Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels the molecular feature of M2 macrophages of head and neck squamous cell carcinoma.

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We gathered gene expression profiles and clinical data from HNSC patients in the TCGA database. Using Consensus Clustering, we categorized these patients into M2 macrophage-related clusters. We developed a M2 macrophage-related signature (MRS) through statistical analyses. Additionally, we assessed gene expression in HNSC cells using single-cell sequencing data (GSE139324). We identified three distinct M2 macrophage-related clusters in HNSC, each with different prognostic outcomes and immune characteristics. Patients with different MRS profiles exhibited variations in immune infiltration, genetic mutations and prognosis. FCGR2A may play a role in creating an immunosuppressive tumour microenvironment and could potentially serve as a therapeutic target for HNSC. Our study demonstrated that M2 macrophage-related genes significantly impact the development and progression of HNSC. The M2 macrophage-related model offered a more comprehensive assessment of HNSC patient prognosis, genetic mutations and immune features. FCGR2A was implicated in immunosuppressive microenvironments and may hold promise for the development of novel immunotherapeutic strategies for HNSC.", "claims": [{"id": "claim-method", "statement": "We developed the M2 macrophage‐related signature (MRS) through a combination of the least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38393307", "locator": "sections[6] \"Prognostic model analysis\" paragraph 2", "quote": "We developed the M2 macrophage‐related signature (MRS) through a combination of the least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox regression analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in TCGA, GEO and TISCH2 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38393307", "locator": "sections[28] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data that support the findings of this study are openly available in TCGA, GEO and TISCH2 datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:38393307"], "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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