Multi-omics comprehensive analyses of programmed cell death patterns to regulate the immune characteristics of head and neck squamous cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38237211", "kind": "science-record", "revision": 3, "content_hash": "sha256:7dfd2335b4035f52681e2b697fa4c958cb1e96be76ecc7e3d4a09eb4ead55fb5", "created_at": "2026-11-01T19:20:09Z", "updated_at": "2026-11-01T22:11:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Multi-omics comprehensive analyses of programmed cell death patterns to regulate the immune characteristics of head and neck squamous cell carcinoma.", "doi": "10.1016/j.tranon.2023.101862", "pmid": "38237211", "authors": ["Yi Jin", "Siwei Huang", "Hongyu Zhou", "Zhanwang Wang", "Yonghong Zhou"], "journal": "Translational oncology", "year": 2024, "abstract": "Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer with high morbidity and mortality. Triggering the programmed cell death (PCD) to enhance the anti-tumor therapies is being applied in multiple cancers. However, the limited understanding of genetic heterogeneity in HNSCC severely hampers the clinical efficacy. We systematically analyzed 14 types of PCD in HNSCC from The Cancer Genome Atlas (TCGA). We utilized ssGSEA to calculate the PCD scores and classify patients into two clusters. Subsequently, we displayed the genomic alteration landscape to unravel the significant differences in copy number alterations and gene mutations. Furthermore, we calculated the IC50 values of targeted drugs to predict the differences in sensitivity. To identify the immune-related prognostic types, we comprehensively estimated the relationship between immune indicators and all prognostic PCD in three datasets (TCGA, GSE65858, GSE41613). Finally, 7 regulators were filtered. Subsequently, we integrated 10 machine learning algorithms and 101 algorithm combinations to test the clinical predictive efficacy. Using WGCNA as a basis, we built a weighted co-expression network to identify modules involved in the immune landscape with different colors. Meanwhile, our results indicated that blue and red modules containing crucial regulators closely related to the CD4+, CD8+ T cells, TMB or PD-L1. FCGR2A from blue module, CSF2, INHBA, and THBS1 from the red module were determined. After verifying in vivo experiments, FCGR2A was identified as hub gene. In conclusion, our findings suggest a potential role of PCD in HNSCC, offering new insights into effective immunotherapy and anti-tumor therapies in HNSCC.", "claims": [{"id": "claim-method", "statement": "We utilized the ssGSEA algorithm with R packages (GSVA, GSEABase, and limma) to comprehensively assess the inherent characteristics of each sample included in the study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38237211", "locator": "sections[4] \"ssGSEA and hierarchical clustering analysis\" paragraph 2", "quote": "We utilized the ssGSEA algorithm with R packages (GSVA, GSEABase, and limma) to comprehensively assess the inherent characteristics of each sample included in the study."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: The raw data and corresponding clinical information were downloaded from the Genomic Data Commons (GDC, https://portal.gdc.cancer.gov/) and Gene Expression Omnibus Database (GEO; https://www.ncbi.n lm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38237211", "locator": "sections[29] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: The raw data and corresponding clinical information were downloaded from the Genomic Data Commons (GDC, https://portal.gdc.cancer.gov/) and Gene Expression Omnibus Database (GEO; https://www.ncbi.n lm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We systematically analyzed 14 types of PCD in HNSCC from The Cancer Genome Atlas (TCGA).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38237211", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "We systematically analyzed 14 types of PCD in HNSCC from The Cancer Genome Atlas (TCGA)."}, {"asset": "source:pmid:38237211", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "We utilized ssGSEA to calculate the PCD scores and classify patients into two clusters."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We systematically analyzed 14 types of PCD in HNSCC from The Cancer Genome Atlas (TCGA).", "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:38237211"], "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:GSE27020"], "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:GSE27020"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38237211", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2023.101862", "sha256": "sha256:586308b8d2b36ba6fcfcabc73bd29739145efeb3f6f957625c4681ab64e2431b", "bytes": 59229, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2023.101862", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10825548", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27020", "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=GSE27020", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27020", "version": null, "note": "Publicly available datasets were analyzed in this study. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:38237211", "data:geo:GSE27020"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27020"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:06:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16553, "completion_tokens": 3018, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38237211", "type": "paper", "label": "pmid:38237211"}, {"id": "source:pmid:38237211", "type": "manuscript", "label": "PMID 38237211 full text"}, {"id": "data:geo:GSE27020", "type": "dataset", "label": "GEO GSE27020"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38237211", "type": "paper", "label": "pmid:38237211"}, {"id": "source:pmid:38237211", "type": "manuscript", "label": "PMID 38237211 full text"}, {"id": "data:geo:GSE27020", "type": "dataset", "label": "GEO GSE27020"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38237211", "type": "extraction", "used": ["source:pmid:38237211"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27020", "type": "accession_resolution", "used": ["data:geo:GSE27020"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38237211", "parent_hash": "sha256:cb378e8a096a5943122974d24b45166ea4f01daa067a6d53b37875ad3981597e", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE27020 licence not read", "asset:data:geo:GSE27020 not downloaded", "asset:data:geo:GSE41613 licence not read", "asset:data:geo:GSE41613 not downloaded", "asset:data:geo:GSE65858 licence not read", "asset:data:geo:GSE65858 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["red module were determined. After verifying in vivo experiments, FCGR2A was identified as hub ge"], "order_basis": "paper_text_order:1614", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}