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Xu Y, Ma Q, Ren J, Chen L, Guo W, Feng K, Zeng Z, Huang T, Cai Y. Using Machine Learning Methods in Identifying Genes Associated with COVID-19 in Cardiomyocytes and Cardiac Vascular Endothelial Cells. Life (Basel) 2023; 13:life13041011. [PMID: 37109540 PMCID: PMC10146712 DOI: 10.3390/life13041011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) not only causes respiratory system damage, but also imposes strain on the cardiovascular system. Vascular endothelial cells and cardiomyocytes play an important role in cardiac function. The aberrant expression of genes in vascular endothelial cells and cardiomyocytes can lead to cardiovascular diseases. In this study, we sought to explain the influence of respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gene expression levels of vascular endothelial cells and cardiomyocytes. We designed an advanced machine learning-based workflow to analyze the gene expression profile data of vascular endothelial cells and cardiomyocytes from patients with COVID-19 and healthy controls. An incremental feature selection method with a decision tree was used in building efficient classifiers and summarizing quantitative classification genes and rules. Some key genes, such as MALAT1, MT-CO1, and CD36, were extracted, which exert important effects on cardiac function, from the gene expression matrix of 104,182 cardiomyocytes, including 12,007 cells from patients with COVID-19 and 92,175 cells from healthy controls, and 22,438 vascular endothelial cells, including 10,812 cells from patients with COVID-19 and 11,626 cells from healthy controls. The findings reported in this study may provide insights into the effect of COVID-19 on cardiac cells and further explain the pathogenesis of COVID-19, and they may facilitate the identification of potential therapeutic targets.
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Affiliation(s)
- Yaochen Xu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
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Jun Q, Youhong L, Yuan Z, Xi Y, Wang B, Xinyi S, Fu Y, Kedan C, Lian J, Jianqing Z. Histone modification of endothelial-mesenchymal transition in cardiovascular diseases. Front Cardiovasc Med 2022; 9:1022988. [PMID: 36568553 PMCID: PMC9768231 DOI: 10.3389/fcvm.2022.1022988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Endothelial-mesenchymal transition (EndMT) is a differentiation process in which endothelial cells lose their own characteristics and acquire mesenchymal-like characteristics, which contributes to the formation and development of atherosclerotic plaques. Until now, there is still a lack of effective measures to treat atherosclerosis (AS), so there is an urgent need to understand the underlying mechanisms of AS. In addition, although various studies have shown that EndMT is involved in the pathological stages of cardiovascular diseases, such as myocardial fibrosis, myocardial hypertrophy, and hypertension, the specific molecular mechanisms driving EndMT are still in the exploratory stage. In this review, we review the role of histone modifications (methylation, demethylation and acetylation, deacetylation) on EndMT in cardiovascular disease, aiming to target histone-modifying enzymes to guide cardiovascular disease therapy.
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Affiliation(s)
- Qiu Jun
- Medicine School of Ningbo University, Ningbo, China
| | - Li Youhong
- Li Huili Hospital Affiliated to Ningbo University, Ningbo, China
| | - Zhong Yuan
- Ningbo Medical-Industrial Integration Innovation Research Institute, Ningbo, China
| | - Yang Xi
- Medicine School of Ningbo University, Ningbo, China
| | - Bingyu Wang
- Medicine School of Ningbo University, Ningbo, China
| | - Sun Xinyi
- Medicine School of Ningbo University, Ningbo, China
| | - Yin Fu
- Medicine School of Ningbo University, Ningbo, China
| | - Cen Kedan
- Medicine School of Ningbo University, Ningbo, China
| | - Jiangfang Lian
- Medicine School of Ningbo University, Ningbo, China,Jiangfang Lian,
| | - Zhou Jianqing
- Li Huili Hospital Affiliated to Ningbo University, Ningbo, China,Medicine School of Ningbo University, Ningbo, China,*Correspondence: Zhou Jianqing,
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Wang B, Yang X, Sun X, Liu J, Fu Y, Liu B, Qiu J, Lian J, Zhou J. ATF3 in atherosclerosis: a controversial transcription factor. J Mol Med (Berl) 2022; 100:1557-1568. [PMID: 36207452 DOI: 10.1007/s00109-022-02263-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022]
Abstract
Atherosclerosis, the pathophysiological basis of most malignant cardiovascular diseases, remains a global concern. Transcription factors play a key role in regulating cell function and disease progression in developmental signaling pathways involved in atherosclerosis. Activated transcription factor (ATF) 3 is an adaptive response gene in the ATF/cAMP response element binding (CREB) protein family that acts as a transcription suppressor or activator by forming homodimers or heterodimers with other ATF/CREB members. Appropriate ATF3 expression is vital for normal physiological cell function. Notably, ATF3 exhibits distinct roles in vascular endothelial cells, macrophages, and the liver, which will also be described in detail. This review provides a new perspective for atherosclerosis therapy by summarizing the mechanism of ATF3 in atherosclerosis, as well as the structure and pathophysiological properties of ATF3. KEY MESSAGES: • In endothelial cells, ATF3 overexpression aggravates oxidative stress and inflammation. • In macrophages and liver cells, ATF3 can act as a negative regulator of inflammation and promote cholesterol metabolism. • ATF3 can be used as a potential therapeutic factor in the treatment of atherosclerosis.
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Affiliation(s)
- Bingyu Wang
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
| | - Xi Yang
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China.,Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Xinyi Sun
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
| | - Jianhui Liu
- Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Yin Fu
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
| | - Bingyang Liu
- Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Jun Qiu
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China
| | - Jiangfang Lian
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China.,Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China.,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China
| | - Jianqing Zhou
- Department of Cardiovascular, Medical College, Ningbo University, Ningbo, China. .,Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, China. .,Central Laboratory, Ningbo Institute of Innovation for Combined Medicine and Engineering, Ningbo, China.
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