1
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Voskamp SM, Hammonds MA, Knapp TM, Pekmezian AL, Hadley D, Nelson JS. Meta-analysis reveals differential gene expression in tetralogy of Fallot versus controls. Birth Defects Res 2024; 116:e2293. [PMID: 38146097 DOI: 10.1002/bdr2.2293] [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: 09/27/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023]
Abstract
OBJECTIVES Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect in the United States. We aimed to identify genetic variations associated with TOF using meta-analysis of publicly available digital samples to spotlight targets for prevention, screening, and treatment strategies. METHODS We used the Search Tag Analyze Resource for Gene Expression Omnibus (STARGEO) platform to identify 39 TOF and 19 non-TOF right ventricle tissue samples from microarray data and identified upregulated and downregulated genes. Associated gene expression data were analyzed using ingenuity pathway analysis and restricted to genes with a statistically significant (p < .05) difference and an absolute experimental log ratio >0.1 between disease and control samples. RESULTS Our analysis identified 220 genes whose expression profiles were significantly altered in TOF vs. non-TOF samples. The most striking differences identified in gene expression included genes FBXO32, PTGES, MYL12a, and NR2F2. Some top associated canonical pathways included adrenergic signaling, estrogen receptor signaling, and the role of NFAT in cardiac hypertrophy. In general, genes involved in adaptive, defensive, and reparative cardiovascular responses showed altered expression in TOF vs. non-TOF samples. CONCLUSIONS We introduced the interpretation of open "big data" using the STARGEO platform to define robust genomic signatures of congenital heart disease pathology of TOF. Overall, our meta-analysis results indicated increased metabolism, inflammation, and altered gene expression in TOF patients. Estrogen receptor signaling and the role of NFAT in cardiac hypertrophy represent unique pathways upregulated in TOF patients and are potential targets for future pharmacologic treatments.
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Affiliation(s)
- Sarah Mae Voskamp
- University of Central Florida College of Medicine, Orlando, Florida, USA
| | | | - Thomas M Knapp
- University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Ashley L Pekmezian
- University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Dexter Hadley
- University of Central Florida College of Medicine, Orlando, Florida, USA
- Department of Clinical Sciences, University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Jennifer S Nelson
- University of Central Florida College of Medicine, Orlando, Florida, USA
- Department of Cardiovascular Services, Nemours Children's Health, Orlando, Florida, USA
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2
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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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3
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Epigenetic Evaluation of the TBX20 Gene and Environmental Risk Factors in Mexican Paediatric Patients with Congenital Septal Defects. Cells 2023; 12:cells12040586. [PMID: 36831251 PMCID: PMC9953838 DOI: 10.3390/cells12040586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The TBX20 gene has a key role during cardiogenesis, and it has been related to epigenetic mechanisms in congenital heart disease (CHD). The purpose of this study was to assess the association between DNA methylation status and congenital septal defects. The DNA methylation of seven CpG sites in the TBX20 gene promoter was analyzed through pyrosequencing as a quantitative method in 48 patients with congenital septal defects and 104 individuals with patent ductus arteriosus (PDA). The average methylation was higher in patients than in PDA (p < 0.001). High methylation levels were associated with a higher risk of congenital septal defects (OR = 4.59, 95% CI = 1.57-13.44, p = 0.005). The ROC curve analysis indicated that methylation of the TBX20 gene could be considered a risk marker for congenital septal defects (AUC = 0.682; 95% CI = 0.58-0.77; p < 0.001). The analysis of environmental risk factors in patients with septal defects and PDA showed an association between the consumption of vitamins (OR = 0.10; 95% CI = 0.01-0.98; p = 0.048) and maternal infections (OR = 3.10; 95% CI = 1.26-7.60; p = 0.013). These results suggest that differences in DNA methylation of the TBX20 gene can be associated with septal defects.
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4
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Comparison of
DNA
methylation patterns across tissue types in infants with tetralogy of Fallot. Birth Defects Res 2022; 114:1101-1111. [DOI: 10.1002/bdr2.2090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 11/07/2022]
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5
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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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6
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Accelerated Growth, Differentiation, and Ploidy with Reduced Proliferation of Right Ventricular Cardiomyocytes in Children with Congenital Heart Defect Tetralogy of Fallot. Cells 2022; 11:cells11010175. [PMID: 35011735 PMCID: PMC8750260 DOI: 10.3390/cells11010175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 02/06/2023] Open
Abstract
The myocardium of children with tetralogy of Fallot (TF) undergoes hemodynamic overload and hypoxemia immediately after birth. Comparative analysis of changes in the ploidy and morphology of the right ventricular cardiomyocytes in children with TF in the first years of life demonstrated their significant increase compared with the control group. In children with TF, there was a predominantly diffuse distribution of Connexin43-containing gap junctions over the cardiomyocytes sarcolemma, which redistributed into the intercalated discs as cardiomyocytes differentiation increased. The number of Ki67-positive cardiomyocytes varied greatly and amounted to 7.0–1025.5/106 cardiomyocytes and also were decreased with increased myocytes differentiation. Ultrastructural signs of immaturity and proliferative activity of cardiomyocytes in children with TF were demonstrated. The proportion of interstitial tissue did not differ significantly from the control group. The myocardium of children with TF under six months of age was most sensitive to hypoxemia, it was manifested by a delay in the intercalated discs and myofibril assembly and the appearance of ultrastructural signs of dystrophic changes in the cardiomyocytes. Thus, the acceleration of ontogenetic growth and differentiation of the cardiomyocytes, but not the reactivation of their proliferation, was an adaptation of the immature myocardium of children with TF to hemodynamic overload and hypoxemia.
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7
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González-Peña SM, Calvo-Anguiano G, Martínez-de-Villarreal LE, Ancer-Rodríguez PR, Lugo-Trampe JJ, Saldivar-Rodríguez D, Hernández-Almaguer MD, Calzada-Dávila M, Guerrero-Orjuela LS, Campos-Acevedo LD. Maternal Folic Acid Intake and Methylation Status of Genes Associated with Ventricular Septal Defects in Children: Case-Control Study. Nutrients 2021; 13:nu13062071. [PMID: 34204335 PMCID: PMC8234530 DOI: 10.3390/nu13062071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Background: DNA methylation is the best epigenetic mechanism for explaining the interactions between nutrients and genes involved in intrauterine growth and development programming. A possible contributor of methylation abnormalities to congenital heart disease is the folate methylation regulatory pathway; however, the mechanisms and methylation patterns of VSD-associated genes are not fully understood. Objective: To determine if maternal dietary intake of folic acid (FA) is related to the methylation status (MS) of VSD-associated genes (AXIN1, MTHFR, TBX1, and TBX20). Methods: Prospective case–control study; 48 mothers and their children were evaluated. The mothers’ dietary variables were collected through a food frequency questionnaire focusing on FA and the consumption of supplements with FA. The MS of promoters of genes was determined in the children. Results: The intake of FA supplements was significantly higher in the control mothers. In terms of maternal folic acid consumption, significant differences were found in the first trimester of pregnancy. Significant differences were observed in the MS of MTHFR and AXIN1 genes in VSD and control children. A correlation between maternal FA supplementation and MS of AXIN1 and TBX20 genes was found in control and VSD children, respectively. Conclusions: A lower MS of AXIN1 genes and a higher MS of TBX20 genes is associated with FA maternal supplementation.
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Affiliation(s)
- Sandra M. González-Peña
- Clinical Nutrition, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (S.M.G.-P.); (P.R.A.-R.)
- International Iberoamerican University of México, Campeche 24560, Mexico
| | - Geovana Calvo-Anguiano
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
| | - Laura E. Martínez-de-Villarreal
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
| | - Patricia R. Ancer-Rodríguez
- Clinical Nutrition, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (S.M.G.-P.); (P.R.A.-R.)
| | - José J. Lugo-Trampe
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
| | - Donato Saldivar-Rodríguez
- Gynecology and Obstetrics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico;
| | - María D. Hernández-Almaguer
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
- Medicine Faculty, Autonomous University of Baja California, Mexicali 21000, Mexico
| | - Melissa Calzada-Dávila
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
| | | | - Luis D. Campos-Acevedo
- Genetics Department, Hospital Universitario “Dr. José Eleuterio González” and Medicine Faculty, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (G.C.-A.); (L.E.M.-d.-V.); (J.J.L.-T.); (M.D.H.-A.); (M.C.-D.)
- Correspondence: ; Tel.: +52-01-81-8348-3704
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8
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Wang J, Ma X, Zhang Q, Chen Y, Wu D, Zhao P, Yu Y. The Interaction Analysis of SNP Variants and DNA Methylation Identifies Novel Methylated Pathogenesis Genes in Congenital Heart Diseases. Front Cell Dev Biol 2021; 9:665514. [PMID: 34041244 PMCID: PMC8143053 DOI: 10.3389/fcell.2021.665514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defect (CHD) is a rare and complicated disease with a high mortality rate. Its etiology remains unclear and includes many aspects. DNA methylation has been indicated to be involved in heart development in the early stage of life, and aberrant methylation level was related to CHDs. This study provides the first evidence of the cross talk of SNP variants and DNA methylation in clarifying CHD underlying genomic cause. We gathered whole exome sequencing (WES) data for Group 1 consisting of patients with PA (n = 78), TOF (n = 20), TAPVC (n = 78), and PDA (n = 40), and 100 healthy children as control group. Rare non-synonymous mutations and novel genes were found and highlighted. Meanwhile, we carried out the second analysis of DNA methylation data from patients with PA (n = 3), TAPVC (n = 3), TOF (n = 3), and PDA (n = 2), and five healthy controls using 850 K array in Group 2. DNA methylation was linked to WES data, and we explored an obvious overlap of hyper/hypomethylated genes. Next, we identified some candidate genes by Fisher’s exact test and Burden analysis; then, those methylated genes were figured out by the criteria of the mutation located in the CpG islands of the genome, differential methylation sites (DMS), and DNA methylation quantitative trait loci (meQTLs) in the database, respectively. Also, the interaction of differentially methylated candidate genes with known CHD pathogenetic genes was depicted in a molecular network. Taken together, our findings show that nine novel genes (ANGPTL4, VEGFA, PAX3, MUC4, HLA-DRB1, TJP2, BCR, PKD1, and HK2) in methylation level are critical to CHD and reveal a new insight into the molecular pathogenesis of CHD.
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Affiliation(s)
- Jing Wang
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China.,Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqin Ma
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Qi Zhang
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinghui Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Wu
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Pengjun Zhao
- Department of Pediatric Cardiology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Yu
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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9
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Rufaihah AJ, Chen CK, Yap CH, Mattar CNZ. Mending a broken heart: In vitro, in vivo and in silico models of congenital heart disease. Dis Model Mech 2021; 14:dmm047522. [PMID: 33787508 PMCID: PMC8033415 DOI: 10.1242/dmm.047522] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Birth defects contribute to ∼0.3% of global infant mortality in the first month of life, and congenital heart disease (CHD) is the most common birth defect among newborns worldwide. Despite the significant impact on human health, most treatments available for this heterogenous group of disorders are palliative at best. For this reason, the complex process of cardiogenesis, governed by multiple interlinked and dose-dependent pathways, is well investigated. Tissue, animal and, more recently, computerized models of the developing heart have facilitated important discoveries that are helping us to understand the genetic, epigenetic and mechanobiological contributors to CHD aetiology. In this Review, we discuss the strengths and limitations of different models of normal and abnormal cardiogenesis, ranging from single-cell systems and 3D cardiac organoids, to small and large animals and organ-level computational models. These investigative tools have revealed a diversity of pathogenic mechanisms that contribute to CHD, including genetic pathways, epigenetic regulators and shear wall stresses, paving the way for new strategies for screening and non-surgical treatment of CHD. As we discuss in this Review, one of the most-valuable advances in recent years has been the creation of highly personalized platforms with which to study individual diseases in clinically relevant settings.
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Affiliation(s)
- Abdul Jalil Rufaihah
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228
| | - Ching Kit Chen
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228
| | - Choon Hwai Yap
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat -National University Children's Medical Institute, National University Health System, Singapore 119228
- Department of Bioengineering, Imperial College London, London, UK
| | - Citra N Z Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
- Department of Obstetrics and Gynaecology, National University Health System, Singapore 119228
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10
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Lim TB, Foo SYR, Chen CK. The Role of Epigenetics in Congenital Heart Disease. Genes (Basel) 2021; 12:genes12030390. [PMID: 33803261 PMCID: PMC7998561 DOI: 10.3390/genes12030390] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Congenital heart disease (CHD) is the most common birth defect among newborns worldwide and contributes to significant infant morbidity and mortality. Owing to major advances in medical and surgical management, as well as improved prenatal diagnosis, the outcomes for these children with CHD have improved tremendously so much so that there are now more adults living with CHD than children. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. For this reason, the complex process of cardiogenesis, which is governed by multiple interlinked and dose-dependent pathways, is a well investigated process. In addition to the sequence of the genome, the contribution of epigenetics to cardiogenesis is increasingly recognized. Significant progress has been made dissecting the epigenome of the heart and identified associations with cardiovascular diseases. The role of epigenetic regulation in cardiac development/cardiogenesis, using tissue and animal models, has been well reviewed. Here, we curate the current literature based on studies in humans, which have revealed associated and/or causative epigenetic factors implicated in CHD. We sought to summarize the current knowledge on the functional role of epigenetics in cardiogenesis as well as in distinct CHDs, with an aim to provide scientists and clinicians an overview of the abnormal cardiogenic pathways affected by epigenetic mechanisms, for a better understanding of their impact on the developing fetal heart, particularly for readers interested in CHD research.
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Affiliation(s)
- Tingsen Benson Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Sik Yin Roger Foo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children’s Medical Institute, National University Health System, Singapore 119228, Singapore
- Correspondence:
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11
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Cui T, Huang J, Sun Y, Ning B, Mu F, You X, Guo Y, Li H, Wang N. KLF2 Inhibits Chicken Preadipocyte Differentiation at Least in Part via Directly Repressing PPARγ Transcript Variant 1 Expression. Front Cell Dev Biol 2021; 9:627102. [PMID: 33634127 PMCID: PMC7901985 DOI: 10.3389/fcell.2021.627102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is the master regulatory factor of preadipocyte differentiation. As a result of alternative splicing and alternative promoter usage, PPARγ gene generates multiple transcript variants encoding two protein isoforms. Krüppel-like factor 2 (KLF2) plays a negative role in preadipocyte differentiation. However, its underlying mechanism remains incompletely understood. Here, we demonstrated that KLF2 inhibited the P1 promoter activity of the chicken PPARγ gene. Bioinformatics analysis showed that the P1 promoter harbored a conserved putative KLF2 binding site, and mutation analysis showed that the KLF2 binding site was required for the KLF2-mediated transcription inhibition of the P1 promoter. ChIP, EMSA, and reporter gene assays showed that KLF2 could directly bind to the P1 promoter regardless of methylation status and reduced the P1 promoter activity. Consistently, histone modification analysis showed that H3K9me2 was enriched and H3K27ac was depleted in the P1 promoter upon KLF2 overexpression in ICP1 cells. Furthermore, gene expression analysis showed that KLF2 overexpression reduced the endogenous expression of PPARγ transcript variant 1 (PPARγ1), which is driven by the P1 promoter, in DF1 and ICP1 cells, and that the inhibition of ICP1 cell differentiation by KLF2 overexpression was accompanied by the downregulation of PPARγ1 expression. Taken together, our results demonstrated that KLF2 inhibits chicken preadipocyte differentiation at least inpart via direct downregulation of PPARγ1 expression.
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Affiliation(s)
- Tingting Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Jiaxin Huang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yingning Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Bolin Ning
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Fang Mu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Xin You
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Yaqi Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Hui Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
| | - Ning Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China
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12
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Zhu Y, Ye M, Xu H, Gu R, Ma X, Chen M, Li X, Sheng W, Huang G. Methylation status of CpG sites in the NOTCH4 promoter region regulates NOTCH4 expression in patients with tetralogy of Fallot. Mol Med Rep 2020; 22:4412-4422. [PMID: 33000281 PMCID: PMC7533461 DOI: 10.3892/mmr.2020.11535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease (CHD). Although a lower methylation level of whole genome has been demonstrated in TOF patients, little is known regarding the DNA methylation changes in specific gene and its associations with TOF development. NOTCH4 is a mediator of the Notch signalling pathway that plays an important role in normal cardiac development. However, the role of epigenetic regulation of the NOTCH4 gene in the pathogenesis of TOF remains unclear. Considering the NOTCH4 low mutation frequency and reduced expression in the TOF patients, we hypothesized that abnormal DNA methylation change of NOTCH4 gene may influence its expression and responsible for TOF development. In this study, we measured the promoter methylation status of NOTCH4 and was measured and its regulation mechanism was explored, which may be related to TOF disease. Additionally, the promoter methylation statuses of NOTCH4 was measured in order to further understand epigenetic mechanisms that may serve a role in the development of TOF. Immunohistochemical analysis was used to examine NOTCH4 expression in right ventricular outflow tract myocardial tissues in patients with TOF. Compared with healthy controls, patients with TOF displayed significantly reduced in NOTCH4 expression (P=0.0055). Moreover, bisulphite sequencing suggested that the methylation levels of CpG site 2 in the NOTCH4 promoter was significantly higher in the patients than in the controls (P=0.0459). NOTCH4 expression was negatively associated with CpG site 2 methylation levels (r=−0.51; P=0.01). ETS1 transcription factor can serve as transcriptional activators by binding to specific DNA sequences of target genes, such as DLL4 and NOTCH4, which serves an important role in normal heart development. Dual-luciferase reporter and electrophoretic mobility shift assays indicated that the ETS1 transcription factor could bind to the NOTCH4 promoter region. However, binding of ETS1 to the NOTCH4 promoter was abrogated by methylation at the putative ETS1 binding sites. These findings suggested that decreased NOTCH4 expression in patients with TOF may be associated with hypermethylation of CpG site 2 in the NOTCH4 promoter region, due to impaired binding of ETS1.
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Affiliation(s)
- Yanjie Zhu
- Institute of Paediatrics, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Ming Ye
- Cardiovascular Centre, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Hongfei Xu
- Department of Forensic Medicine, Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Ruoyi Gu
- Cardiovascular Centre, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Xiaojing Ma
- Cardiovascular Centre, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Mingwu Chen
- Division of Life Sciences and Medicine, The First Affiliated Hospital of The University of Science and Technology of China, Hefei, Anhui 230036, P.R. China
| | - Xiaodi Li
- Institute of Paediatrics, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Wei Sheng
- Institute of Paediatrics, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
| | - Guoying Huang
- Institute of Paediatrics, Children's Hospital of Fudan University, Shanghai 201102, P.R. China
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