Comprehensive analysis of the relationship between RNA modification writers and immune microenvironment 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:39533178", "kind": "science-record", "revision": 2, "content_hash": "sha256:03c3804418317beec5357ad0ec593c8cc1e450d00a76f662c05a91f48b8b863a", "created_at": "2026-11-01T20:29:48Z", "updated_at": "2026-11-01T21:34:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of the relationship between RNA modification writers and immune microenvironment in head and neck squamous cell carcinoma.", "doi": "10.1186/s12865-024-00667-3", "pmid": "39533178", "authors": ["Wei Li", "Ying Chen", "Yao Zhang", "Wen Wen", "Yingying Lu"], "journal": "BMC immunology", "year": 2024, "abstract": "OBJECTIVES: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Four types of RNA modification writers (m6A, m1A, A-I editing, and APA) are widely involved in tumorigenesis and the TME. We aimed to comprehensively explore the role of the four RNA modification writers in the progression and immune microenvironment of HNSCC.\nMATERIALS AND METHODS: We first obtained transcription profile data and transcriptional variation of the four types of RNA modification writers from The Cancer Genome Atlas (TCGA) database. HNSCC patients in TCGA dataset were divided into different clusters based on the four types of RNA modification writers. Univariate Cox and Least absolute shrinkage and selection operator (LASSO) analyses were performed to conduct a Writer-score scoring system, which was successfully verified in the GSE65858 dataset and our clinical sample dataset. Finally, we evaluated the relationship between different RNA modification clusters (Writer-score) and immunological characteristics of HNSCC.\nRESULTS: Two different RNA modification clusters (A and B) were obtained. These RNA modification clusters (Writer-score) were strongly associated with immunological characteristics (immunomodulators, cancer immunity cycles, infiltrating immune cells (TIICs), inhibitory immune checkpoints, and T cell inflamed score (TIS)) of HNSCC.\nCONCLUSIONS: This study identified two different RNA modification clusters and explored the potential relationship between RNA modification clusters (Writer-score) and immunological characteristics, offering a new theoretical basis for precision immunotherapy in patients with HNSCC.", "claims": [{"id": "claim-method", "statement": "Univariate Cox and Least absolute shrinkage and selection operator (LASSO) analyses were performed to conduct a Writer-score scoring system, which was successfully verified in the GSE65858 dataset and our clinical sample dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39533178", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Univariate Cox and Least absolute shrinkage and selection operator (LASSO) analyses were performed to conduct a Writer-score scoring system, which was successfully verified in the GSE65858 dataset and our clinical sample dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article and its supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39533178", "locator": "sections[24] \"notes\" paragraph 1", "quote": "All data generated or analyzed during this study are included in this published article and its supplementary information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The Writer-score scoring system had independent prognostic value for overall survival in HNSCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39533178", "locator": "sections[14] \"Construction and validation of a Writer-score scoring system\" paragraph 2", "quote": "Finally, univariate and multivariate Cox regression analyses of the training and testing datasets revealed that the Writer-score scoring system has an independent prognostic value (HR > 1, Writer-score represents risk factors for the prognosis of HNSCC) (Fig. 4H-J)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The Writer-score scoring system had independent prognostic value for overall survival in HNSCC.", "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:39533178"], "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:GSE65858"], "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:GSE65858"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39533178", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12865-024-00667-3", "sha256": 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Sixteen hours after transfection, the knockdown lentivirus (10 infections) wa", "us (10 infections) was screened and a stable transfection cell line was confirmed. 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