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pmid:37288756
Macrophage polarization induces endothelium-to-myofibroblast transition in chronic allograft dysfunction.
Zeping Gui · Xiang Zhang · Qianguang Han · Zhou Hang · Ruoyun Tan · Min Gu · Zijie Wang
Renal failure · 2023 doi:10.1080/0886022X.2023.2220418
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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Transplanted nephrectomy specimens from CAD patients were collected and studied to explore the infiltration of M1 and M2 macrophages using immunofluorescence, PCR, and Western blotting (WB). A co-culture model of M1 macrophages, polarized from mouse bone marrow-derived macrophages (BMDM) or Raw264.7, and aortic endothelial cells was established, and EndMT was tested using PCR and WB. RNA-sequencing was performed on the macrophages from the mouse BMDM. The TNF-α secreted from the polarized M1 macrophages was verified using ELISA. Based on the GEO public database, it was observed that macrophages were significantly infiltrated in CAD allograft tissues, with CD68(+) iNOS(+) M1 macrophages significantly infiltrating the glomeruli of allograft tissues, and CD68(+)CD206(+) M2 macrophages notably infiltrating the allograft interstitial area. 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RNA-sequencing was performed on the macrophages from the mo", "ficantly promote the EndMT process in vitro. RNA-Sequencing analysis revealed that TNF signaling could b", "hronic allograft dysfunction (CAD). GSE21374 transcriptome sequencing data were obtained. Transplanted", "nd homogenized, and differential analysis of transcriptome information between patients with stable all"], "order_basis": "paper_text_order:223", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["infiltration of M1 and M2 macrophages using immunofluorescence, PCR, and Western blotting (WB). A co-cultur", "nford.edu). Immunofluorescence intensity and immunohistochemical positive regions were calculated using the I", "oftware Cibersort (cibersortx.stanford.edu). Immunofluorescence intensity and immunohistochemical positive r", "function (CAD; n = 5); (F-G) Indirect double immunofluorescence staining of CD68(+) iNOS(+) M1 macrophages ("], "order_basis": "paper_text_order:408", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["crophages using immunofluorescence, PCR, and Western blotting (WB). A co-culture model of M1 macrophages,"], "order_basis": "paper_text_order:436", "id": "assay:3"}, {"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": ["ture model of M1 macrophages, polarized from mouse bone marrow-derived macrophages (BMDM) or Ra", "ng was performed on the macrophages from the mouse BMDM. The TNF-α secreted from the polarized"], "order_basis": "paper_text_order:512", "id": "assay:4"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["polarized M1 macrophages was verified using ELISA. Based on the GEO public database, it was ob"], "order_basis": "paper_text_order:797", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We employed R3.6.1 to analyze all data, using the Limma package to differentially analyze public transcriptome data, and the Clusterprofiler package to analyze gene enrichment based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. Each sample’s immune cell infiltration status was also fitted (number of fits = 100) using the bioinformatics software Cibersort (cibersortx.stanford.edu)."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}