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pmid:36311801
Significance of macrophage infiltration in the prognosis of lung adenocarcinoma patients evaluated by scRNA and bulkRNA analysis.
Huaiyang Zhu · Chunning Zheng · Hongtao Liu · Fanhua Kong · Shuai Kong · Feng Chen · Yuan Tian
Frontiers in immunology · 2022 doi:10.3389/fimmu.2022.1028440
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Complete file
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Marker genes of macrophage subtypes were identified using single-cell sequencing of lung adenocarcinoma tissue. Risk score models were constructed and validated using external data cohorts and clinical samples.\nResults: Analysis of cohorts TCGA-LUAD, GSE11969, GSE31210, GSE50081, GSE72094 and GSE8894, revealed a negative correlation between macrophage infiltration and survival. Immunohistochemical analyses of clinical samples were consistent with these data. Based on cell-cluster-markers and TAMs-related-genes, TOP8 genes were obtained (C1QTNF6, CCNB1, FSCN1, HMMR, KPNA2, PRC1, RRM2, and TK1) with a significant association to prognosis. Risk score models including 9 factors (C1QTNF6, FSCN1, KPNA2, GLI2, TYMS, BIRC3, RBBP7, KRT8, GPR65) for prognosis were constructed. The efficacy, stability and generalizability of the risk score models were validated using multiple data cohorts (GSE19188, GSE26939, GSE31210, GSE50081, GSE42127, and GSE72094).\nConclusions: Macrophage infiltration negatively correlates with prognosis in patients with lung adenocarcinoma. Based on cell-cluster-markers and TAMs-related-genes, both TOP8 genes (C1QTNF6, CCNB1, FSCN1, HMMR, KPNA2, PRC1, RRM2, TK1) and risk score models using C1QTNF6, FSCN1, KPNA2, GLI2, TYMS, BIRC3, RBBP7, KRT8, GPR65 could predict disease prognosis.", "claims": [{"id": "claim-method", "statement": "CIBERSORT was used to evaluate the levels of immune-infiltration from different lung adenocarcinoma datasets (TCGA-LUAD, GSE11969, GSE31210, GSE50081, GSE72094, and GSE8894).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36311801", "locator": "sections[16] \"3.1 Proportion of immune infiltrating cells and the prognostic efficacy of macrophages\" paragraph 2", "quote": "CIBERSORT was used to evaluate the levels of immune-infiltration from different lung adenocarcinoma datasets (TCGA-LUAD, GSE11969, GSE31210, GSE50081, GSE72094, and GSE8894)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. 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{"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE11969", "GSE19188", "GSE26939", "GSE31210", "GSE42127", "GSE50081", "GSE72094", "GSE8894", "GSE131907", "GSE13213"], "resolved_accessions": ["GSE11969", "GSE19188", "GSE26939", "GSE31210", "GSE42127", "GSE50081", "GSE72094", "GSE8894", "GSE131907", "GSE13213"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE11969, GSE19188, GSE26939, GSE31210, GSE42127, GSE50081, GSE72094, GSE8894, GSE131907, GSE13213 in GEO database and the accession resolves in the repository. 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Immunohistochemical analyses of clinical samples were consistent", "cal sample validation (sample collection and immunohistochemistry) Lung Cancer samples were collected from the", "for histological evaluation. HE-stained and immunohistochemical (IHC) slides were examined by two independen", "rker for M2 macrophages (31). Double-labeled immunohistochemical staining was performed using alkaline phosph"], "order_basis": "paper_text_order:757", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["WHO criteria. Samples were IHC stained with mouse anti-human CD68 monoclonal antibodies (MAB-0", "lonal antibodies (MAB-0863, clone MX075) and mouse anti-human CD163 monoclonal antibodies (MAB-"], "order_basis": "paper_text_order:3294", "id": "assay:2"}, {"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": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}