Novel Stemness-Related Gene Signature Predicting Prognosis and Indicating a Different Immune Microenvironment in HNSCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35360859", "kind": "science-record", "revision": 3, "content_hash": "sha256:6cb1701d8ee8be5a79f51ef0aa5a9ef543ebf6d7fd95f8a7ee3ab3ace9644759", "created_at": "2026-11-01T18:14:10Z", "updated_at": "2026-11-01T21:27:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Novel Stemness-Related Gene Signature Predicting Prognosis and Indicating a Different Immune Microenvironment in HNSCC.", "doi": "10.3389/fgene.2022.822115", "pmid": "35360859", "authors": ["Yi Luo", "Wei-Bo Xu", "Ben Ma", "Yu Wang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: The head and neck squamous cell carcinomas (HNSCC) is one of the most frequent cancers in the world, with an unfavorable prognosis. Cancer stem cells (CSCs) have been found to be responsible for HNSCC recurrence and therapeutic resistance. Methods: The stemness of HNSCC was measured using a stemness index based on mRNA expression (mRNAsi). Stemness-related genes were discovered using weighted gene co-expression network analysis, least absolute shrinkage and selection operator analysis, and Cox regression, and a stemness-related prognostic index (SPI) was constructed. This research was based on TCGA and GSE65858. Results: Stemness was found upregulated in HNSCC compared with normal tissues. The risk score model including five stemness-related genes exhibited a good accuracy in predicting outcomes. High SPI predicted a shorter overall survival (OS) in HNSCC patients, in the meantime, also demonstrated a lower CD8+ T cell infiltration and a higher enrichment of macrophages and fibroblasts than the low-SPI group, focusing on several up-regulated pathways such as epithelial mesenchymal transition (EMT), MYC targets v1, E2F targets, mTORC1 signaling, hypoxia, MYC targets v2, angiogenesis, G2M checkpoint, and glycolysis. Conclusion: The SPI signature, which includes five stemness-related genes, could be utilized as a prognostic biomarker for HNSCC, implying that stemness may impact HNSCC immunologic profiles and be a feasible therapeutic target.", "claims": [{"id": "claim-method", "statement": "The LASSO regression with 10-fold cross-validation was then used to filter prognostic genes, and a stemness-related prognostic index (SPI) was constructed using regression coefficients from the multivariate cox regression in the trial set, where the Akaike information criterion (AIC) was utilized to optimize the data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35360859", "locator": "sections[5] \"Prognostic Gene Screening and Validation\" paragraph 2", "quote": "The LASSO regression with 10-fold cross-validation was then used to filter prognostic genes, and a stemness-related prognostic index (SPI) was constructed using regression coefficients from the multivariate cox regression in the trial set, where the Akaike information criterion (AIC) was utilized to optimize the data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35360859", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The five-gene stemness-related prognostic index predicted poorer overall survival in HNSCC, with multivariate survival HRs of 2.63 in the training set, 2.14 in the TCGA validation set, and 1.85 in the GSE65858 validation set.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Furthermore, multivariate survival analysis was performed in training and validation sets, taking into account clinical characteristics such as age, gender, and TNM stage, suggesting a substantial influence of SPI on the OS of HNSCC patients (training set: HR = 2.63, 95% CI = 1.74–3.98, p < 0.001; validation set of TCGA: HR = 2.14, 95% CI = 1.43–3.20, p < 0.001; validation set of GSE65858, HR = 1.85, 95% CI = 1.16–2.95, p = 0.001) (Supplementary Table S3)."}, "evidence": [{"asset": "source:pmid:35360859", "locator": "sections[15] \"Validation of the Prognostic Model\" paragraph 2", "quote": "Furthermore, multivariate survival analysis was performed in training and validation sets, taking into account clinical characteristics such as age, gender, and TNM stage, suggesting a substantial influence of SPI on the OS of HNSCC patients (training set: HR = 2.63, 95% CI = 1.74–3.98, p < 0.001; validation set of TCGA: HR = 2.14, 95% CI = 1.43–3.20, p < 0.001; validation set of GSE65858, HR = 1.85, 95% CI = 1.16–2.95, p = 0.001) (Supplementary Table S3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The five-gene stemness-related prognostic index predicted poorer overall survival in HNSCC, with multivariate survival HRs of 2.63 in the training set, 2.14 in the TCGA validation set, and 1.85 in the GSE65858 validation set.", "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:35360859"], "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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