Immune Infiltration Characteristics and a Gene Prognostic Signature Associated With the Immune Infiltration in Head and Neck Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35586567", "kind": "science-record", "revision": 4, "content_hash": "sha256:d4ebaf50bf8eb5774a0eefeb88f730aed5cc5fcfeaac6992cc7e0a19e6bce064", "created_at": "2026-11-01T18:14:29Z", "updated_at": "2026-11-01T22:06:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immune Infiltration Characteristics and a Gene Prognostic Signature Associated With the Immune Infiltration in Head and Neck Squamous Cell Carcinoma.", "doi": "10.3389/fgene.2022.848841", "pmid": "35586567", "authors": ["Chunmei Zhu", "Qiuji Wu", "Ningning Yang", "Zhewen Zheng", "Fuxiang Zhou", "Yunfeng Zhou"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Immunotherapy has become the new standard of care for recurrent and metastatic head and neck squamous cell carcinoma (HNSCC), and PD-L1 is a widely used biomarker for immunotherapeutic response. However, PD-L1 expression in most cancer patients is low, and alternative biomarkers used to screen the population benefiting from immunotherapy are still being explored. Tumor microenvironment (TME), especially tumor immune-infiltrating cells, regulates the body's immunity, affects the tumor growth, and is expected to be a promising biomarker for immunotherapy. Purpose: This article mainly discussed how the immune-infiltrating cell patterns impacted immunity, thereby affecting HNSCC patients' prognosis. Method: The immune-infiltrating cell profile was generated by the CIBERSORT algorithm based on the transcriptomic data of HNSCC. Consensus clustering was used to divide groups with different immune cell infiltration patterns. Differentially expressed genes (DEGs) obtained from the high and low immune cell infiltration (ICI) groups were subjected to Kaplan-Meier and univariate Cox analysis. Significant prognosis-related DEGs were involved in the construction of a prognostic signature using multivariate Cox analysis. Results: In our study, 408 DEGs were obtained from high- and low-ICI groups, and 59 of them were significantly associated with overall survival (OS). Stepwise multivariate Cox analysis developed a 16-gene prognostic signature, which could distinguish favorable and poor prognosis of HNSCC patients. An ROC curve and nomogram verified the sensitivity and accuracy of the prognostic signature. The AUC values for 1 year, 2 years, and 3 years were 0.712, 0.703, and 0.700, respectively. TCGA-HNSCC cohort, GSE65858 cohort, and an independent GSE41613 cohort proved a similar prognostic significance. Notably, the prognostic signature distinguished the expression of promising immune inhibitory receptors (IRs) well and could predict the response to immunotherapy. Conclusion: We established a tumor immune cell infiltration (TICI)-based 16-gene signature, which could distinguish patients with different prognosis and help predict the response to immunotherapy.", "claims": [{"id": "claim-method", "statement": "With multivariate Cox analysis, we developed a prognostic signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35586567", "locator": "sections[7] \"Establishment of the Prognostic Signature and Preliminary Exploration of the Genes of the Signature\" paragraph 2", "quote": "With multivariate Cox analysis, we developed a prognostic signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35586567", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "An ROC curve and nomogram verified the sensitivity and accuracy of the prognostic signature.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35586567", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "An ROC curve and nomogram verified the sensitivity and accuracy of the prognostic signature. The AUC values for 1 year, 2 years, and 3 years were 0.712, 0.703, and 0.700, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "An ROC curve and nomogram verified the sensitivity and accuracy of the prognostic signature.", "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:35586567"], "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:GSE41613"], "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:GSE41613"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35586567", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.848841", "sha256": "sha256:bddd481ff96765ab3b8b5a2bf9278714df053b706475aac0370d9afb5ab7277c", "bytes": 64859, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.848841", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9108548", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE41613", "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=GSE41613", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41613", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1020099", "GSM1020100", "GSM1020101", "GSM1020102", "GSM1020103", "GSM1020104", "GSM1020105", "GSM1020106", "GSM1020107", "GSM1020108", "GSM1020109", "GSM1020110", "GSM1020111", "GSM1020112", "GSM1020113", "GSM1020114", "GSM1020115", "GSM1020116", "GSM1020117", "GSM1020118", "GSM1020119", "GSM1020120", "GSM1020121", "GSM1020122", "GSM1020123", "GSM1020124", "GSM1020125", "GSM1020126", "GSM1020127", "GSM1020128", "GSM1020129", "GSM1020130", "GSM1020131", "GSM1020132", "GSM1020133", "GSM1020134", "GSM1020135", "GSM1020136", "GSM1020137", "GSM1020138", "GSM1020139", "GSM1020140", "GSM1020141", "GSM1020142", "GSM1020143", "GSM1020144", "GSM1020145", "GSM1020146", "GSM1020147", "GSM1020148", "GSM1020149", "GSM1020150", "GSM1020151", "GSM1020152", "GSM1020153", "GSM1020154", "GSM1020155", "GSM1020156", "GSM1020157", "GSM1020158", "GSM1020159", "GSM1020160", "GSM1020161", "GSM1020162", "GSM1020163", "GSM1020164", "GSM1020165", "GSM1020166", "GSM1020167", "GSM1020168", "GSM1020169", "GSM1020170", "GSM1020171", "GSM1020172", "GSM1020173", "GSM1020174", "GSM1020175", "GSM1020176", "GSM1020177", "GSM1020178", "GSM1020179", "GSM1020180", "GSM1020181", "GSM1020182", "GSM1020183", "GSM1020184", "GSM1020185", "GSM1020186", "GSM1020187", "GSM1020188", "GSM1020189", "GSM1020190", "GSM1020191", "GSM1020192", "GSM1020193", "GSM1020194", "GSM1020195"], "sample_count": 97, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65858", "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=GSE65858", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65858", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1607684", "GSM1607685", "GSM1607686", "GSM1607687", "GSM1607688", "GSM1607689", "GSM1607690", "GSM1607691", "GSM1607692", "GSM1607693", "GSM1607694", "GSM1607695", "GSM1607696", "GSM1607697", "GSM1607698", "GSM1607699", "GSM1607700", "GSM1607701", "GSM1607702", "GSM1607703", "GSM1607704", "GSM1607705", "GSM1607706", "GSM1607707", "GSM1607708", "GSM1607709", "GSM1607710", "GSM1607711", "GSM1607712", "GSM1607713", "GSM1607714", "GSM1607715", "GSM1607716", "GSM1607717", "GSM1607718", "GSM1607719", "GSM1607720", "GSM1607721", "GSM1607722", "GSM1607723", "GSM1607724", "GSM1607725", "GSM1607726", "GSM1607727", "GSM1607728", "GSM1607729", "GSM1607730", "GSM1607731", "GSM1607732", "GSM1607733", "GSM1607734", "GSM1607735", "GSM1607736", "GSM1607737", "GSM1607738", "GSM1607739", "GSM1607740", "GSM1607741", "GSM1607742", "GSM1607743", "GSM1607744", "GSM1607745", "GSM1607746", "GSM1607747", "GSM1607748", "GSM1607749", "GSM1607750", "GSM1607751", "GSM1607752", "GSM1607753", "GSM1607754", "GSM1607755", "GSM1607756", "GSM1607757", "GSM1607758", "GSM1607759", "GSM1607760", "GSM1607761", "GSM1607762", "GSM1607763", "GSM1607764", "GSM1607765", "GSM1607766", "GSM1607767", "GSM1607768", "GSM1607769", "GSM1607770", "GSM1607771", "GSM1607772", "GSM1607773", "GSM1607774", "GSM1607775", "GSM1607776", "GSM1607777", "GSM1607778", "GSM1607779", "GSM1607780", "GSM1607781", "GSM1607782", "GSM1607783", "GSM1607784", "GSM1607785", "GSM1607786", "GSM1607787", "GSM1607788", "GSM1607789", "GSM1607790", "GSM1607791", "GSM1607792", "GSM1607793", "GSM1607794", "GSM1607795", "GSM1607796", "GSM1607797", "GSM1607798", "GSM1607799", "GSM1607800", "GSM1607801", "GSM1607802", "GSM1607803", "GSM1607804", "GSM1607805", "GSM1607806", "GSM1607807", "GSM1607808", "GSM1607809", "GSM1607810", "GSM1607811", "GSM1607812", "GSM1607813", "GSM1607814", "GSM1607815", "GSM1607816", "GSM1607817", "GSM1607818", "GSM1607819", "GSM1607820", "GSM1607821", "GSM1607822", "GSM1607823", "GSM1607824", "GSM1607825", "GSM1607826", "GSM1607827", "GSM1607828", "GSM1607829", "GSM1607830", "GSM1607831", "GSM1607832", "GSM1607833", "GSM1607834", "GSM1607835", "GSM1607836", "GSM1607837", "GSM1607838", "GSM1607839", "GSM1607840", "GSM1607841", "GSM1607842", "GSM1607843", "GSM1607844", "GSM1607845", "GSM1607846", "GSM1607847", "GSM1607848", "GSM1607849", "GSM1607850", "GSM1607851", "GSM1607852", "GSM1607853", "GSM1607854", "GSM1607855", "GSM1607856", "GSM1607857", "GSM1607858", "GSM1607859", "GSM1607860", "GSM1607861", "GSM1607862", "GSM1607863", "GSM1607864", "GSM1607865", "GSM1607866", "GSM1607867", "GSM1607868", "GSM1607869", "GSM1607870", "GSM1607871", "GSM1607872", "GSM1607873", "GSM1607874", "GSM1607875", "GSM1607876", "GSM1607877", "GSM1607878", "GSM1607879", "GSM1607880", "GSM1607881", "GSM1607882", "GSM1607883", "GSM1607884", "GSM1607885", "GSM1607886", "GSM1607887", "GSM1607888", "GSM1607889", "GSM1607890", "GSM1607891", "GSM1607892", "GSM1607893", "GSM1607894", "GSM1607895", "GSM1607896", "GSM1607897", "GSM1607898", "GSM1607899", "GSM1607900", "GSM1607901", "GSM1607902", "GSM1607903", "GSM1607904", "GSM1607905", "GSM1607906", "GSM1607907", "GSM1607908", "GSM1607909", "GSM1607910", "GSM1607911", "GSM1607912", "GSM1607913", "GSM1607914", "GSM1607915", "GSM1607916", "GSM1607917", "GSM1607918", "GSM1607919", "GSM1607920", "GSM1607921", "GSM1607922", "GSM1607923", "GSM1607924", "GSM1607925", "GSM1607926", "GSM1607927", "GSM1607928", "GSM1607929", "GSM1607930", "GSM1607931", "GSM1607932", "GSM1607933", "GSM1607934", "GSM1607935", "GSM1607936", "GSM1607937", "GSM1607938", "GSM1607939", "GSM1607940", "GSM1607941", "GSM1607942", "GSM1607943", "GSM1607944", "GSM1607945", "GSM1607946", "GSM1607947", "GSM1607948", "GSM1607949", "GSM1607950", "GSM1607951", "GSM1607952", "GSM1607953"], "sample_count": 270, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression patterns and TP53 mutations are associated with HPV RNA status, lymph node metastasis, and survival in head and neck cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE41613 not downloaded", "asset:data:geo:GSE41613 licence not read", "asset:data:geo:GSE65858 not downloaded", "asset:data:geo:GSE65858 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.7, "band": "medium", "quote": "ROC curve"}}, {"id": "method-6", "family": null, "specific": null, "label": "Multivariate Cox analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "With multivariate Cox analysis, we developed a prognostic signature."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65858", "GSE41613"], "resolved_accessions": ["GSE65858", "GSE41613"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE65858, GSE41613 in Gene Expression Omnibus database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:35586567", "data:geo:GSE41613"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE41613"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:46:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19155, "completion_tokens": 1250, "cached_tokens": 128}}, "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:35586567", "type": "paper", "label": "pmid:35586567"}, {"id": "source:pmid:35586567", "type": "manuscript", "label": "PMID 35586567 full text"}, {"id": "data:geo:GSE41613", "type": "dataset", "label": "GEO GSE41613"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35586567", "type": "paper", "label": "pmid:35586567"}, {"id": "source:pmid:35586567", "type": "manuscript", "label": "PMID 35586567 full text"}, {"id": "data:geo:GSE41613", "type": "dataset", "label": "GEO GSE41613"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35586567", "type": "extraction", "used": ["source:pmid:35586567"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE41613", "type": "accession_resolution", "used": ["data:geo:GSE41613"], "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:35586567", "parent_hash": "sha256:19c8617d704294b51af163abbd1d4dfb12fd1b2f2d7e148cca88884ffde4e6e9", "fork_of": null, "generation": 3}, "gaps": ["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": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}