Integration RNA bulk and single cell RNA sequencing to explore the change of glycolysis-related immune microenvironment and construct prognostic signature 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:38850799", "kind": "science-record", "revision": 3, "content_hash": "sha256:22da74adb19ce398595160290aa2d13ef9de7808f13af913078a444d246d6511", "created_at": "2026-11-01T19:20:47Z", "updated_at": "2026-11-01T21:33:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integration RNA bulk and single cell RNA sequencing to explore the change of glycolysis-related immune microenvironment and construct prognostic signature in head and neck squamous cell carcinoma.", "doi": "10.1016/j.tranon.2024.102021", "pmid": "38850799", "authors": ["Qian Nie", "Huan Cao", "Jianwang Yang", "Tao Liu", "Baoshan Wang"], "journal": "Translational oncology", "year": 2024, "abstract": "BACKGROUND: Glycolysis is an indispensable process for tumor cell,but the effect of glycolysis on the prognosis and immune cell infiltration of head and neck squamous cell carcinoma is not clear.\nMETHODS: Based on RNA bulk and single cell RNA sequencing data of head and neck squamous cell carcinoma from The Cancer Genome Atlas(TCGA) and GSE195832, the effect of glycolysis level on immune cell infiltration was analyzed. Then, we obtained the prognostic genes related to glycolysis through survival analysis to construct prognostic risk signature. Our sample and GSE65858 datasets are used as external verification datasets to verify the validity of the signature. Finally, we used Western blot and cell function assays to determine the relationship between risk genes and glycolysis and the function of prognostic genes.\nRESULT: The level of glycolysis was related to the prognosis of head and neck tumors (P = 0.0044). The results of immune infiltration analysis of TCGA database showed that high level glycolysis subgroup had less infiltration of macrophages, T cells and monocytes. Results of single cell sequencing analysis validates the above results. Additionally, Five risk genes(MUCL1,TRIML2,RAB3B,SPINK6,IGSF11) were selected to construct signature.Risk score was an independent prognostic factor(P < 0.01). The external validation set also shows the same result. In vitro functional and Western blot assays confirmed that the above five genes affect tumor function and related to the process of glycolysis.\nCONCLUSION: Glycolysis-related risk signatures can be used to predict the prognosis and immune infiltration of head and neck squamous cell carcinoma.", "claims": [{"id": "claim-method", "statement": "Then, according to the death and survival time of the patients with head and neck squamous cell carcinoma, Kaplan-Meier survival analysis was performed on the high and low risk groups, and the survival differences of the three high and low expression groups were obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38850799", "locator": "sections[5] \"Principal components and Kaplan-Meier survival analysis\" paragraph 2", "quote": "Then, according to the death and survival time of the patients with head and neck squamous cell carcinoma, Kaplan-Meier survival analysis was performed on the high and low risk groups, and the survival differences of the three high and low expression groups were obtained."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analysed during the current study are available in the GDC repository [TCGA-HNSC] [https://portal.gdc.cancer.gov/], GSE195832 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195832] and GSE65858 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65858].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38850799", "locator": "sections[27] \"Data availability\" paragraph 2", "quote": "The datasets analysed during the current study are available in the GDC repository [TCGA-HNSC] [https://portal.gdc.cancer.gov/], GSE195832 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195832] and GSE65858 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65858]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The result showed that risk score excluded the effect of age,sex and stage were still independent prognostic factors (P < 0.01) (Fig. 6B).", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "The result showed that risk score excluded the effect of age,sex and stage were still independent prognostic factors (P < 0.01) (Fig. 6B)."}, "evidence": [{"asset": "source:pmid:38850799", "locator": "sections[22] \"Glycolysis-related risk score is an independent prognostic factor\" paragraph 2", "quote": "The result showed that risk score excluded the effect of age,sex and stage were still independent prognostic factors (P < 0.01) (Fig. 6B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The result showed that risk score excluded the effect of age,sex and stage were still independent prognostic factors (P < 0.01) (Fig. 6B).", "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:38850799"], "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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METHODS: Based on RNA bulk and single cell RNA sequencing data of head and neck squamous cell carcinom", "cessing GSE195832: We downloaded Single cell transcriptome data of 4 untreated patients from the GEO we"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["validity of the signature. Finally, we used Western blot and cell function assays to determine the re", "ows the same result. In vitro functional and Western blot assays confirmed that the above five genes a"], "order_basis": "paper_text_order:837", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["of Biotechnology in Beijing. The cells were cultured in RPMI 1640 and DMEM containing 10 % fetal bov"], "order_basis": "paper_text_order:3339", "id": "assay:3"}, {"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": 1.0, "evidence": ["Then, according to the death and survival time of the patients with head and neck squamous cell carcinoma, Kaplan-Meier survival analysis was performed on the high and low risk groups, and the survival differences of the three high and low expression groups were obtained."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}