ScRNA-seq reveals the correlation between M2 phenotype of tumor-associated macrophages and lymph node metastasis of breast cancer.

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This study aimed to investigate the role of the M2 phenotype of tumor-associated macrophages and mine the key M2 macrophages-related genes for lymph node metastasis in BC. We downloaded the GSE158399 dataset from the Gene Expression Omnibus (GEO) database, which includes transcriptomic profiles of individual cells from primary tumors, negative lymph nodes (NLNs), and positive lymph nodes (PLNs) of breast cancer patients. The cell subsets were identified by clustering analysis after quality control of the scRNA-seq using Seurat. The activation and migration capability of M2 macrophages were evaluated with R package \"GSVA\". The key M2 macrophages-related genes were screened from the differential expressed genes (DEGs) and M2 macrophages activation and migration gene sets collected from MSigDB database. Our analysis identified three main cell types in primary tumors, NLNs, and PLNs: basal cells, luminal cells, and immune cell subsets. The further cell type classification of immune cell subsets indicated M2 macrophages accumulation in NLs and PLs. The GSVA enrichment scores for activation and migration capability were increased significantly in M2 macrophages from primary tumors than NLNs and PLNs (p-value < 0.001). Seven M2 macrophages activation-related and 15 M2 macrophages migration-related genes were significantly up-regulated in primary tumors than NLNs and PLNs. The proportion and GSVA enrichment scores for activation and migration of M2 macrophages may be potential markers for lymph node metastasis in breast cancer. Our study demonstrated that twenty-two up-regulated mRNA may be possible therapeutic targets for lymph node metastasis in breast cancer.", "claims": [{"id": "claim-method", "statement": "Relevant gene sets were collected through the MSigDB (https://www.gsea-msigdb.org/gsea/msigdb) database, and the R package “GSVA” was used to score the functional activity of M2 macrophages from the three samples using the Wilcoxon rank sum test compares differences among them.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37744272", "locator": "sections[5] \"GSVA-gene set enrichment analysis\" paragraph 2", "quote": "Relevant gene sets were collected through the MSigDB (https://www.gsea-msigdb.org/gsea/msigdb) database, and the R package “GSVA” was used to score the functional activity of M2 macrophages from the three samples using the Wilcoxon rank sum test compares differences among them."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The single-cell sequencing data GSE158399 of lymph node metastasis in breast cancer was obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158399).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37744272", "locator": "sections[3] \"Data preparation and quality control\" paragraph 2", "quote": "The single-cell sequencing data GSE158399 of lymph node metastasis in breast cancer was obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158399)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The GSVA enrichment scores for activation and migration capability were increased significantly in M2 macrophages from primary tumors than NLNs and PLNs (p-value < 0.001).", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "The GSVA enrichment scores for activation and migration capability were increased significantly in M2 macrophages from primary tumors than NLNs and PLNs (p-value < 0.001)."}, "evidence": [{"asset": "source:pmid:37744272", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The GSVA enrichment scores for activation and migration capability were increased significantly in M2 macrophages from primary tumors than NLNs and PLNs (p-value < 0.001)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The GSVA enrichment scores for activation and migration capability were increased significantly in M2 macrophages from primary tumors than NLNs and PLNs (p-value < 0.001).", "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:37744272"], "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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