Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts
Cardiac fibrosis is a common pathological feature in cardiac remodeling. This study aimed to explore the role of KDM5A in cardiac fibrosis via bioinformatics analysis. Cardiac fibroblasts (CFs) were harvested and cultured from 10 dilated cardiomyopathy (DCM) patients who underwent heart transplantat...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-07-01
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| Series: | Frontiers in Cardiovascular Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcvm.2022.929030/full |
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| author | Yiyao Jiang Yiyao Jiang Xu Zhang Ting Wei Xianjie Qi Isah Amir Abba Nana Zhang Yao Chen Ran Wang Chao Shi |
| author_facet | Yiyao Jiang Yiyao Jiang Xu Zhang Ting Wei Xianjie Qi Isah Amir Abba Nana Zhang Yao Chen Ran Wang Chao Shi |
| author_sort | Yiyao Jiang |
| collection | DOAJ |
| description | Cardiac fibrosis is a common pathological feature in cardiac remodeling. This study aimed to explore the role of KDM5A in cardiac fibrosis via bioinformatics analysis. Cardiac fibroblasts (CFs) were harvested and cultured from 10 dilated cardiomyopathy (DCM) patients who underwent heart transplantation. Western blotting was applied to verify that KDM5A is regulated by angiotensin II (Ang II) via the PI3k/AKT signaling pathway. The differentially expressed genes (DEGs) were analyzed by transcriptomics. ChIP-seq and ChIP-qPCR were used to identify the genes bound by KDM5A. In integrative analysis, weighted gene coexpression network analysis (WGCNA) was performed to identify highly relevant gene modules. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for the key genes in modules. The STRING database, Cytoscape, and MCODE were applied to construct the protein–protein interaction (PPI) network and screen hub genes. To verify the expression of DEGs regulated by KDM5A, Western blotting and immunofluorescence were performed in myocardial tissue samples. Immunofluorescence verified the vimentin positivity of CFs. Ang II upregulated the expression of KDM5A in CFs via the PI3K/AKT signaling pathway. GO analysis of DEGs indicated that regulation of vasoconstriction, extracellular region, and calcium ion binding were enriched when KDM5A interfered with CPI or Ang II. KEGG analysis of the DEGs revealed the involvement of ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, cell adhesion, and arrhythmogenic right ventricular cardiomyopathy pathways. Three hub genes (IGF1, MYH11, and TGFB3) were identified via four different algorithms. Subsequent verification in patient samples demonstrated that the hub genes, which were regulated by KDM5A, were downregulated in DCM samples. KDM5A is a key regulator in the progression of cardiac fibrosis. In this successful integrative analysis, IGF1, MYH11, and TGFB3 were determined to be coordinately expressed to participate in cardiac fibrosis. |
| first_indexed | 2024-12-11T17:26:32Z |
| format | Article |
| id | doaj.art-a795de612b9c4cbfb4bf0d0820d2dc28 |
| institution | Directory Open Access Journal |
| issn | 2297-055X |
| language | English |
| last_indexed | 2024-12-11T17:26:32Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Cardiovascular Medicine |
| spelling | doaj.art-a795de612b9c4cbfb4bf0d0820d2dc282022-12-22T00:56:57ZengFrontiers Media S.A.Frontiers in Cardiovascular Medicine2297-055X2022-07-01910.3389/fcvm.2022.929030929030Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac FibroblastsYiyao Jiang0Yiyao Jiang1Xu Zhang2Ting Wei3Xianjie Qi4Isah Amir Abba5Nana Zhang6Yao Chen7Ran Wang8Chao Shi9Department of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Surgery, Tianjin First Center Hospital and NanKai University, Tianjin, ChinaDepartment of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Medicine, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Medicine, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Emergency Medicine, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaDepartment of Cardiovascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, ChinaCardiac fibrosis is a common pathological feature in cardiac remodeling. This study aimed to explore the role of KDM5A in cardiac fibrosis via bioinformatics analysis. Cardiac fibroblasts (CFs) were harvested and cultured from 10 dilated cardiomyopathy (DCM) patients who underwent heart transplantation. Western blotting was applied to verify that KDM5A is regulated by angiotensin II (Ang II) via the PI3k/AKT signaling pathway. The differentially expressed genes (DEGs) were analyzed by transcriptomics. ChIP-seq and ChIP-qPCR were used to identify the genes bound by KDM5A. In integrative analysis, weighted gene coexpression network analysis (WGCNA) was performed to identify highly relevant gene modules. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for the key genes in modules. The STRING database, Cytoscape, and MCODE were applied to construct the protein–protein interaction (PPI) network and screen hub genes. To verify the expression of DEGs regulated by KDM5A, Western blotting and immunofluorescence were performed in myocardial tissue samples. Immunofluorescence verified the vimentin positivity of CFs. Ang II upregulated the expression of KDM5A in CFs via the PI3K/AKT signaling pathway. GO analysis of DEGs indicated that regulation of vasoconstriction, extracellular region, and calcium ion binding were enriched when KDM5A interfered with CPI or Ang II. KEGG analysis of the DEGs revealed the involvement of ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, cell adhesion, and arrhythmogenic right ventricular cardiomyopathy pathways. Three hub genes (IGF1, MYH11, and TGFB3) were identified via four different algorithms. Subsequent verification in patient samples demonstrated that the hub genes, which were regulated by KDM5A, were downregulated in DCM samples. KDM5A is a key regulator in the progression of cardiac fibrosis. In this successful integrative analysis, IGF1, MYH11, and TGFB3 were determined to be coordinately expressed to participate in cardiac fibrosis.https://www.frontiersin.org/articles/10.3389/fcvm.2022.929030/fullKDM5Acardiac fibrosisdifferentially expressed genesintegrative bioinformatics analysiscardiac fibroblasts |
| spellingShingle | Yiyao Jiang Yiyao Jiang Xu Zhang Ting Wei Xianjie Qi Isah Amir Abba Nana Zhang Yao Chen Ran Wang Chao Shi Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts Frontiers in Cardiovascular Medicine KDM5A cardiac fibrosis differentially expressed genes integrative bioinformatics analysis cardiac fibroblasts |
| title | Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts |
| title_full | Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts |
| title_fullStr | Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts |
| title_full_unstemmed | Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts |
| title_short | Transcriptomic and ChIP-seq Integrative Analysis Identifies KDM5A-Target Genes in Cardiac Fibroblasts |
| title_sort | transcriptomic and chip seq integrative analysis identifies kdm5a target genes in cardiac fibroblasts |
| topic | KDM5A cardiac fibrosis differentially expressed genes integrative bioinformatics analysis cardiac fibroblasts |
| url | https://www.frontiersin.org/articles/10.3389/fcvm.2022.929030/full |
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