Immune Gene Networks from Lung Cancer Patients Treated with Immune Checkpoint Inhibitors.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38540240", "kind": "science-record", "revision": 4, "content_hash": "sha256:fba70f90baf25b8383675134445a40442eaba9a2f70d21917380a4847ec76591", "created_at": "2026-11-01T19:20:29Z", "updated_at": "2026-11-01T22:11:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune Gene Networks from Lung Cancer Patients Treated with Immune Checkpoint Inhibitors.", "doi": "10.3390/biomedicines12030628", "pmid": "38540240", "authors": ["Kyung Soo Kim", "Taewon Kang", "Dong Wook Jekarl"], "journal": "Biomedicines", "year": 2024, "abstract": "The association between immune checkpoint inhibitors (ICIs) and immune gene networks in squamous lung cancer (LUSC) and lung adenocarcinoma (LUAD) was studied. Immune gene networks were constructed using RNA-seq data from the gene expression omnibus (GEO) database. Datasets with more than 10 samples of normal control and tumor tissues were selected; of these, GSE87340, GSE120622, and GSE111907 were suitable for analysis. Gene set enrichment for pathway analysis was performed. For immune gene network construction, 998 unique immune genes were selected from 21 pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene function annotation was performed based on the KEGG, Gene Ontology, and Reactome databases. Tumor tissues showed decreased coagulation, hematopoiesis, and innate immune pathways, whereas complement- and coagulation-related genes were prominent in the tumor immune gene network. The average numbers of neighbors, clustering coefficients, network diameters, path lengths, densities, and heterogeneities were highest for normal tissue, followed by LUAD and LUSC. Decreased coagulation genes, which were prominent in tumor immune networks, imply functional attenuation. LUAD was deviated from normal tissue, based on network parameters. Tumor tissues showed decreased immune function, and the deviation of LUSC from normal tissue might explain LUSC's better therapeutic response to ICI treatment.", "claims": [{"id": "claim-method", "statement": "After selecting normal controls and an equal number of tumor tissues, gene set enrichment for pathway analysis was performed using the GAGE R package [26], which utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [18,27].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38540240", "locator": "sections[3] \"2.1. Gene Set Enrichment for Pathway Analysis\" paragraph 2", "quote": "After selecting normal controls and an equal number of tumor tissues, gene set enrichment for pathway analysis was performed using the GAGE R package [26], which utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [18,27]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are contained within the article and Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38540240", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "Data are contained within the article and Supplementary Materials."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LUSC tissues deviated more from normal samples than LUAD tissues based on Euclidean, Manhattan, and cosine distances.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38540240", "locator": "sections[7] \"3. Results\" paragraph 19", "quote": "These analysis results indicate that LUAD tissues are closer to normal tissues compared with LUSC, and LUSC tissues deviated more from the normal samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "LUSC tissues deviated more from normal samples than LUAD tissues based on Euclidean, Manhattan, and cosine distances.", "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:38540240"], "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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