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Toro V, Jutras-Beaudoin N, Boucherat O, Bonnet S, Provencher S, Potus F. Right Ventricle and Epigenetics: A Systematic Review. Cells 2023; 12:2693. [PMID: 38067121 PMCID: PMC10705252 DOI: 10.3390/cells12232693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
There is an increasing recognition of the crucial role of the right ventricle (RV) in determining the functional status and prognosis in multiple conditions. In the past decade, the epigenetic regulation (DNA methylation, histone modification, and non-coding RNAs) of gene expression has been raised as a critical determinant of RV development, RV physiological function, and RV pathological dysfunction. We thus aimed to perform an up-to-date review of the literature, gathering knowledge on the epigenetic modifications associated with RV function/dysfunction. Therefore, we conducted a systematic review of studies assessing the contribution of epigenetic modifications to RV development and/or the progression of RV dysfunction regardless of the causal pathology. English literature published on PubMed, between the inception of the study and 1 January 2023, was evaluated. Two authors independently evaluated whether studies met eligibility criteria before study results were extracted. Amongst the 817 studies screened, 109 studies were included in this review, including 69 that used human samples (e.g., RV myocardium, blood). While 37 proposed an epigenetic-based therapeutic intervention to improve RV function, none involved a clinical trial and 70 are descriptive. Surprisingly, we observed a substantial discrepancy between studies investigating the expression (up or down) and/or the contribution of the same epigenetic modifications on RV function or development. This exhaustive review of the literature summarizes the relevant epigenetic studies focusing on RV in human or preclinical setting.
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Affiliation(s)
| | | | | | | | | | - François Potus
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Québec, QC G1V 4G5, Canada; (V.T.); (N.J.-B.); (O.B.); (S.B.); (S.P.)
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2
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Schiano C, Balbi C, Burrello J, Ruocco A, Infante T, Fiorito C, Panella S, Barile L, Mauro C, Vassalli G, Napoli C. De novo DNA methylation induced by circulating extracellular vesicles from acute coronary syndrome patients. Atherosclerosis 2022; 354:41-52. [PMID: 35830762 DOI: 10.1016/j.atherosclerosis.2022.06.1026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND AIMS DNA methylation is associated with gene silencing, but its clinical role in cardiovascular diseases (CVDs) remains to be elucidated. We hypothesized that extracellular vesicles (EVs) may carry epigenetic changes, showing themselves as a potentially valuable non-invasive diagnostic liquid biopsy. We isolated and characterized circulating EVs of acute coronary syndrome (ACS) patients and assessed their role on DNA methylation in epigenetic modifications. METHODS EVs were recovered from plasma of 19 ACS patients and 50 healthy subjects (HS). Flow cytometry, qRT-PCR, and Western blot (WB) were performed to evaluate both intra-vesicular and intra-cellular signals. ShinyGO, PANTHER, and STRING tools were used to perform GO and PPI network analyses. RESULTS ACS-derived EVs showed increased levels of DNA methyltransferases (DNMTs) (p<0.001) and Ten-eleven translocation (TET) genes reduction. Specifically, de novo methylation transcripts, as DNMT3A and DNMT3B, were significantly increased in plasma ACS-EVs. DNA methylation analysis on PBMCs from healthy donors treated with HS- and ACS-derived EVs showed an important role of DNMTs carried by EVs. PPI network analysis evidenced that ACS-EVs induced changes in PBMC methylome. In the most enriched subnetwork, the hub gene SRC was connected to NOTCH1, FOXO3, CDC42, IKBKG, RXRA, DGKG, BAIAP2 genes that were showed to have many molecular effects on various cell types into onset of several CVDs. Modulation in gene expression after ACS-EVs treatment was confirmed for SRC, NOTCH1, FOXO3, RXRA, DGKG and BAIAP2 (p<0.05). CONCLUSIONS Our data showed an important role for ACS-derived EVs in gene expression modulation through de novo DNA methylation signals, and modulating signalling pathways in target cells.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy; Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland.
| | - Carolina Balbi
- Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Center for Molecular Cardiology, Zurich, Switzerland
| | - Jacopo Burrello
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Antonio Ruocco
- Unit of Cardiovascular Diseases and Arrhythmias, Antonio Cardarelli Hospital, Naples, Italy
| | - Teresa Infante
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Stefano Panella
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Lucio Barile
- Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Cardiovascular Theranostics, Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland
| | - Ciro Mauro
- Unit of Cardiovascular Diseases and Arrhythmias, Antonio Cardarelli Hospital, Naples, Italy
| | - Giuseppe Vassalli
- Cellular and Molecular Cardiology lab Istituto Cardiocentro Ticino-EOC, Lugano, Switzerland; Laboratories for Translation Research, EOC, Bellinzona, Switzerland; Center for Molecular Cardiology, Zurich, Switzerland
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania Luigi Vanvitelli, Naples, Italy; Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology (SIMT), Regional Reference Laboratory of Transplant Immunology (LIT), Azienda Universitaria Policlinico (AOU), Naples, Italy
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3
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Nana L, Lu L, Zhen L, Ying D, Meixian W, Zhao J, Zeng S, Hong K, Yanping W, Jun Z, Jianxin Z, Ping Y. The effect of maternal polycyclic aromatic hydrocarbons exposure and methylation levels of CHDs-candidate genes on the risk of congenital heart diseases. Prenat Diagn 2022; 42:1142-1154. [PMID: 35556253 DOI: 10.1002/pd.6167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/27/2022] [Accepted: 05/08/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To evaluate the impact of maternal exposure to polycyclic aromatic hydrocarbons (PAHs) and methylation levels of CHDs-candidate genes on the risk of congenital heart diseases (CHDs), and the effect of PAHs exposure on DNA methylation states. METHODS A case-control study involving 60 mother -fetus pairs was performed by measuring 1-OHPG concentration in maternal urine and methylation levels of 20 CHDs-candidate genes in cord bloods. Logistic regression models were applied to determine the effect of maternal PAHs exposure and fetal methylation levels on the risk of CHDs. Spearman correlation was performed to correlate PAHs exposure and methylation levels. RESULTS Maternal higher PAHs exposure was associated with the risk of CHDs (aOR = 3.245, 95% CI: 1.060, 9.937) or some subtypes. The methylation levels of 23 amplicons within 11 genes exhibited significant differences between CHDs and controls. Higher methylation of NKX2-5_M1 was associated with decreased risk of CHDs (aOR=0.182, 95% CI:0.034, 0.983). No significant correlations were found between 1-OHPG concentration and methylation levels of NKX2-5_M1. CONCLUSIONS Maternal PAHs exposure was linked with CHDs. Higher methylation of the upstream sequence of NKX2-5 promoter decreased the risk of CHDs. There was no correlation between maternal PAHs exposure and the methylation level of NKX2-5. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Li Nana
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Li Lu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Liu Zhen
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Deng Ying
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Wang Meixian
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Jinju Zhao
- Department of Gynecology and Obstetrics, Xichang people's Hospital, Xichang, China
| | - Shengli Zeng
- Department of Gynecology and Obstetrics, Rongchang Maternal and Child care Hospital, Chongqing, China
| | - Kang Hong
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Wang Yanping
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Zhu Jun
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Zhao Jianxin
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yu Ping
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec.3 No.17, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
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Abstract
Embryonic heart development is an intricate process that mainly involves morphogens, transcription factors, and cardiac genes. The precise spatiotemporal expression of these genes during different developmental stages underlies normal heart development. Thus, mutation or aberrant expression of these genes may lead to congenital heart disease (CHD). However, evidence demonstrates that the mutation of genes accounts for only a small portion of CHD cases, whereas the aberrant expression regulated by epigenetic modification plays a predominant role in the pathogenesis of CHD. In this review, we provide essential knowledge on the aberrant epigenetic modification involved in the pathogenesis of CHD. Then, we discuss recent advances in the identification of novel epigenetic biomarkers. Last, we highlight the epigenetic roles in some adverse intrauterine environment‐related CHD, which may help the prevention, diagnosis, and treatment of these kinds of CHD.
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Affiliation(s)
- Guanglei Wang
- Department of Obstetrics, Gynecology, & Reproductive Sciences University of Maryland School of Medicine Baltimore MD
| | - Bingbing Wang
- Department of Obstetrics, Gynecology, & Reproductive Sciences University of Maryland School of Medicine Baltimore MD
| | - Peixin Yang
- Department of Obstetrics, Gynecology, & Reproductive Sciences University of Maryland School of Medicine Baltimore MD
- Department of Biochemistry & Molecular Biology University of Maryland School of Medicine Baltimore MD
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DNA Methylation Levels of the TBX5 Gene Promoter Are Associated with Congenital Septal Defects in Mexican Paediatric Patients. BIOLOGY 2022; 11:biology11010096. [PMID: 35053095 PMCID: PMC8773106 DOI: 10.3390/biology11010096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 11/17/2022]
Abstract
The TBX5 gene regulates morphological changes during heart development, and it has been associated with epigenetic abnormalities observed in congenital heart defects (CHD). The aim of this research was to evaluate the association between DNA methylation levels of the TBX5 gene promoter and congenital septal defects. DNA methylation levels of six CpG sites in the TBX5 gene promoter were evaluated using pyrosequencing analysis in 35 patients with congenital septal defects and 48 controls. Average methylation levels were higher in individuals with congenital septal defects than in the controls (p < 0.004). In five CpG sites, we also found higher methylation levels in patients than in the controls (p < 0.05). High methylation levels were associated with congenital septal defects (OR = 3.91; 95% CI = 1.02–14.8; p = 0.045). The analysis of Receiver Operating Characteristic (ROC) showed that the methylation levels of the TBX5 gene could be used as a risk marker for congenital septal defects (AUC = 0.68, 95% CI = 0.56–0.80; p = 0.004). Finally, an analysis of environmental factors indicated that maternal infections increased the risk (OR = 2.90; 95% CI = 1.01–8.33; p = 0.048) of congenital septal defects. Our data suggest that a high DNA methylation of the TBX5 gene could be associated with congenital septal defects.
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Zhou J, Xiong Y, Dong X, Wang H, Qian Y, Ma D, Li X. Genome-wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development-associated genes in fetuses with cardiac defects. Exp Ther Med 2021; 22:1032. [PMID: 34373718 PMCID: PMC8343574 DOI: 10.3892/etm.2021.10464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
DNA methylation, as an epigenetic mechanism, has a vital role in heart development. An increasing number of studies have investigated aberrant DNA methylation in pediatric or adult heart samples from patients with congenital heart defects (CHD). Placenta tissue, umbilical cord blood, or newborn blood have also been used to detect DNA methylation biomarkers for CHD. However, few studies have compared the methylation levels in fetal heart tissue with cardiac defects with that in normal controls. The present study conducted an integrative whole-genome and CpG site-specific DNA methylation analysis of fetal heart samples from 17 isolated cardiac defect cases, 14 non-isolated cardiac defect cases, and 22 controls with normal hearts, using methylated DNA immunoprecipitation microarray and MassARRAY EpiTYPER assays. Expression of genes adjacent to differentially methylated regions (DMRs) was measured by RT-qPCR and western blot analysis. The results revealed that fetuses with cardiac defects presented global hypomethylation. Genomic analysis of DMRs revealed that a proportion of DMRs were located in exons (12.4%), distal intergenic regions (11.14%), and introns (8.97%). Only 55.7% of DMRs were observed at promoter regions. Functional enrichment analysis for genes adjacent to these DMRs revealed that hypomethylated genes were involved in embryonic heart tube morphogenesis and immune-related regulation functions. Intergenic hypermethylation of EGFR and solute carrier family 19 member 1 (SLC19A1), and intragenic hypomethylation of NOTCH1 were validated in fetal heart tissues with cardiac defects. Only SLC19A1 expression was significantly decreased at the mRNA level, while EGFR, NOTCH1, and SLC19A1 expression were all significantly decreased at the protein level. In conclusion, the present study demonstrated that fetal cardiac defects may be associated with alterations in regional and single CpG site methylation outside of promoter regions, resulting in differentiated expression of corresponding genes associated with heart development. These results present new insights into the epigenetic mechanisms underlying abnormal heart development.
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Affiliation(s)
- Jizi Zhou
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China
| | - Yu Xiong
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China
| | - Xinran Dong
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Huijun Wang
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Yanyan Qian
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Xiaotian Li
- Department of Prenatal Diagnosis and Fetal Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, P.R. China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China.,The Shanghai Key Laboratory of Birth Defects, Fudan University, Shanghai 200032, P.R. China
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7
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Wu Y, Jin X, Zhang Y, Zheng J, Yang R. Genetic and epigenetic mechanisms in the development of congenital heart diseases. WORLD JOURNAL OF PEDIATRIC SURGERY 2021; 4:e000196. [DOI: 10.1136/wjps-2020-000196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common of congenital cardiovascular malformations associated with birth defects, and it results in significant morbidity and mortality worldwide. The classification of CHD is still elusive owing to the complex pathogenesis of CHD. Advances in molecular medicine have revealed the genetic basis of some heart anomalies. Genes associated with CHD might be modulated by various epigenetic factors. Thus, the genetic and epigenetic factors are gradually accepted as important triggers in the pathogenesis of CHD. However, few literatures have comprehensively elaborated the genetic and epigenetic mechanisms of CHD. This review focuses on the etiology of CHD from genetics and epigenetics to discuss the role of these factors in the development of CHD. The interactions between genetic and epigenetic in the pathogenesis of CHD are also elaborated. Chromosome abnormalities and gene mutations in genetics, and DNA methylations, histone modifications and on-coding RNAs in epigenetics are summarized in detail. We hope the summative knowledge of these etiologies may be useful for improved diagnosis and further elucidation of CHD so that morbidity and mortality of children with CHD can be reduced in the near future.
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8
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Shao M, Lu L, Wang Q, Ma L, Tian X, Li C, Li C, Guo D, Wang Q, Wang W, Wang Y. The multi-faceted role of retinoid X receptor in cardiovascular diseases. Biomed Pharmacother 2021; 137:111264. [PMID: 33761589 DOI: 10.1016/j.biopha.2021.111264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 01/14/2023] Open
Abstract
Retinoid X receptors (RXRs) are members of ligand-dependent transcription factors whose effects on a diversity of cellular processes, including cellular proliferation, the immune response, and lipid and glucose metabolism. Knock out of RXRα causes a hypoplasia of the myocardium which is lethal during fetal life. In addition, the heart maintains a well-orchestrated balances in utilizing fatty acids (FAs) and other substrates to meet the high energy requirements. As the master transcriptional regulators of lipid metabolism, RXRs become particularly important for the energy needs of the heart. Accumulating evidence suggested that RXRs may exert direct beneficial effects in the heart both through heterodimerization with other nuclear receptors (NRs) and homodimerization, thus standing as suitable targets for treating in cardiovascular diseases. Although compounds that target RXRs are promising drugs, their use is limited by toxicity. A better understanding of the structural biology of RXRs in cardiovascular disease should enable the rational design of more selective nuclear receptor modulators to overcome these problems. Here, this review summarizes a brief overview of RXRs structure and versatility of RXR action in the control of cardiovascular diseases. And we also discussed the therapeutic potential of RXR ligand.
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Affiliation(s)
- Mingyan Shao
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Linghui Lu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Lin Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xue Tian
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Changxiang Li
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chun Li
- Modern Research Center of Traditional Chinese Medicine, School of Traditional Chinese Material Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Dongqing Guo
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qiyan Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Wei Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Yong Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing, 100029, China; College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Ma J, Chen S, Hao L, Sheng W, Chen W, Ma X, Zhang B, Ma D, Huang G. Hypermethylation-mediated down-regulation of lncRNA TBX5-AS1:2 in Tetralogy of Fallot inhibits cell proliferation by reducing TBX5 expression. J Cell Mol Med 2020; 24:6472-6484. [PMID: 32368852 PMCID: PMC7294119 DOI: 10.1111/jcmm.15298] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/06/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common complex congenital heart disease (CHD) with uncertain cause. Although long non‐coding RNAs (lncRNAs) have been implicated in heart development and several CHDs, their role in TOF is not well understood. This study aimed to investigate how dysregulated lncRNAs contribute to TOF. Using Gene Expression Omnibus data mining, bioinformatics analysis and clinical heart tissue sample detecting, we identified a novel antisense lncRNA TBX5‐AS1:2 with unknown function that was significantly down‐regulated in injured cardiac tissues from TOF patients. LncRNA TBX5‐AS1:2 was mainly located in the nucleus of the human embryonic kidney 293 (HEK293T) cells and formed an RNA‐RNA double‐stranded structure in the overlapping region with its sense mRNA T‐box transcription factor 5 (TBX5), which is an important regulator in heart development. Knock‐down of lncRNA TBX5‐AS1:2 via promoter hypermethylation reduced TBX5 expression at both the mRNA and protein levels by affecting its mRNA stability through RNA‐RNA interaction. Moreover, lncRNA TBX5‐AS1:2 knock‐down inhibited the proliferation of HEK293T cells. In conclusion, these results indicated that lncRNA TBX5‐AS1:2 may be involved in TOF by affecting cell proliferation by targeting TBX5.
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Affiliation(s)
- Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University, Shanghai, China.,Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shiyu Chen
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lili Hao
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai, China
| | - WeiCheng Chen
- Children's Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, China
| | - Bowen Zhang
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, China
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Using Network Pharmacology to Explore Potential Treatment Mechanism for Coronary Heart Disease Using Chuanxiong and Jiangxiang Essential Oils in Jingzhi Guanxin Prescriptions. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:7631365. [PMID: 31772600 PMCID: PMC6854988 DOI: 10.1155/2019/7631365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/30/2019] [Accepted: 09/14/2019] [Indexed: 01/06/2023]
Abstract
Background To predict the active components and potential targets of traditional Chinese medicine and to determine the mechanism behind the curative effect of traditional Chinese medicine, a multitargeted method was used. Jingzhi Guanxin prescriptions expressed a high efficacy for coronary heart disease (CHD) patients of which essential oils from Chuanxiong and Jiangxiang were confirmed to be the most important effective substance. However, the interaction between the active components and the targets for the treatment of CHD has not been clearly explained in previous studies. Materials and Methods Genes associated with the disease and the treatment strategy were searched from the electronic database and analyzed by Cytoscape (version 3.2.1). Protein-protein interaction network diagram of CHD with Jiangxiang and Chuanxiong essential oils was constructed by Cytoscape. Pathway functional enrichment analysis was executed by clusterProfiler package in R platform. Results 121 ingredients of Chuanxiong and Jiangxiang essential oils were analyzed, and 393 target genes of the compositions and 912 CHD-related genes were retrieved. 15 coexpression genes were selected, including UGT1A1, DPP4, RXRA, ADH1A, RXRG, UGT1A3, PPARA, TRPC3, CYP1A1, ABCC2, AHR, and ADRA2A. The crucial pathways of occurrence and treatment molecular mechanism of CHD were analyzed, including retinoic acid metabolic process, flavonoid metabolic process, response to xenobiotic stimulus, cellular response to xenobiotic stimulus, cellular response to steroid hormone stimulus, retinoid binding, retinoic acid binding, and monocarboxylic acid binding. Finally, we elucidate the underlying role and mechanism behind these genes in the pathogenesis and treatment of CHD. Conclusions Generally speaking, the nodes in subnetwork affect the pathological process of CHD, thus indicating the mechanism of Jingzhi Guanxin prescriptions containing Chuanxiong and Jiangxiang essential oils in the treatment of CHD.
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11
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Gong J, Sheng W, Ma D, Huang G, Liu F. DNA methylation status of TBX20 in patients with tetralogy of Fallot. BMC Med Genomics 2019; 12:75. [PMID: 31138201 PMCID: PMC6540552 DOI: 10.1186/s12920-019-0534-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background TBX20 plays an important role in heart development; however, its epigenetic regulation in the pathogenesis of tetralogy of Fallot (TOF) remains unclear. Methods The methylation levels of the TBX20 promoter region in the right ventricular myocardial tissues of TOF and control samples were measured by the Sequenom MassARRAY platform. Bisulphite-sequencing PCR (BSP) was used to confirm the TBX20 methylation of CpG sites in cells. Dual-luciferase reporter assays were performed to detect the influence of TBX20 methylation and Sp1 transcription factors on gene activity. An electrophoretic mobility shift assay (EMSA) was used to explore the binding of the Sp1 transcription factor to the TBX20 promoter. Results TOF cases had a significantly lower TBX20_M1 methylation level than controls (median methylation: 20.40% vs. 38.73%; p = 0.0047). The Sp1 transcription factor, which binds to Sp1 binding sites in the TBX20_M1 region and promotes TBX20 gene activity, was blocked by the methylation of Sp1 binding sites in normal controls. With decreasing methylation in the TOF cases, the Sp1 transcription factor can bind to its binding site within the TBX20 promoter M1 region and promote TBX20 gene expression. Conclusions Hypomethylation of the TBX20 promoter region was observed in the TOF cases, and the high expression of the TBX20 gene may be caused by activated Sp1 transcription factor binding because of the decreasing methylation at the Sp1 transcription factor binding sites within TBX20_M1.
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Affiliation(s)
- Juan Gong
- Children Hospital of Fudan University, Shanghai, 201102, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, 201102, China
| | - Wei Sheng
- Children Hospital of Fudan University, Shanghai, 201102, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, 201102, China
| | - Duan Ma
- Shanghai Key Laboratory of Birth Defects, Shanghai, 201102, China
| | - Guoying Huang
- Children Hospital of Fudan University, Shanghai, 201102, China. .,Shanghai Key Laboratory of Birth Defects, Shanghai, 201102, China.
| | - Fang Liu
- Children Hospital of Fudan University, Shanghai, 201102, China. .,Shanghai Key Laboratory of Birth Defects, Shanghai, 201102, China.
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12
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Yang X, Kong Q, Li Z, Xu M, Cai Z, Zhao C. Association between the promoter methylation of the TBX20 gene and tetralogy of fallot. SCAND CARDIOVASC J 2018; 52:287-291. [PMID: 30084275 DOI: 10.1080/14017431.2018.1499955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To investigate the association between promoter methylation of the TBX20 gene and tetralogy of Fallot (TOF). Methods. The methylation level of TBX20 promoter regions in 23 patients with TOF and five controls were analyzed through bisulfite sequencing polymerase chain reaction. Meanwhile, the expression of TBX20 mRNA was measured using real time fluorescence quantitative polymerase chain reaction. RESULTS The region -400 to -48 in the TBX20 promoter consisting of 42 CpG sites was predicted to contain multiple transcription factor binding sites. In this study, the overall methylation level in this region was lower in patients with TOF than in the controls (P = .035). Among the 42 CpG sites, the methylation percentages of the CpG 26 site in the TOF cases were lower than those in the controls (P = .016). The mRNA expression of TBX20 in the right ventricular outflow tract myocardium was increased in TOF cases in contrast to those in the controls (P < .001). The methylation levels in TOF cases were correlated with mRNA expression values (r = -0.81, P < .001). CONCLUSION The downregulated methylation level at TBX20 promoter may be responsible for the elevated mRNA expression levels in patients with TOF. The abnormal methylation status of the TBX20 promoter may contribute to the pathogenesis of TOF.
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Affiliation(s)
- Xiaofei Yang
- a Department of Pediatrics , Qilu Hospital of Shandong University , Jinan , China.,b Department of Pediatrics , Yidu central hospital of Weifang , Weifang , China
| | - Qingyu Kong
- a Department of Pediatrics , Qilu Hospital of Shandong University , Jinan , China
| | - Zhenghao Li
- b Department of Pediatrics , Yidu central hospital of Weifang , Weifang , China
| | - Min Xu
- c Department of Pediatrics , The People's Hospital of Yucheng City , Dezhou , China
| | - Zhifeng Cai
- a Department of Pediatrics , Qilu Hospital of Shandong University , Jinan , China
| | - Cuifen Zhao
- a Department of Pediatrics , Qilu Hospital of Shandong University , Jinan , China
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13
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DNA Methylation Variability in a Single Locus of the RXRα Promoter from Umbilical Vein Blood at Term Pregnancy. Biochem Genet 2018; 56:210-224. [PMID: 29305749 DOI: 10.1007/s10528-017-9838-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/29/2017] [Indexed: 12/26/2022]
Abstract
DNA methylation status of RXRα gene promoter has been correlated with maternal diet during early pregnancy, and associated with offspring's adiposity and bone mineral content. In adult life, increased methylation of RXRα promoter region is associated with myocardium pathologies. Early growth response proteins (EGR) are zinc finger transcription factors associated with several cellular pathways such as inflammation, apoptosis, and cardiopathies. DNA-binding sequences of EGR proteins have been reported in the RXRα gene promoter using chromatin immunoprecipitation methods. Here, we used correlations between the maternal pre-pregnancy body mass index (p-BMI), gestational weight gain (GWG), and birth weight (BW) as indirect indicators of the maternal nutritional status as modifier of DNA methylation in the offspring. DNA methylation status from newborns' umbilical vein blood in full-term pregnancy was evaluated in a short sequence (116 pb) of the RXRα gene promoter that contains the elements of response sequence for EGR proteins. Fifty-three bisulfite-modified DNA samples were assessed through methyl-sensitive high-resolution melting (MS-HRM) analysis. To validate the results, we directly sequenced MS-HRM samples to confirm the presence of CpG-methylated positions. In addition, the RXRα protein levels in extracts of umbilical vein blood were evaluated by western blot. We found differential methylation in a specific locus of the RXRα promoter surrounding the EGR-binding sequence; however, no correlation was found with the level of RXRα protein expression. Variability in the methylation status of the RXRα promoter near the EGR transcription factor binding site in newborn cord blood provides controversial epigenetic insights into RXRα regulation via EGR proteins.
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14
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Yue H, Yan W, Ji X, Gao R, Ma J, Rao Z, Li G, Sang N. Maternal Exposure of BALB/c Mice to Indoor NO2 and Allergic Asthma Syndrome in Offspring at Adulthood with Evaluation of DNA Methylation Associated Th2 Polarization. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:097011. [PMID: 28935613 PMCID: PMC5903874 DOI: 10.1289/ehp685] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 06/07/2017] [Accepted: 06/19/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fetal stress has been proposed to be associated with diseases in both children and adults. Epidemiological studies suggest that maternal exposure to nitrogen dioxide (NO2) contributes to increased morbidity and mortality of offspring with allergic asthma later in life. OBJECTIVES We aimed to test whether maternal NO2 exposure causes allergic asthma-related consequences in offspring absent any subsequent lung provocation and whether this exposure enhances the likelihood of developing allergic asthma or the intensity of developed allergic airway disease following postnatal allergic sensitization and challenge. In addition, if such consequences and enhancements occurred, we sought to determine the mechanism(s) of these responses. METHODS Pregnant BALB/c mice were exposed to either NO2 (2.5 ppm, 5 h/day) or air daily throughout the gestation period. Offspring were sacrificed on postnatal days (PNDs) 1, 7, 14, 21, and 42, and remaining offspring were sensitized by ovalbumin (OVA) injection followed by OVA aerosol challenge during postnatal wk 7-9. We analyzed the lung histopathology, inflammatory cell infiltration, airway hyper-responsiveness (AHR), immune responses, and gene methylation under different treatment conditions. RESULTS Maternal exposure to NO2 caused a striking increase in inflammatory cell infiltration and the release of type 2 cytokines in the lungs of offspring at PNDs 1 and 7; however, these alterations were reversed during postnatal development. Following OVA sensitization and challenge, the exposure enhanced the levels of allergic asthma-characterized OVA-immunoglobulin (Ig) E, AHR, and airway inflammation in adult offspring. Importantly, differentiation of T-helper (Th) 2 cells and demethylation of the interleukin-4 (IL4) gene occurred during the process. CONCLUSIONS Maternal exposure to indoor environmental NO2 causes allergic asthma-related consequences in offspring absent any subsequent lung provocation and potentiates the symptoms of allergic asthma in adult offspring following postnatal allergic sensitization and challenge; this response is associated with the Th2-based immune response and DNA methylation of the IL4 gene. https://doi.org/10.1289/EHP685.
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Affiliation(s)
- Huifeng Yue
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
| | - Wei Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
| | - Xiaotong Ji
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
| | - Rui Gao
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
| | - Juan Ma
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, People's Republic of China
| | - Ziyu Rao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, People's Republic of China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University , Taiyuan, Shanxi, People's Republic of China
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15
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Gu R, Xu J, Lin Y, Zhang J, Wang H, Sheng W, Ma D, Ma X, Huang G. Liganded retinoic acid X receptor α represses connexin 43 through a potential retinoic acid response element in the promoter region. Pediatr Res 2016; 80:159-68. [PMID: 26991262 DOI: 10.1038/pr.2016.47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022]
Abstract
INTRODUCTION Retinoic acid X receptor alpha (RXRα) and Connexin 43 (Cx43) both play a crucial role in cardiogenesis. However, little is known about the interplay mechanism between the RXRα and Cx43. METHODS The activations of retinoic acid response element (RARE) in Cx43 were measured by luciferase transfection assay. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) was performed to prove that RXRα can directly bind to the RARE sequence. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting were used to analyze the RXRα and Cx43 mRNA level and protein level in cells. RESULTS In this study, we confirmed the negative association of the gene expression between the RXRα and Cx43 in the cell level. Interestingly, a functional RARE was detected in the region from -1,426 to -314 base pairs upstream from the transcriptional start site of Cx43. Moreover, we also prove that RXRα can directly bind to this RARE sequence in vitro and in vivo. CONCLUSIONS RXRα negatively regulates the transcription and expression by directly binding to the RARE in the promoter of Cx43. The RARE-like sequence harbored in the Cx43 promoter region may serve as a functional RARE in the retinoic acid (RA) signaling pathway.
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Affiliation(s)
- Ruoyi Gu
- Children's Hospital of Fudan University, Shanghai, China
| | - Jun Xu
- Children's Hospital of Fudan University, Shanghai, China
| | - Yixiang Lin
- Children's Hospital of Fudan University, Shanghai, China
| | - Jing Zhang
- Children's Hospital of Fudan University, Shanghai, China.,Present address: Department of Pediatrics, Chengdu Women and Children's Medical Center, Sichuan, China
| | - Huijun Wang
- Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Duan Ma
- Shanghai Key Laboratory of Birth Defects, Shanghai, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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16
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Zhu C, Fan H, Yuan Z, Hu S, Ma X, Xuan J, Wang H, Zhang L, Wei C, Zhang Q, Zhao F, Du L. Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays. Sci Rep 2016; 6:27822. [PMID: 27282145 PMCID: PMC4901276 DOI: 10.1038/srep27822] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/24/2016] [Indexed: 01/08/2023] Open
Abstract
Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the genetic mechanisms underlying the phenotypic differences among Chinese indigenous sheep with tails of three different types, we used ovine high-density 600K SNP arrays to detect genome-wide copy number variation (CNV). In large-tailed Han sheep, Altay sheep, and Tibetan sheep, 371, 301, and 66 CNV regions (CNVRs) with lengths of 71.35 Mb, 51.65 Mb, and 10.56 Mb, respectively, were identified on autosomal chromosomes. Ten CNVRs were randomly chosen for confirmation, of which eight were successfully validated. The detected CNVRs harboured 3130 genes, including genes associated with fat deposition, such as PPARA, RXRA, KLF11, ADD1, FASN, PPP1CA, PDGFA, and PEX6. Moreover, multilevel bioinformatics analyses of the detected candidate genes were significantly enriched for involvement in fat deposition, GTPase regulator, and peptide receptor activities. This is the first high-resolution sheep CNV map for Chinese indigenous sheep breeds with three types of tails. Our results provide valuable information that will support investigations of genomic structural variation underlying traits of interest in sheep.
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Affiliation(s)
- Caiye Zhu
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongying Fan
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zehu Yuan
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shijin Hu
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaomeng Ma
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junli Xuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hongwei Wang
- Beijing Compass Biotechnology Co., Ltd., Beijing 100192, China
| | - Li Zhang
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Caihong Wei
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qin Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fuping Zhao
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixin Du
- National Center for Molecular Genetics and Breeding of Animals, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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17
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Amarillo IE, O'Connor S, Lee CK, Willing M, Wambach JA. De novo 9q gain in an infant with tetralogy of Fallot with absent pulmonary valve: Patient report and review of congenital heart disease in 9q duplication syndrome. Am J Med Genet A 2015; 167A:2966-74. [PMID: 26768185 DOI: 10.1002/ajmg.a.37296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 08/05/2015] [Indexed: 12/14/2022]
Abstract
Genomic disruptions, altered epigenetic mechanisms, and environmental factors contribute to the heterogeneity of congenital heart defects (CHD). In recent years, chromosomal microarray analysis (CMA) has led to the identification of numerous copy number variations (CNV) in patients with CHD. Genes disrupted by and within these CNVs thus represent excellent candidate genes for CHD. Microduplications of 9q (9q+) have been described in patients with CHD, however, the critical gene locus remains undetermined. Here we discuss an infant with tetralogy of Fallot with absent pulmonary valve, fetal hydrops, and a 3.76 Mb de novo contiguous gain of 9q34.2-q34.3 detected by CMA, and confirmed by karyotype and FISH studies. This duplicated interval disrupted RXRA (retinoid X receptor alpha; OMIM #180245) at intron 1. We also review CHD findings among previously reported patients with 9q (9q+) duplication syndrome. This is the first report implicating RXRA in CHD with 9q duplication, providing additional data in understanding the genetic etiology of tetralogy of Fallot, CHD, and disorders linked to 9q microduplication syndrome. This report also highlights the significance of CMA in the clinical diagnosis and genetic counseling of patients and families with complex CHD.
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Affiliation(s)
- Ina E Amarillo
- Department of Pathology and Immunology, Cytogenomics Laboratory, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Shawn O'Connor
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Caroline K Lee
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marcia Willing
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Jennifer A Wambach
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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18
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Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev 2015; 7:141-159. [PMID: 28509974 DOI: 10.1007/s12551-014-0145-3] [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: 09/09/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.
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