Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics
Abstract Background DCM is a common cardiomyopathy worldwide, which is characterized by ventricular dilatation and systolic dysfunction. DCM is one of the most widespread diseases contributing to sudden death and heart failure. However, our understanding of its molecular mechanisms is limited becaus...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | Proteome Science |
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| Online Access: | https://doi.org/10.1186/s12953-023-00214-9 |
| _version_ | 1797453820256583680 |
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| author | Hongli Xiong Zhe Zheng Congcong Zhao Minzhu Zhao Qi Wang Peng Zhang Yongguo Li Ying Zhu Shisheng Zhu Jianbo Li |
| author_facet | Hongli Xiong Zhe Zheng Congcong Zhao Minzhu Zhao Qi Wang Peng Zhang Yongguo Li Ying Zhu Shisheng Zhu Jianbo Li |
| author_sort | Hongli Xiong |
| collection | DOAJ |
| description | Abstract Background DCM is a common cardiomyopathy worldwide, which is characterized by ventricular dilatation and systolic dysfunction. DCM is one of the most widespread diseases contributing to sudden death and heart failure. However, our understanding of its molecular mechanisms is limited because of its etiology and underlying mechanisms. Hence, this study explored the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics Methods DCM target genes were downloaded from the public databases. Next, DCM was induced in 20 rats by 8 weeks doxorubicin treatment (2.5 mg/kg/week). We applied isobaric tags for a relative and absolute quantification (iTRAQ) coupled with proteomics approach to identify differentially expressed proteins (DEPs) in myocardial tissue. After association analysis of the DEPs and the key target genes, subsequent analyses, including functional annotation, pathway enrichment, validation, were performed. Results Nine hundred thirty-five genes were identified as key target genes from public databases. Meanwhile, a total of 782 DEPs, including 348 up-regulated and 434 down-regulated proteins, were identified in our animal experiment. The functional annotation of these DEPs revealed complicated molecular mechanisms including TCA cycle, Oxidative phosphorylation, Cardiac muscle contraction. Moreover, the DEPs were analyzed for association with the key target genes screened in the public dataset. We further determined the importance of these three pathways. Conclusion Our results demonstrate that TCA cycle, Oxidative phosphorylation, Cardiac muscle contraction played important roles in the detailed molecular mechanisms of DCM. |
| first_indexed | 2024-03-09T15:28:23Z |
| format | Article |
| id | doaj.art-8762914b76fe4c2f89234c3d8f5833fc |
| institution | Directory Open Access Journal |
| issn | 1477-5956 |
| language | English |
| last_indexed | 2024-03-09T15:28:23Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Proteome Science |
| spelling | doaj.art-8762914b76fe4c2f89234c3d8f5833fc2023-11-26T12:22:58ZengBMCProteome Science1477-59562023-09-0121111310.1186/s12953-023-00214-9Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformaticsHongli Xiong0Zhe Zheng1Congcong Zhao2Minzhu Zhao3Qi Wang4Peng Zhang5Yongguo Li6Ying Zhu7Shisheng Zhu8Jianbo Li9Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityDepartment of Forensic Medicine, Henan University of Science and TechnologyDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityDepartment of Forensic Medicine, Hainan Medical UniversityDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityFaculty of Basic Medical Sciences, Chongqing Medical and Pharmaceutical CollegeDepartment of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical UniversityAbstract Background DCM is a common cardiomyopathy worldwide, which is characterized by ventricular dilatation and systolic dysfunction. DCM is one of the most widespread diseases contributing to sudden death and heart failure. However, our understanding of its molecular mechanisms is limited because of its etiology and underlying mechanisms. Hence, this study explored the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics Methods DCM target genes were downloaded from the public databases. Next, DCM was induced in 20 rats by 8 weeks doxorubicin treatment (2.5 mg/kg/week). We applied isobaric tags for a relative and absolute quantification (iTRAQ) coupled with proteomics approach to identify differentially expressed proteins (DEPs) in myocardial tissue. After association analysis of the DEPs and the key target genes, subsequent analyses, including functional annotation, pathway enrichment, validation, were performed. Results Nine hundred thirty-five genes were identified as key target genes from public databases. Meanwhile, a total of 782 DEPs, including 348 up-regulated and 434 down-regulated proteins, were identified in our animal experiment. The functional annotation of these DEPs revealed complicated molecular mechanisms including TCA cycle, Oxidative phosphorylation, Cardiac muscle contraction. Moreover, the DEPs were analyzed for association with the key target genes screened in the public dataset. We further determined the importance of these three pathways. Conclusion Our results demonstrate that TCA cycle, Oxidative phosphorylation, Cardiac muscle contraction played important roles in the detailed molecular mechanisms of DCM.https://doi.org/10.1186/s12953-023-00214-9Dilated cardiomyopathyMolecular pathwaysGene networkBioinformaticsMechanisms |
| spellingShingle | Hongli Xiong Zhe Zheng Congcong Zhao Minzhu Zhao Qi Wang Peng Zhang Yongguo Li Ying Zhu Shisheng Zhu Jianbo Li Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics Proteome Science Dilated cardiomyopathy Molecular pathways Gene network Bioinformatics Mechanisms |
| title | Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics |
| title_full | Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics |
| title_fullStr | Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics |
| title_full_unstemmed | Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics |
| title_short | Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics |
| title_sort | insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining itraq prm proteomics and bioinformatics |
| topic | Dilated cardiomyopathy Molecular pathways Gene network Bioinformatics Mechanisms |
| url | https://doi.org/10.1186/s12953-023-00214-9 |
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