Identification and Validation of an Immune-Related RNA Signature to Predict Survival of Patients With Head and Neck Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31921296", "kind": "science-record", "revision": 6, "content_hash": "sha256:a1c0610e474268a7ab4f03bd5822edb722fb070074065dbf16b134d8451c07aa", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T21:22:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of an Immune-Related RNA Signature to Predict Survival of Patients With Head and Neck Squamous Cell Carcinoma.", "doi": "10.3389/fgene.2019.01252", "pmid": "31921296", "authors": ["Shuo Wu", "Xinyi Dai", "Dielai Xie"], "journal": "Frontiers in genetics", "year": 2019, "abstract": "Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease characterized by different molecular subgroups and clinical features. Therefore, it is important to uncover reliable molecular biomarkers for distinguishing different risk patient subgroup. Here, we conducted a multi-omics analysis to examine the joint predictive power of a multi-type RNA signature in the prognosis of HNSCC patients through integration analysis of mRNA, miRNA, and lncRNA expression profiles and clinical data in a large number of HNSCC patients. A multi-type RNA signature (15SigRS) was constructed which can classify patients into the high-risk group and low-risk group with the significantly different outcome [hazard ratio (HR) = 2.718, 95% confidence interval (CI), 2.258-3.272, p < 0.001] in the discovery data set, and subsequently validated in the Cancer Genome Atlas (TCGA) testing data set (HR = 1.299, 95% CI, 1.170-1.442, p < 0.001) and another independent GSE65858 data set (HR = 1.077, 95% CI, 1.016-1.143, p = 0.013). Further multivariate Cox regression analysis and stratification analysis demonstrated the independence of predictive performance of the 15SigRS relative to conventional clinicopathological factors. Furthermore, the 15SigRS has a prior performance in prognostic prediction than other single RNA type-based signatures. Functional analysis suggested that the 15SigRS are involved in immune- or metabolism-related KEGG pathways. In summary, our study demonstrated the potential application of mixed RNA types as molecular markers for predicting the outcome of cancer patients.", "claims": [{"id": "claim-method", "statement": "Then all these candidate prognostic mRNAs, miRNAs, and lncRNAs were fitted into multivariate Cox regression analysis, 15 of 39 genes were identified as independent prognostic gene biomarkers.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31921296", "locator": "sections[8] \"Identification of Independent Survival-Related mRNAs, miRNAs, and lncRNAs\" paragraph 2", "quote": "Then all these candidate prognostic mRNAs, miRNAs, and lncRNAs were fitted into multivariate Cox regression analysis, 15 of 39 genes were identified as independent prognostic gene biomarkers."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data analyzed in this study was obtained from the Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/) and Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65858).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31921296", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The data analyzed in this study was obtained from the Cancer Genome Atlas (TCGA) database (https://cancergenome.nih.gov/) and Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65858)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31921296"], "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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["", "<60", "113 (46.1)", "103 (42.2)", "216 (44.2)", "153 (56.7)"], ["Gender, n (%)", "Female", "64 (26.1)", "66 (27.0)", "130 (26.6)", "47 (17.4)"], ["", "Male", "181 (73.9)", "178 (73.0)", "359 (73.4)", "223 (82.6)"], ["Stage, n (%)", "Stage I/II", "57 (23.3)", "37 (15.2)", "94 (19.2)", "55 (20.4)"], ["", "Stage III/IV", "157 (64.1)", "171 (70.1)", "328 (67.1)", "215 (79.6)"], ["", "NA", "31 (12.6)", "36 (14.7)", "67 (13.7)", ""], ["Grade, n (%)", "G1", "29 (11.8)", "32 (13.1)", "61 (12.5)", ""], ["", "G2", "147 (60)", "144 (59.0)", "291 (59.5)", ""], ["", "G3", "59 (24.1)", "58 (23.8)", "117 (23.9)", ""], ["", "NA", "10 (4.1)", "10 (4.1)", "20 (4.1)", ""], ["Race, n (%)", "White", "201 (82)", "216 (88.5)", "417 (85.3)", ""], ["", "Other_race", "34 (13.9)", "24 (9.8)", "58 (11.9)"], ["", "NA", "10 (4.1)", "4 (1.7)", "14 (2.9)", ""], ["ANGIOLYMPHATIC_INVASION, n (%)", "Yes", "54 (22)", "61 (25)", "115 (23.5)", ""], ["", "No", "112 (45.7)", "104 (42.6)", "216 (44.2)", ""], ["", "NA", "79 (32.2)", "79 (32.4)", "158 (32.3)", ""], ["PERINEURAL_INVASION, n (%)", "Yes", "72 (29.4)", "86 (35.2)", "158 (32.3)", ""], ["", "No", "98 (40)", "86 (35.2)", "184 (37.6)", ""], ["", "NA", "75 (30.6)", "72 (29.5)", "147 (30.1)", ""], ["Smoking_pack_years, n (%)", "> = 40", "82 (33.5)", "78 (32.0)", "160 (32.7)", "222 (YES, 82.2)"], ["", "<40", "61 (24.9)", "58 (23.8)", "119 (24.3)", "48 (NO, 17.8)"], ["", "NA", "102 (41.6)", "108 (44.2)", "210 (42.9)", ""], ["ALCOHOL_HISTORY_DOCUMENTED, n (%)", "Yes", "159 (64.9)", "165 (67.6)", "324 (66.3)", ""], ["", "No", "81 (33.1)", "73 (29.9)", "154 (31.5)", ""], ["", "NA", "5 (2)", "6 (2.5)", "11 (2.2)", ""], ["HPV_STATUS_P16, n (%)", "Negative", "37 (15.1)", "32 (13.1)", "69 (14.1)", ""], ["", "Positive", "15 (6.1)", "15 (6.1)", "30 (6.1)", ""], ["", "NA", "193 (78.8)", "197 (80.8)", "390 (79.8)", ""]], "row_count": 32, "column_count": 6, "numeric_cells": 112, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": 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["15SigRS", "2.718", "2.258–3.272", "<0.001", "2.562", "1.999–3.284", "<0.001"], ["Age", "1.043", "1.024–1.063", "0.000", "1.016", "0.991–1.042", "0.218"], ["Gender (male/female)", "0.643", "0.42–0.984", "0.042", "0.499", "0.272–0.916", "0.025"], ["Stage (III&IV/I&II)", "1.254", "0.753–2.088", "0.385", "1.187", "0.352–4.001", "0.783"], ["Grade (G2/G1)", "1.362", "0.703–2.640", "0.360", "1.685", "0.584–4.861", "0.334"], ["Grade (G3/G1)", "1.139", "0.554–2.343", "0.723", "1.829", "0.599–5.582", "0.289"], ["Race (White/other race)", "0.578", "0.329–1.014", "0.056", "1.623", "0.679–3.880", "0.276"], ["ALCOHOL_HISTORY_DOCUMENTED (yes/no)", "0.734", "0.483–1.113", "0.145", "1.010", "0.562–1.815", "0.974"], ["ANGIOLYMPHATIC_INVASION (yes/no)", "1.687", "0.988–2.881", "0.056", "", "", ""], ["PERINEURAL_INVASION (yes/no)", "2.879", "1.689–4.907", "0.000", "", "", ""], ["SMOKING_PACK_YEARS", "1.001", "0.995–1.008", "0.737", "", "", ""], ["Validation data set (n = 244)"], ["15SigRS", "1.299", "1.170–1.442", "<0.001", "1.311", "1.158–1.484", "<0.001"], ["Age", "1.003", "0.986–1.02", "0.721", "1.020", "0.996–1.045", "0.111"], ["Gender (male/female)", "0.904", "0.605–1.352", "0.624", "1.063", "0.606–1.866", "0.832"], ["Stage (III & IV/I & II)", "3.294", "1.595–6.805", "0.001", "3.102", "0.569–16.905", "0.191"], ["Grade (G2/G1)", "2.264", "1.157–4.430", "0.017", "1.326", "0.593–2.967", "0.492"], ["Grade (G3/G1)", "1.927", "0.936–3.964", "0.075", "1.248", "0.520–2.993", "0.620"], ["Race (White/other race)", "0.871", "0.477–1.587", "0.651", "0.900", "0.452–1.790", "0.763"], ["ALCOHOL_HISTORY_DOCUMENTED (yes/no)", "1.185", "0.788–1.78", "0.415", "1.536", "0.882–2.675", "0.130"], ["ANGIOLYMPHATIC_INVASION (yes/no)", "1.809", "1.138–2.874", "0.012", "", "", ""], ["PERINEURAL_INVASION (yes/no)", "1.698", "1.061–2.716", "0.027", "", "", ""], ["SMOKING_PACK_YEARS", "1.001", "0.992–1.011", "0.801", "", "", ""], ["TCGA data set (n = 489)"], ["15SigRS", "1.496", "1.393–1.606", "<0.001", "1.482", "1.348–1.629", "<0.001"], ["Age", "1.022", "1.009–1.035", "0.001", "1.027", "1.010–1.044", "0.002"], ["Gender (male/female)", "0.759", "0.568–1.016", "0.064", "0.786", "0.526–1.174", "0.239"], ["Stage (III & IV/I & II)", "1.812", "1.216–2.701", "0.003", "1.846", "0.768–4.437", "0.171"], ["Grade (G2/G1)", "1.749", "1.102–2.777", "0.018", "1.240", "0.679–2.264", "0.483"], ["Grade (G3/G1)", "1.507", "0.913–2.487", "0.109", "1.441", "0.754–2.754", "0.269"], ["Race (White/other race)", "0.710", "0.473–1.065", "0.098", "0.811", "0.492–1.335", "0.410"], ["ALCOHOL_HISTORY_DOCUMENTED (yes/no)", "0.951", "0.712–1.27", "0.734", "1.165", "0.792–1.714", "0.437"], ["ANGIOLYMPHATIC_INVASION (yes/no)", "1.750", "1.239–2.473", "0.001", "", "", ""], ["PERINEURAL_INVASION (yes/no)", "2.222", "1.563–3.16", "0.000", "", "", ""], ["SMOKING_PACK_YEARS", "1.001", "0.995–1.006", "0.765", "", "", ""], ["HPV_STATUS_P16 (yes/no)", "0.504", "0.172–1.477", "0.212", "", "", ""], ["GSE65858 data set (n = 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