Role of Monocyte/Macrophage-Associated Gene Ccl9 in Acute Myocardial Infarction Analysis: Based on Bulk and Single Cell RNA Sequencing Data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41195292", "kind": "science-record", "revision": 4, "content_hash": "sha256:2dc5c9a3713eb2603423c9c0b0e5aae29babca3073e5a5bcffdce7b663b4d38b", "created_at": "2026-11-01T20:31:13Z", "updated_at": "2026-11-01T22:57:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Role of Monocyte/Macrophage-Associated Gene Ccl9 in Acute Myocardial Infarction Analysis: Based on Bulk and Single Cell RNA Sequencing Data.", "doi": "10.2147/JIR.S516092", "pmid": "41195292", "authors": ["Qiang Yang", "Ziyue Luo", "Xinyi Cheng", "Tianyu Wang", "Pengfei Hu"], "journal": "Journal of inflammation research", "year": 2025, "abstract": "Background: Acute myocardial infarction (AMI) is one of the major causes of sudden cardiac death, resulting in severe complications. Therefore, it is of great significance to find new therapeutic targets.\nMethods: AMI datasets, Bulk RNA sequencing (Bulk RNA seq) GSE158157 and GSE23294, scRNA-seq GSE163129 datasets were downloaded from GEO. In this study, GSE163129 was subjected to dimensionality reduction analysis, subpopulation identification, enrichment analysis, and cellular communication analysis. Subsequently, we performed differential expression and immune infiltration analysis on GSE158157 and GSE23294 datasets to obtain seven monocyte/macrophage-related core genes. Finally, the mechanism of Ccl9 in AMI was explored through a series of animal and cellular experiments, which involved the establishment of AMI mouse model and isolation of primary mouse cardiomyocytes.\nResults: The t-distributed stochastic neighbor embedding (tSNE) analysis of GSE163129 identified 18 cell clusters, divided into six cell types. Monocytes and neutrophils were highly active. Differential expression analysis of GSE158157 and GSE23294 identified 2362 differentially expressed genes (DEGs). Immune infiltration analysis showed macrophage presence, with notable differences in M2 monocytes and other immune cells between AMI and Sham groups. Nine monocyte-associated hub genes were identified. qRT-PCR validation in AMI mouse models revealed significant upregulation of B2M, SPP1, Ccl4, LGALS3, MRC1, Ccl9, and FN1. Co-culture of primary cardiomyocytes and RAW264.7 cells indicated that low Ccl9 expression promoted M2 macrophage polarization and reduced OGD-induced cardiomyocyte injury.\nConclusion: This study identified seven monocyte/macrophage-related genes in AMI and highlighted Ccl9's potential role in regulating M2 macrophage polarization and mitigating OGD-induced cardiomyocyte injury in AMI.", "claims": [{"id": "claim-method", "statement": "Differentially Expressed Genes (DEGs) analysis was performed using FindAllMarkers to find DEGs in each cell cluster, and the Top 10 DEGs of each cell cluster were selected to draw heatmaps.\nDEG analysis of samples was performed using the limma package of R (V 4.3.0), with thresholds set to |log2FC|>1 and adjust pvalue<0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41195292", "locator": "sections[4] \"Dimensionality Reduction Analysis and Subpopulation Identification of Single-Cell Datasets\" paragraph 2", "quote": "Differentially Expressed Genes (DEGs) analysis was performed using FindAllMarkers to find DEGs in each cell cluster, and the Top 10 DEGs of each cell cluster were selected to draw heatmaps."}, {"asset": "source:pmid:41195292", "locator": "sections[8] \"Screening of Bulk Dataset DEGs\" paragraph 2", "quote": "DEG analysis of samples was performed using the limma package of R (V 4.3.0), with thresholds set to |log2FC|>1 and adjust pvalue<0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets GSE158157, GSE23294 and GSE163129 used in the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41195292", "locator": "sections[39] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets GSE158157, GSE23294 and GSE163129 used in the current study are available in the GEO repository (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified seven monocyte/macrophage-related genes in acute myocardial infarction and highlighted Ccl9's potential role in regulating M2 macrophage polarization and mitigating OGD-induced cardiomyocyte injury.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41195292", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified seven monocyte/macrophage-related genes in AMI and highlighted Ccl9’s potential role in regulating M2 macrophage polarization and mitigating OGD-induced cardiomyocyte injury in AMI."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified seven monocyte/macrophage-related genes in acute myocardial infarction and highlighted Ccl9's potential role in regulating M2 macrophage polarization and mitigating OGD-induced cardiomyocyte injury.", "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:41195292"], "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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