohort (0.704, 0.676, and 0.617, respectively) (Fig. 10C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The eight-gene prognostic model achieved AUC values of 0.729, 0.723, and 0691 for predicting survival at 1, 3, and 5 years, respectively.", "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:38533005"], "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:GSE11969"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE11969"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38533005", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e28236", "sha256": "sha256:b966c3366977ed70f90831bf78947f68ae2800a8b81231f5766e59bee6dca81c", "bytes": 58174, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e28236", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10963648", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11969", "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=GSE11969", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11969", "version": null, "note": "The code is provided in the Supplementary code Material. Source data are provided with this paper. All other datasets generated and analysed in the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The code is provided in the Supplementary code Material. Source data are provided with this paper. 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