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Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq
BACKGROUND: The pathogenic mechanism of dilated cardiomyopathy (DCM) remains to be defined. This study aimed to identify hub genes and immune cells that could serve as potential therapeutic targets for DCM. METHODS: We downloaded four datasets from the Gene Expression Omnibus (GEO) database: GSE1419...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9290235/ https://www.ncbi.nlm.nih.gov/pubmed/35850644 http://dx.doi.org/10.1186/s12872-022-02759-7 |
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author | Fang, Chenggang Lv, Zhan Yu, Zhimin Wang, Kexin Xu, Chengkai Li, Yixuan Wang, Yanggan |
author_facet | Fang, Chenggang Lv, Zhan Yu, Zhimin Wang, Kexin Xu, Chengkai Li, Yixuan Wang, Yanggan |
author_sort | Fang, Chenggang |
collection | PubMed |
description | BACKGROUND: The pathogenic mechanism of dilated cardiomyopathy (DCM) remains to be defined. This study aimed to identify hub genes and immune cells that could serve as potential therapeutic targets for DCM. METHODS: We downloaded four datasets from the Gene Expression Omnibus (GEO) database: GSE141910, GSE3585, GSE42955 and GSE79962. Weighted gene coexpression network analysis (WGCNA) and differential expression analysis were performed to identify gene panels related to DCM. Meanwhile, the CIBERSORT algorithm was used to estimate the immune cells in DCM tissues. Multiple machine learning approaches were used to screen the hub genes and immune cells. Finally, the diagnostic value of the hub genes was assessed by receiver operating characteristic (ROC) analysis. An experimental mouse model of dilated cardiomyopathy was used to validate the bioinformatics results. RESULTS: FRZB and EXT1 were identified as hub biomarkers, and the ROC curves suggested an excellent diagnostic ability of the above genes for DCM. In addition, naive B cells were upregulated in DCM tissues, while eosinophils, M2 macrophages, and memory CD4 T cells were downregulated in DCM tissues. The increase in two hub genes and naive B cells was validated in animal experiments. CONCLUSION: These results indicated that FRZB and EXT1 could be used as promising biomarkers, and eosinophils, M2 macrophages, resting memory CD4 T cells and naive B cells may also affect the occurrence of DCM. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12872-022-02759-7. |
format | Online Article Text |
id | pubmed-9290235 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-92902352022-07-19 Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq Fang, Chenggang Lv, Zhan Yu, Zhimin Wang, Kexin Xu, Chengkai Li, Yixuan Wang, Yanggan BMC Cardiovasc Disord Research BACKGROUND: The pathogenic mechanism of dilated cardiomyopathy (DCM) remains to be defined. This study aimed to identify hub genes and immune cells that could serve as potential therapeutic targets for DCM. METHODS: We downloaded four datasets from the Gene Expression Omnibus (GEO) database: GSE141910, GSE3585, GSE42955 and GSE79962. Weighted gene coexpression network analysis (WGCNA) and differential expression analysis were performed to identify gene panels related to DCM. Meanwhile, the CIBERSORT algorithm was used to estimate the immune cells in DCM tissues. Multiple machine learning approaches were used to screen the hub genes and immune cells. Finally, the diagnostic value of the hub genes was assessed by receiver operating characteristic (ROC) analysis. An experimental mouse model of dilated cardiomyopathy was used to validate the bioinformatics results. RESULTS: FRZB and EXT1 were identified as hub biomarkers, and the ROC curves suggested an excellent diagnostic ability of the above genes for DCM. In addition, naive B cells were upregulated in DCM tissues, while eosinophils, M2 macrophages, and memory CD4 T cells were downregulated in DCM tissues. The increase in two hub genes and naive B cells was validated in animal experiments. CONCLUSION: These results indicated that FRZB and EXT1 could be used as promising biomarkers, and eosinophils, M2 macrophages, resting memory CD4 T cells and naive B cells may also affect the occurrence of DCM. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12872-022-02759-7. BioMed Central 2022-07-18 /pmc/articles/PMC9290235/ /pubmed/35850644 http://dx.doi.org/10.1186/s12872-022-02759-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Fang, Chenggang Lv, Zhan Yu, Zhimin Wang, Kexin Xu, Chengkai Li, Yixuan Wang, Yanggan Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title | Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title_full | Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title_fullStr | Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title_full_unstemmed | Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title_short | Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq |
title_sort | exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from rna-seq |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9290235/ https://www.ncbi.nlm.nih.gov/pubmed/35850644 http://dx.doi.org/10.1186/s12872-022-02759-7 |
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