1
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Munguia-Galaviz FJ, Gutierrez-Mercado YK, Miranda-Diaz AG, Portilla de Buen E, Flores-Soto ME, Echavarria R. Cardiac transcriptomic changes induced by early CKD in mice reveal novel pathways involved in the pathogenesis of Cardiorenal syndrome type 4. Heliyon 2024; 10:e27468. [PMID: 38509984 PMCID: PMC10950824 DOI: 10.1016/j.heliyon.2024.e27468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Background Cardiorenal syndrome (CRS) type 4 is prevalent among the chronic kidney disease (CKD) population, with many patients dying from cardiovascular complications. However, limited data regarding cardiac transcriptional changes induced early by CKD is available. Methods We used a murine unilateral ureteral obstruction (UUO) model to evaluate renal damage, cardiac remodeling, and transcriptional regulation at 21 days post-surgery through histological analysis, RT-qPCR, RNA-seq, and bioinformatics. Results UUO leads to significant kidney injury, low uremia, and pathological cardiac remodeling, evidenced by increased collagen deposition and smooth muscle alpha-actin 2 expression. RNA-seq analysis identified 76 differentially expressed genes (DEGs) in UUO hearts. Upregulated DEGs were significantly enriched in cell cycle and cell division pathways, immune responses, cardiac repair, inflammation, proliferation, oxidative stress, and apoptosis. Gene Set Enrichment Analysis further revealed mitochondrial oxidative bioenergetic pathways, autophagy, and peroxisomal pathways are downregulated in UUO hearts. Vimentin was also identified as an UUO-upregulated transcript. Conclusions Our results emphasize the relevance of extensive transcriptional changes, mitochondrial dysfunction, homeostasis deregulation, fatty-acid metabolism alterations, and vimentin upregulation in CRS type 4 development.
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Affiliation(s)
- Francisco Javier Munguia-Galaviz
- Departamento de Fisiologia, CUCS, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Division de Ciencias de la Salud, CUSUR, Universidad de Guadalajara, Ciudad Guzman 49000, Jalisco, Mexico
| | | | | | - Eliseo Portilla de Buen
- Division de Investigacion Quirurgica, Centro de Investigacion Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico
| | - Mario Eduardo Flores-Soto
- Division de Neurociencias, Centro de Investigacion Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Jalisco, Mexico
| | - Raquel Echavarria
- CONAHCYT-Centro de Investigacion Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Jalisco, Mexico
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2
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Bridges J, Ramirez-Guerrero JA, Rosa-Garrido M. Gender-specific genetic and epigenetic signatures in cardiovascular disease. Front Cardiovasc Med 2024; 11:1355980. [PMID: 38529333 PMCID: PMC10962446 DOI: 10.3389/fcvm.2024.1355980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Cardiac sex differences represent a pertinent focus in pursuit of the long-awaited goal of personalized medicine. Despite evident disparities in the onset and progression of cardiac pathology between sexes, historical oversight has led to the neglect of gender-specific considerations in the treatment of patients. This oversight is attributed to a predominant focus on male samples and a lack of sex-based segregation in patient studies. Recognizing these sex differences is not only relevant to the treatment of cisgender individuals; it also holds paramount importance in addressing the healthcare needs of transgender patients, a demographic that is increasingly prominent in contemporary society. In response to these challenges, various agencies, including the National Institutes of Health, have actively directed their efforts toward advancing our comprehension of this phenomenon. Epigenetics has proven to play a crucial role in understanding sex differences in both healthy and disease states within the heart. This review presents a comprehensive overview of the physiological distinctions between males and females during the development of various cardiac pathologies, specifically focusing on unraveling the genetic and epigenetic mechanisms at play. Current findings related to distinct sex-chromosome compositions, the emergence of gender-biased genetic variations, and variations in hormonal profiles between sexes are highlighted. Additionally, the roles of DNA methylation, histone marks, and chromatin structure in mediating pathological sex differences are explored. To inspire further investigation into this crucial subject, we have conducted global analyses of various epigenetic features, leveraging data previously generated by the ENCODE project.
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Affiliation(s)
| | | | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
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3
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Baker MR, Lee AS, Rajadhyaksha AM. L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. Channels (Austin) 2023; 17:2176984. [PMID: 36803254 PMCID: PMC9980663 DOI: 10.1080/19336950.2023.2176984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/01/2023] [Indexed: 02/21/2023] Open
Abstract
Recent human genetic studies have linked a variety of genetic variants in the CACNA1C and CACNA1D genes to neuropsychiatric and neurodevelopmental disorders. This is not surprising given the work from multiple laboratories using cell and animal models that have established that Cav1.2 and Cav1.3 L-type calcium channels (LTCCs), encoded by CACNA1C and CACNA1D, respectively, play a key role in various neuronal processes that are essential for normal brain development, connectivity, and experience-dependent plasticity. Of the multiple genetic aberrations reported, genome-wide association studies (GWASs) have identified multiple single nucleotide polymorphisms (SNPs) in CACNA1C and CACNA1D that are present within introns, in accordance with the growing body of literature establishing that large numbers of SNPs associated with complex diseases, including neuropsychiatric disorders, are present within non-coding regions. How these intronic SNPs affect gene expression has remained a question. Here, we review recent studies that are beginning to shed light on how neuropsychiatric-linked non-coding genetic variants can impact gene expression via regulation at the genomic and chromatin levels. We additionally review recent studies that are uncovering how altered calcium signaling through LTCCs impact some of the neuronal developmental processes, such as neurogenesis, neuron migration, and neuron differentiation. Together, the described changes in genomic regulation and disruptions in neurodevelopment provide possible mechanisms by which genetic variants of LTCC genes contribute to neuropsychiatric and neurodevelopmental disorders.
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Affiliation(s)
- Madelyn R. Baker
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, USA
| | - Andrew S. Lee
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Anjali M. Rajadhyaksha
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine, New York, USA
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4
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Yu R, Roseman S, Siegenfeld AP, Nguyen SC, Joyce EF, Liau BB, Krantz ID, Alexander KA, Berger SL. CTCF/cohesin organize the ground state of chromatin-nuclear speckle association. bioRxiv 2023:2023.07.22.550178. [PMID: 37961560 PMCID: PMC10634669 DOI: 10.1101/2023.07.22.550178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The interchromatin space in the cell nucleus contains various membrane-less nuclear bodies. Recent findings indicate that nuclear speckles, comprising a distinct nuclear body, exhibit interactions with certain chromatin regions in a ground state. Key questions are how this ground state of chromatin-nuclear speckle association is established and what are the gene regulatory roles of this layer of nuclear organization. We report here that chromatin structural factors CTCF and cohesin are required for full ground state association between DNA and nuclear speckles. Disruption of ground state DNA-speckle contacts via either CTCF depletion or cohesin depletion had minor effects on basal level expression of speckle-associated genes, however we show strong negative effects on stimulus-dependent induction of speckle-associated genes. We identified a putative speckle targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association. In contrast to reduction of CTCF or RAD21, depletion of the cohesin releasing factor WAPL stabilized cohesin on chromatin and DNA-speckle contacts, resulting in enhanced inducibility of speckle-associated genes. In addition, we observed disruption of chromatin-nuclear speckle association in patient derived cells with Cornelia de Lange syndrome (CdLS), a congenital neurodevelopmental diagnosis involving defective cohesin pathways, thus revealing nuclear speckles as an avenue for therapeutic inquiry. In summary, our findings reveal a mechanism to establish the ground organizational state of chromatin-speckle association, to promote gene inducibility, and with relevance to human disease.
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5
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Wołowiec A, Wołowiec Ł, Grześk G, Jaśniak A, Osiak J, Husejko J, Kozakiewicz M. The Role of Selected Epigenetic Pathways in Cardiovascular Diseases as a Potential Therapeutic Target. Int J Mol Sci 2023; 24:13723. [PMID: 37762023 PMCID: PMC10531432 DOI: 10.3390/ijms241813723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetics is a rapidly developing science that has gained a lot of interest in recent years due to the correlation between characteristic epigenetic marks and cardiovascular diseases (CVDs). Epigenetic modifications contribute to a change in gene expression while maintaining the DNA sequence. The analysis of these modifications provides a thorough insight into the cardiovascular system from its development to its further functioning. Epigenetics is strongly influenced by environmental factors, including known cardiovascular risk factors such as smoking, obesity, and low physical activity. Similarly, conditions affecting the local microenvironment of cells, such as chronic inflammation, worsen the prognosis in cardiovascular diseases and additionally induce further epigenetic modifications leading to the consolidation of unfavorable cardiovascular changes. A deeper understanding of epigenetics may provide an answer to the continuing strong clinical impact of cardiovascular diseases by improving diagnostic capabilities, personalized medical approaches and the development of targeted therapeutic interventions. The aim of the study was to present selected epigenetic pathways, their significance in cardiovascular diseases, and their potential as a therapeutic target in specific medical conditions.
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Affiliation(s)
- Anna Wołowiec
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Łukasz Wołowiec
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Grzegorz Grześk
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Albert Jaśniak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Joanna Osiak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jakub Husejko
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Mariusz Kozakiewicz
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
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6
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McKinsey TA, Foo R, Anene-Nzelu CG, Travers JG, Vagnozzi RJ, Weber N, Thum T. Emerging epigenetic therapies of cardiac fibrosis and remodelling in heart failure: from basic mechanisms to early clinical development. Cardiovasc Res 2023; 118:3482-3498. [PMID: 36004821 DOI: 10.1093/cvr/cvac142] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/02/2022] [Accepted: 08/21/2022] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular diseases and specifically heart failure (HF) impact global health and impose a significant economic burden on society. Despite current advances in standard of care, the risks for death and readmission of HF patients remain unacceptably high and new therapeutic strategies to limit HF progression are highly sought. In disease settings, persistent mechanical or neurohormonal stress to the myocardium triggers maladaptive cardiac remodelling, which alters cardiac function and structure at both the molecular and cellular levels. The progression and magnitude of maladaptive cardiac remodelling ultimately leads to the development of HF. Classical therapies for HF are largely protein-based and mostly are targeted to ameliorate the dysregulation of neuroendocrine pathways and halt adverse remodelling. More recently, investigation of novel molecular targets and the application of cellular therapies, epigenetic modifications, and regulatory RNAs has uncovered promising new avenues to address HF. In this review, we summarize the current knowledge on novel cellular and epigenetic therapies and focus on two non-coding RNA-based strategies that reached the phase of early clinical development to counteract cardiac remodelling and HF. The current status of the development of translating those novel therapies to clinical practice, limitations, and future perspectives are additionally discussed.
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Affiliation(s)
- Timothy A McKinsey
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Roger Foo
- NUHS Cardiovascular Disease Translational Research Programme, NUS Yong Loo Lin School of Medicine, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Cardiovascular Research Institute, National University Heart Centre, 14 Medical Drive, Level 8, 117599 Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- NUHS Cardiovascular Disease Translational Research Programme, NUS Yong Loo Lin School of Medicine, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Cardiovascular Research Institute, National University Heart Centre, 14 Medical Drive, Level 8, 117599 Singapore, Singapore.,Montreal Heart Institute, 5000 Rue Belanger, H1T 1C8, Montreal, Canada
| | - Joshua G Travers
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Ronald J Vagnozzi
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, 12700 E.19th Ave, Aurora, CO, 80045-2507, USA
| | - Natalie Weber
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.,REBIRTH Center for Translational Regenerative Therapies, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.,Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Straße 1, 30625 Hannover, Germany
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7
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Zhang J, Ouyang Z, Xia L, Wang Q, Zheng F, Xu K, Xing Y, Wei K, Shi S, Li C, Yang J. Dynamic chromatin landscape encodes programs for perinatal transition of cardiomyocytes. Cell Death Dis 2023; 9:11. [PMID: 36653336 PMCID: PMC9849264 DOI: 10.1038/s41420-023-01322-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
The perinatal period occurring immediately before and after birth is critical for cardiomyocytes because they must change rapidly to accommodate the switch from fetal to neonatal circulation after birth. This transition is a well-orchestrated process, and any perturbation leads to unhealthy cardiomyocytes and heart disease. Despite its importance, little is known about how this transition is regulated and controlled. Here, by mapping the genome-wide chromatin accessibility, transcription-centered long-range chromatin interactions and gene expression in cardiomyocytes undergoing perinatal transition, we discovered two key transcription factors, MEF2 and AP1, that are crucial for driving the phenotypic changes within the perinatal window. Thousands of dynamic regulatory elements were found in perinatal cardiomyocytes and we show these elements mediated the transcriptional reprogramming through an elegant chromatin high-order architecture. We recompiled transcriptional program of induced stem cell-derived cardiomyocytes according to our discovered network, and they showed adult cardiomyocyte-like electrophysiological expression. Our work provides a comprehensive regulatory resource of cardiomyocytes perinatal reprogramming, and aids the gap-filling of cardiac translational research.
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Affiliation(s)
- Jing Zhang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Zhaohui Ouyang
- grid.24516.340000000123704535Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092 Shanghai, China
| | - Limei Xia
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Qi Wang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Feng Zheng
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Kun Xu
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Yuexian Xing
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Ke Wei
- grid.24516.340000000123704535Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092 Shanghai, China
| | - Shaolin Shi
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Chaojun Li
- grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine and China International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, 211166 Nanjing, China
| | - Jingping Yang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
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8
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Yang Y, Chen Z, Le H. CTCF-mediated H3K27me3 enrichment on the LncRNA MALAT1 promoter regulates the cardiomyocytes from I/R-induced apoptosis through targeting miR-26b-5p. Mol Cell Toxicol 2023. [DOI: 10.1007/s13273-022-00246-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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9
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Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. Cell Regen 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
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Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
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10
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Xi X, Li H, Chen S, Lv T, Ma T, Jiang R, Zhang P, Wong WH, Zhang X. Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling. iScience 2022; 25:104790. [PMID: 35992073 PMCID: PMC9386115 DOI: 10.1016/j.isci.2022.104790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/26/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
Complex traits such as cardiovascular diseases (CVD) are the results of complicated processes jointly affected by genetic and environmental factors. Genome-wide association studies (GWAS) identified genetic variants associated with diseases but usually did not reveal the underlying mechanisms. There could be many intermediate steps at epigenetic, transcriptomic, and cellular scales inside the black box of genotype-phenotype associations. In this article, we present a machine-learning-based cross-scale framework GRPath to decipher putative causal paths (pcPaths) from genetic variants to disease phenotypes by integrating multiple omics data. Applying GRPath on CVD, we identified 646 and 549 pcPaths linking putative causal regions, variants, and gene expressions in specific cell types for two types of heart failure, respectively. The findings suggest new understandings of coronary heart disease. Our work promoted the modeling of tissue- and cell type-specific cross-scale regulation to uncover mechanisms behind disease-associated variants, and provided new findings on the molecular mechanisms of CVD. We defined one type of cross-scale genotype-to-phenotype regulation path We designed a framework GRPath to uncover putative regulation paths for diseases GRPath helped uncover molecular mechanisms for two major types of heart failure
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Affiliation(s)
- Xi Xi
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shengquan Chen
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Tingting Lv
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Tianxing Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ping Zhang
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Wing Hung Wong
- Departments of Statistics and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST / Department of Automation, Tsinghua University, Beijing 100084, China
- School of Medicine, Tsinghua University, Beijing 100084, China
- Corresponding author
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Wang M, Tu X. The Genetics and Epigenetics of Ventricular Arrhythmias in Patients Without Structural Heart Disease. Front Cardiovasc Med 2022; 9:891399. [PMID: 35783865 PMCID: PMC9240357 DOI: 10.3389/fcvm.2022.891399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/25/2022] [Indexed: 12/19/2022] Open
Abstract
Ventricular arrhythmia without structural heart disease is an arrhythmic disorder that occurs in structurally normal heart and no transient or reversible arrhythmia factors, such as electrolyte disorders and myocardial ischemia. Ventricular arrhythmias without structural heart disease can be induced by multiple factors, including genetics and environment, which involve different genetic and epigenetic regulation. Familial genetic analysis reveals that cardiac ion-channel disorder and dysfunctional calcium handling are two major causes of this type of heart disease. Genome-wide association studies have identified some genetic susceptibility loci associated with ventricular tachycardia and ventricular fibrillation, yet relatively few loci associated with no structural heart disease. The effects of epigenetics on the ventricular arrhythmias susceptibility genes, involving non-coding RNAs, DNA methylation and other regulatory mechanisms, are gradually being revealed. This article aims to review the knowledge of ventricular arrhythmia without structural heart disease in genetics, and summarizes the current state of epigenetic regulation.
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12
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Hu S, Vondriska TM. How Chromatin Stiffens Fibroblasts. Current Opinion in Physiology 2022; 26. [DOI: 10.1016/j.cophys.2022.100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Anene-nzelu CG, Li PY, Luu TDA, Ng SL, Tiang Z, Pan B, Tan WLW, Ackers-johnson M, Chen CK, Lim YP, Qin RWM, Chua WW, Yi LX, Foo RS, Nakabeppu Y, Virág L. 8-Oxoguanine DNA Glycosylase (OGG1) Deficiency Exacerbates Doxorubicin-Induced Cardiac Dysfunction. Oxidative Medicine and Cellular Longevity 2022; 2022:1-11. [PMID: 35391931 PMCID: PMC8981022 DOI: 10.1155/2022/9180267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/13/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
Doxorubicin is an anthracycline widely used for the treatment of various cancers; however, the drug has a common deleterious side effect, namely a dose-dependent cardiotoxicity. Doxorubicin treatment increases the generation of reactive oxygen species, which leads to oxidative stress in the cardiac cells and ultimately DNA damage and cell death. The most common DNA lesion produced by oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoguanine), and the enzyme responsible for its repair is the 8-oxoguanine DNA glycosylase (OGG1), a base excision repair enzyme. Here, we show that the OGG1 deficiency has no major effect on cardiac function at baseline or with pressure overload; however, we found an exacerbation of cardiac dysfunction as well as a higher mortality in Ogg1 knockout mice treated with doxorubicin. Our transcriptomic analysis also showed a more extensive dysregulation of genes in the hearts of Ogg1 knockout mice with an enrichment of genes involved in inflammation. These results demonstrate that OGG1 attenuates doxorubicin-induced cardiotoxicity and thus plays a role in modulating drug-induced cardiomyopathy.
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Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
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15
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Chapski DJ, Cabaj M, Morselli M, Mason RJ, Soehalim E, Ren S, Pellegrini M, Wang Y, Vondriska TM, Rosa-Garrido M. Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart. J Mol Cell Cardiol 2021; 160:73-86. [PMID: 34273410 DOI: 10.1016/j.yjmcc.2021.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022]
Abstract
The temporal nature of chromatin structural changes underpinning pathologic transcription are poorly understood. We measured chromatin accessibility and DNA methylation to study the contribution of chromatin remodeling at different stages of cardiac hypertrophy and failure. ATAC-seq and reduced representation bisulfite sequencing were performed in cardiac myocytes after transverse aortic constriction (TAC) or depletion of the chromatin structural protein CTCF. Early compensation to pressure overload showed changes in chromatin accessibility and DNA methylation preferentially localized to intergenic and intronic regions. Most methylation and accessibility changes observed in enhancers and promoters at the late phase (3 weeks after TAC) were established at an earlier time point (3 days after TAC), before heart failure manifests. Enhancers were paired with genes based on chromatin conformation capture data: while enhancer accessibility generally correlated with changes in gene expression, this feature, nor DNA methylation, was alone sufficient to predict transcription of all enhancer interacting genes. Enrichment of transcription factors and active histone marks at these regions suggests that enhancer activity coordinates with other epigenetic factors to determine gene transcription. In support of this hypothesis, ChIP-qPCR demonstrated increased enhancer and promoter occupancy of GATA4 and NKX2.5 at Itga9 and Nppa, respectively, concomitant with increased transcription of these genes in the diseased heart. Lastly, we demonstrate that accessibility and DNA methylation are imperfect predictors of chromatin structure at the scale of A/B compartmentalization-rather, accessibility, DNA methylation, transcription factors and other histone marks work within these domains to determine gene expression. These studies establish that chromatin reorganization during early compensation after pathologic stimuli is maintained into the later decompensatory phases of heart failure. The findings reveal the rules for how local chromatin features govern gene expression in the context of global genomic structure and identify chromatin remodeling events for therapeutic targeting in disease.
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16
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Chapski DJ, Vondriska TM. Taking Data Science to Heart: Next Scale of Gene Regulation. Curr Cardiol Rep 2021; 23:46. [PMID: 33721129 DOI: 10.1007/s11886-021-01467-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE OF REVIEW Technical advances have facilitated high-throughput measurements of the genome in the context of cardiovascular biology. These techniques bring a deluge of gargantuan datasets, which in turn present two fundamentally new opportunities for innovation-data processing and knowledge integration-toward the goal of meaningful basic and translational discoveries. RECENT FINDINGS Big data, integrative analyses, and machine learning have brought cardiac investigations to the cutting edge of chromatin biology, not only to reveal basic principles of gene regulation in the heart, but also to aid in the design of targeted epigenetic therapies. SUMMARY Cardiac studies using big data are only beginning to integrate the millions of recorded data points and the tools of machine learning are aiding this process. Future experimental design should take into consideration insights from existing genomic datasets, thereby focusing on heretofore unexplored epigenomic contributions to disease pathology.
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Funamoto M, Sunagawa Y, Katanasaka Y, Shimizu K, Miyazaki Y, Sari N, Shimizu S, Mori K, Wada H, Hasegawa K, Morimoto T. Histone Acetylation Domains Are Differentially Induced during Development of Heart Failure in Dahl Salt-Sensitive Rats. Int J Mol Sci 2021; 22:1771. [PMID: 33578969 PMCID: PMC7916721 DOI: 10.3390/ijms22041771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/06/2021] [Accepted: 02/07/2021] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation by epigenetic regulators has been shown to activate the transcription of hypertrophic response genes, which subsequently leads to the development and progression of heart failure. However, nothing is known about the acetylation of the histone tail and globular domains in left ventricular hypertrophy or in heart failure. The acetylation of H3K9 on the promoter of the hypertrophic response gene was significantly increased in the left ventricular hypertrophy stage, whereas the acetylation of H3K122 did not increase in the left ventricular hypertrophy stage but did significantly increase in the heart failure stage. Interestingly, the interaction between the chromatin remodeling factor BRG1 and p300 was significantly increased in the heart failure stage, but not in the left ventricular hypertrophy stage. This study demonstrates that stage-specific acetylation of the histone tail and globular domains occurs during the development and progression of heart failure, providing novel insights into the epigenetic regulatory mechanism governing transcriptional activity in these processes.
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Affiliation(s)
- Masafumi Funamoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Yoichi Sunagawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Yasufumi Katanasaka
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Kana Shimizu
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Yusuke Miyazaki
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Nurmila Sari
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
| | - Satoshi Shimizu
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Kiyoshi Mori
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
| | - Hiromichi Wada
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Koji Hasegawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
| | - Tatsuya Morimoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (M.F.); (Y.S.); (Y.K.); (K.S.); (Y.M.); (N.S.); (S.S.); (K.H.)
- Kyoto Medical Center, Clinical Research Institute, National Hospital Organization, 1-1 Fukakusa Mukaihatacho, Fushimi-ku, Kyoto 612-8555, Japan;
- Shizuoka General Hospital, 4-27-1 Kitaando, Aoi-ku, Shizuoka 420-8527, Japan;
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Bertero A, Rosa-Garrido M. Three-dimensional chromatin organization in cardiac development and disease. J Mol Cell Cardiol 2021; 151:89-105. [PMID: 33242466 PMCID: PMC11056610 DOI: 10.1016/j.yjmcc.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Recent technological advancements in the field of chromatin biology have rewritten the textbook on nuclear organization. We now appreciate that the folding of chromatin in the three-dimensional space (i.e. its 3D "architecture") is non-random, hierarchical, and highly complex. While 3D chromatin structure is partially encoded in the primary sequence and thereby broadly conserved across cell types and states, a substantial portion of the genome seems to be dynamic during development or in disease. Moreover, there is growing evidence that at least some of the 3D structure of chromatin is functionally linked to gene regulation, both being modulated by and impacting on multiple nuclear processes (including DNA replication, transcription, and RNA splicing). In recent years, these new concepts have nourished several investigations about the functional role of 3D chromatin topology dynamics in the heart during development and disease. This review aims to provide a comprehensive overview of our current understanding in this field, and to discuss how this knowledge can inform further research as well as clinical practice.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA.
| | - Manuel Rosa-Garrido
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, 650 Charles Young Dr, Los Angeles, CA 90095, USA.
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Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 2021; 28:152-161. [PMID: 33398174 PMCID: PMC7913465 DOI: 10.1038/s41594-020-00539-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/06/2020] [Indexed: 01/28/2023]
Abstract
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.
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Affiliation(s)
- Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Haruhiko Ishii
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Xiong Xiong
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Simona Bianco
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - Franz Meitinger
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James D. Hocker
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mattia Conte
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - David Gorkin
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Miao Yu
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Bin Li
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Mario Nicodemi
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant’Angelo, Naples, Italy
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Departments of Chemistry, Biochemistry, and Bioengineering, and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA,Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA,Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA,Correspondence to:
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20
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Man JCK, van Duijvenboden K, Krijger PHL, Hooijkaas IB, van der Made I, de Gier-de Vries C, Wakker V, Creemers EE, de Laat W, Boukens BJ, Christoffels VM. Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart. Circ Res 2021; 128:115-129. [PMID: 33107387 DOI: 10.1161/circresaha.120.317045] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RATIONALE ANP (atrial natriuretic peptide) and BNP (B-type natriuretic peptide), encoded by the clustered genes Nppa and Nppb, are important prognostic, diagnostic, and therapeutic proteins in cardiac disease. The spatiotemporal expression pattern and stress-induction of the Nppa and Nppb are tightly regulated, possibly involving their coregulation by an evolutionary conserved enhancer cluster. OBJECTIVE To explore the physiological functions of the enhancer cluster and elucidate the genomic mechanism underlying Nppa-Nppb coregulation in vivo. METHODS AND RESULTS By analyzing epigenetic data we uncovered an enhancer cluster with super enhancer characteristics upstream of Nppb. Using CRISPR/Cas9 genome editing, the enhancer cluster or parts thereof, Nppb and flanking regions or the entire genomic block spanning Nppa-Nppb, respectively, were deleted from the mouse genome. The impact on gene regulation and phenotype of the respective mouse lines was investigated by transcriptomic, epigenomic, and phenotypic analyses. The enhancer cluster was essential for prenatal and postnatal ventricular expression of Nppa and Nppb but not of any other gene. Enhancer cluster-deficient mice showed enlarged hearts before and after birth, similar to Nppa-Nppb compound knockout mice we generated. Analysis of the other deletion alleles indicated the enhancer cluster engages the promoters of Nppa and Nppb in a competitive rather than a cooperative mode, resulting in increased Nppa expression when Nppb and flanking sequences were deleted. The enhancer cluster maintained its active epigenetic state and selectivity when its target genes are absent. In enhancer cluster-deficient animals, Nppa was induced but remained low in the postmyocardial infarction border zone and in the hypertrophic ventricle, involving regulatory sequences proximal to Nppa. CONCLUSIONS Coordinated ventricular expression of Nppa and Nppb is controlled in a competitive manner by a shared super enhancer, which is also required to augment stress-induced expression and to prevent premature hypertrophy.
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MESH Headings
- Animals
- Atrial Natriuretic Factor/genetics
- Atrial Natriuretic Factor/metabolism
- Binding Sites
- Binding, Competitive
- CRISPR-Cas Systems
- Cell Line
- Disease Models, Animal
- Enhancer Elements, Genetic
- Epigenesis, Genetic
- Gene Expression Regulation, Developmental
- Humans
- Hypertrophy, Left Ventricular/genetics
- Hypertrophy, Left Ventricular/metabolism
- Hypertrophy, Left Ventricular/pathology
- Mice, Knockout
- Multigene Family
- Myocardial Infarction/genetics
- Myocardial Infarction/metabolism
- Myocardial Infarction/pathology
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Natriuretic Peptide, Brain/genetics
- Natriuretic Peptide, Brain/metabolism
- Promoter Regions, Genetic
- Mice
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Karel van Duijvenboden
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (P.H.L.K., W.d.L.)
| | - Ingeborg B Hooijkaas
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Ingeborg van der Made
- Department of Experimental Cardiology (I.v.d.M., E.E.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Corrie de Gier-de Vries
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent Wakker
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Esther E Creemers
- Department of Experimental Cardiology (I.v.d.M., E.E.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands (P.H.L.K., W.d.L.)
| | - Bastiaan J Boukens
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
- Department of Experimental Cardiology (I.v.d.M., E.E.C., B.J.B.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology (J.C.K.M., K.v.D., I.B.H., C.d.G.-d.V., V.W., B.J.B., V.M.C.), Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
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21
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Abstract
Epigenetics refers to changes in phenotypes without changes in genotypes. These changes take place in a number of ways, including via genomic DNA methylation, DNA interacting proteins, and microRNAs. The epigenome is the second dimension of the genome and it contains key information that is specific to every type of cell. Epigenetics is essential for many fundamental processes in biology, but its importance in the development and progression of heart failure, which is one of the major causes of morbidity and mortality worldwide, remains unclear. Our understanding of the underlying molecular mechanisms is incomplete. While epigenetics is one of the most innovative research areas in modern biology and medicine, compounds that directly target the epigenome, such as epidrugs, have not been well translated into therapies. This paper focuses on epigenetics in terms of genomic DNA methylation, such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications. These appear to be more dynamic than previously anticipated and may underlie a wide variety of conditions, including heart failure. We also outline possible new strategies for the development of novel therapies.
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22
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Abstract
Gene expression is needed for the maintenance of heart function under normal conditions and in response to stress. Each cell type of the heart has a specific program controlling transcription. Different types of stress induce modifications of these programs and, if prolonged, can lead to altered cardiac phenotype and, eventually, to heart failure. The transcriptional status of a gene is regulated by the epigenome, a complex network of DNA and histone modifications. Until a few years ago, our understanding of the role of the epigenome in heart disease was limited to that played by histone deacetylation. But over the last decade, the consequences for the maintenance of homeostasis in the heart and for the development of cardiac hypertrophy of a number of other modifications, including DNA methylation and hydroxymethylation, histone methylation and acetylation, and changes in chromatin architecture, have become better understood. Indeed, it is now clear that many levels of regulation contribute to defining the epigenetic landscape required for correct cardiomyocyte function, and that their perturbation is responsible for cardiac hypertrophy and fibrosis. Here, we review these aspects and draw a picture of what epigenetic modification may imply at the therapeutic level for heart failure.
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Affiliation(s)
- Roberto Papait
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Simone Serio
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
| | - Gianluigi Condorelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy; Humanitas Clinical Research Center-IRCCS, Rozzano, Italy; Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Italy; and National Research Council of Italy, Institute of Genetics and Biomedical Research, Milan Unit, Rozzano, Italy
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23
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Cibi DM, Bi-Lin KW, Shekeran SG, Sandireddy R, Tee N, Singh A, Wu Y, Srinivasan DK, Kovalik JP, Ghosh S, Seale P, Singh MK. Prdm16 Deficiency Leads to Age-Dependent Cardiac Hypertrophy, Adverse Remodeling, Mitochondrial Dysfunction, and Heart Failure. Cell Rep 2020; 33:108288. [PMID: 33086060 DOI: 10.1016/j.celrep.2020.108288] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/23/2020] [Accepted: 09/29/2020] [Indexed: 01/09/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a well-established risk factor for cardiovascular mortality worldwide. Although hypertrophy is traditionally regarded as an adaptive response to physiological or pathological stress, prolonged hypertrophy can lead to heart failure. Here we demonstrate that Prdm16 is dispensable for cardiac development. However, it is required in the adult heart to preserve mitochondrial function and inhibit hypertrophy with advanced age. Cardiac-specific deletion of Prdm16 results in cardiac hypertrophy, excessive ventricular fibrosis, mitochondrial dysfunction, and impaired metabolic flexibility, leading to heart failure. We demonstrate that Prdm16 and euchromatic histone-lysine N-methyltransferase factors (Ehmts) act together to reduce expression of fetal genes reactivated in pathological hypertrophy by inhibiting the functions of the pro-hypertrophic transcription factor Myc. Although young Prdm16 knockout mice show normal cardiac function, they are predisposed to develop heart failure in response to metabolic stress. Our study demonstrates that Prdm16 protects the heart against age-dependent cardiac hypertrophy and heart failure.
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Affiliation(s)
- Dasan Mary Cibi
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Kathleen Wung Bi-Lin
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Shamini Guna Shekeran
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Reddemma Sandireddy
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Nicole Tee
- National Heart Research Institute Singapore, National Heart Center Singapore, Singapore 169609
| | - Anamika Singh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Yajun Wu
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594
| | - Dinesh Kumar Srinivasan
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594
| | - Jean-Paul Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Sujoy Ghosh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857
| | - Patrick Seale
- Institute for Diabetes, Obesity, and Metabolism, Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Manvendra K Singh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857; National Heart Research Institute Singapore, National Heart Center Singapore, Singapore 169609.
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24
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Kim YW, Kang Y, Kang J, Kim A. GATA-1-dependent histone H3K27 acetylation mediates erythroid cell-specific chromatin interaction between CTCF sites. FASEB J 2020; 34:14736-14749. [PMID: 32924169 DOI: 10.1096/fj.202001526r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022]
Abstract
CCCTC-binding factor (CTCF) sites interact with each other in the chromatin environment, establishing chromatin domains. Our previous study showed that interaction between CTCF sites is cell type-specific around the β-globin locus and is dependent on erythroid-specific activator GATA-1. To find out molecular mechanisms of the cell type-specific interaction, we directly inhibited GATA-1 binding to the β-globin enhancers by deleting its binding motifs and found that histone H3K27 acetylation (H3K27ac) was decreased at CTCF sites surrounding the β-globin locus, even though CTCF binding itself was maintained at the sites. Forced H3K27ac by Trichostatin A treatment or CBP/p300 KD affected the interactions between CTCF sites around the β-globin locus without changes in CTCF binding. Analysis of public ChIA-PET data revealed that H3K27ac is higher at CTCF sites forming short interactions than long interactions. GATA-1 was identified as a representative transcription factor that relates with genes present inside the short interactions in erythroid K562 cells. Depletion of GATA-1-reduced H3K27ac at CTCF sites near erythroid-specific enhancers. These results indicate that H3K27ac at CTCF sites is required for cell type-specific chromatin interactions between them. Tissue-specific activator GATA-1 appears to play a role in H3K27ac at CTCF sites in erythroid cells.
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Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
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25
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Tan WLW, Anene-Nzelu CG, Wong E, Lee CJM, Tan HS, Tang SJ, Perrin A, Wu KX, Zheng W, Ashburn RJ, Pan B, Lee MY, Autio MI, Morley MP, Tam WL, Cheung C, Margulies KB, Chen L, Cappola TP, Loh M, Chambers J, Prabhakar S, Foo RSY. Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype. Circ Res 2020; 127:761-777. [PMID: 32529949 DOI: 10.1161/circresaha.120.317254] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RATIONALE Identifying genetic markers for heterogeneous complex diseases such as heart failure is challenging and requires prohibitively large cohort sizes in genome-wide association studies to meet the stringent threshold of genome-wide statistical significance. On the other hand, chromatin quantitative trait loci, elucidated by direct epigenetic profiling of specific human tissues, may contribute toward prioritizing subthreshold variants for disease association. OBJECTIVE Here, we captured noncoding genetic variants by performing epigenetic profiling for enhancer H3K27ac chromatin immunoprecipitation followed by sequencing in 70 human control and end-stage failing hearts. METHODS AND RESULTS We have mapped a comprehensive catalog of 47 321 putative human heart enhancers and promoters. Three thousand eight hundred ninety-seven differential acetylation peaks (FDR [false discovery rate], 5%) pointed to pathways altered in heart failure. To identify cardiac histone acetylation quantitative trait loci (haQTLs), we regressed out confounding factors including heart failure disease status and used the G-SCI (Genotype-independent Signal Correlation and Imbalance) test1 to call out 1680 haQTLs (FDR, 10%). RNA sequencing performed on the same heart samples proved a subset of haQTLs to have significant association also to gene expression (expression quantitative trait loci), either in cis (180) or through long-range interactions (81), identified by Hi-C (high-throughput chromatin conformation assay) and HiChIP (high-throughput protein centric chromatin) performed on a subset of hearts. Furthermore, a concordant relationship between the gain or disruption of TF (transcription factor)-binding motifs, inferred from alternative alleles at the haQTLs, implied a surprising direct association between these specific TF and local histone acetylation in human hearts. Finally, 62 unique loci were identified by colocalization of haQTLs with the subthreshold loci of heart-related genome-wide association studies datasets. CONCLUSIONS Disease and phenotype association for 62 unique loci are now implicated. These loci may indeed mediate their effect through modification of enhancer H3K27 acetylation enrichment and their corresponding gene expression differences (bioRxiv: https://doi.org/10.1101/536763). Graphical Abstract: A graphical abstract is available for this article.
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Affiliation(s)
- Wilson Lek Wen Tan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Chukwuemeka George Anene-Nzelu
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Eleanor Wong
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Chang Jie Mick Lee
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Hui San Tan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Arnaud Perrin
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Kan Xing Wu
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
| | - Wenhao Zheng
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Robert John Ashburn
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Bangfen Pan
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - May Yin Lee
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Matias Ilmari Autio
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Michael P Morley
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Wai Leong Tam
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Institute of Molecular and Cell Biology, Singapore (C.C.)
| | - Kenneth B Margulies
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore (S.J.T., W.L.T., L.C.)
| | - Thomas P Cappola
- Cardiovascular Institute, Perlman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia (M.P.M., K.B.M., T.P.C.)
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Epidemiology and Biostatistics, Imperial College London (M.L., J.C.), United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom (M.L., J.C.)
| | - John Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore (K.X.W., C.C., M.L., J.C.)
- Epidemiology and Biostatistics, Imperial College London (M.L., J.C.), United Kingdom
- Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, United Kingdom (J.C.)
- Imperial College Healthcare NHS Trust, London, United Kingdom (M.L., J.C.)
| | - Shyam Prabhakar
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
| | - Roger S Y Foo
- From the Cardiovascular Research Institute, National University Health System, Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., B.P., M.I.A., R.S.Y.F.)
- Genome Institute of Singapore (W.L.W.T., C.G.A.-N., E.W., C.J.M.L., H.S.T., A.P., Z.W., R.J.A., B.P., L.M.Y., M.I.A., W.L.T., S.P., R.S.Y.F.)
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26
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Liu CF, Abnousi A, Bazeley P, Ni Y, Morley M, Moravec CS, Hu M, Tang WHW. Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy. J Mol Cell Cardiol 2020; 145:30-42. [PMID: 32533974 DOI: 10.1016/j.yjmcc.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/18/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Acetylation and methylation of histones alter the chromatin structure and accessibility that affect transcriptional regulators binding to enhancers and promoters. The binding of transcriptional regulators enables the interaction between enhancers and promoters, thus affecting gene expression. However, our knowledge of these epigenetic alternations in patients with heart failure remains limited. METHODS AND RESULTS From the comprehensive analysis of major histone modifications, 3-dimensional chromatin interactions, and transcriptome in left ventricular (LV) tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors, differential active enhancer and promoter regions were identified between NF and DCM. Moreover, the genome-wide average promoter signal is significantly lower in DCM than in NF. Super-enhancer (SE) analysis revealed that fewer SEs were found in DCM LVs than in NF ones, and three unique SE-associated genes between NF and DCM were identified. Moreover, SEs are enriched within the genomic region associated with long-range chromatin interactions. The differential enhancer-promoter interactions were observed in the known heart failure gene loci and are correlated with the gene expression levels. Motif analysis identified known cardiac factors and possible novel players for DCM. CONCLUSIONS We have established the cistrome of four histone modifications and chromatin interactome for enhancers and promoters in NF and DCM tissues. Differential histone modifications and enhancer-promoter interactions were found in DCM, which were associated with gene expression levels of a subset of disease-associated genes in human heart failure.
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Affiliation(s)
- Chia-Feng Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, USA
| | - Armen Abnousi
- Quantitative Health Sciences, Lerner Research Institute, USA
| | - Peter Bazeley
- Quantitative Health Sciences, Lerner Research Institute, USA
| | - Ying Ni
- Taussig Cancer Institute, Heart and Vascular Institute, Cleveland Clinic, OH, USA
| | | | - Christine S Moravec
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, USA
| | - Ming Hu
- Quantitative Health Sciences, Lerner Research Institute, USA
| | - W H Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, USA; Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, OH, USA.
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27
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Abstract
PURPOSE OF REVIEW Development, physiological growth and the response of the heart to injury are accompanied by changes of the transcriptome and epigenome of cardiac myocytes. Recently, cell sorting and next generation sequencing techniques have been applied to determine cardiac myocyte-specific transcriptional and epigenetic mechanisms. This review provides a comprehensive overview of studies analysing the transcriptome and epigenome of cardiac myocytes in mouse and human hearts during development, physiological growth and disease. RECENT FINDINGS Adult cardiac myocytes express > 12,600 genes, and their expression levels correlate positively with active histone marks and inversely with gene body DNA methylation. DNA methylation accompanied the perinatal switch in sarcomere or metabolic isoform gene expression in cardiac myocytes, but remained rather stable in heart disease. DNA methylation and histone marks identified > 100,000 cis-regulatory regions in the cardiac myocyte epigenome with a dynamic spectrum of transcription factor binding sites. The ETS-related transcription factor ETV1 was identified as an atrial-specific element involved in the pathogenesis of atrial fibrillation. Thus, dynamic development of the atrial vs. ventricular cardiac myocyte epigenome provides a basis to identify location and time-dependent mechanisms of epigenetic control to shape pathological gene expression during heart disease. Identifying the four dimensions of the cardiac myocyte epigenome, atrial vs. ventricular location, time during development and growth, and disease-specific signals, may ultimately lead to new treatment strategies for heart disease.
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28
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Abstract
Eukaryotes must balance the metabolic and cell death actions of mitochondria via control of gene expression and cell fate by chromatin, thereby functionally binding the metabolome and epigenome. This interaction has far-reaching implications for chronic diseases in humans, the most common of which are those of the cardiovascular system. The most devastating consequence of cardiovascular disease, heart failure, is not a single disease, diagnosis, or endpoint. Human and animal studies have revealed that, regardless of etiology and symptoms, heart failure is universally associated with abnormal metabolism and gene expression - to frame this as cause or consequence, however, may be to wrongfoot the question. This essay aims to challenge current thinking on metabolic-epigenetic crosstalk in heart failure, presenting hypotheses for how chronic diseases arise, take hold, and persist. We unpack assumptions about the order of operations for gene expression and metabolism, exploring recent findings in noncardiac systems that link metabolic intermediates directly to chromatin remodeling. Lastly, we discuss potential mechanisms by which chromatin may serve as a substrate for metabolic memory, and how changes in cellular transcriptomes (and hence in cellular behavior) in response to stress correspond to global changes in chromatin accessibility and structure.
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Affiliation(s)
- Todd H Kimball
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, USA
| | - Thomas M Vondriska
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, USA.
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29
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Abstract
Most studies describing epigenetic modifications have focused on DNA methylation, but fewer studies have focused on histone modifications and noncoding RNAs. Chromatin architecture and CCCTC-binding factor represent important noncoding regulatory elements that warrant further investigation in order to improve our understanding of the genomic basis of complex diseases such as psychiatric disorders.
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Affiliation(s)
- Florence Thibaut
- University Hospital Cochin - site Tarnier, Paris, France Faculty of Medicine Paris Descartes (Paris University), INSERM U1266, Institute of
Psychiatry and Neuroscience, Paris, France
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30
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Zeng Z, Huang N, Zhang Y, Wang Y, Su Y, Zhang H, An Y. CTCF inhibits endoplasmic reticulum stress and apoptosis in cardiomyocytes by upregulating RYR2 via inhibiting S100A1. Life Sci 2019; 242:117158. [PMID: 31837328 DOI: 10.1016/j.lfs.2019.117158] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
Abstract
AIMS Pediatric heart failure is a common cardiovascular disease in clinical pediatrics. CCCTC-binding factor (CTCF), a novel transcriptional repressor, was reported to participate in the occurrence of various cardiovascular diseases. The present study focuses on exploring the effects of CTCF on tunicamycin (TM)-induced endoplasmic reticulum (ER) stress, and investigating the underlying mechanisms. MATERIALS AND METHOD Expression of CTCF in blood samples of heart failure children and TM-induced cardiomyocytes were evaluated by real-time quantitative PCR (RT-qPCR). Apoptotic rate of cardiomyocytes was detected by Annexin v assay. Western blotting and enzyme-linked immunosorbent assay (ELISA) were applied to examine the effect of CTCF on ER stress. Co-immunoprecipitation and western blotting were devoted to explore the mechanism by which CTCF contributes to ER stress. KEY FINDINGS We proved that CTCF was lowly expressed in blood samples of heart failure children and TM-induced cardiomyocytes, and overexpression of CTCF weaken the TM-induced ER stress. Using co-immunoprecipitation and protein blots, we demonstrated that CTCF upregulates RYR2 by inhibiting S100A1, thus mediating the PERK signaling pathway and regulating ER stress. SIGNIFICANCE Our data revealed that CTCF protects cardiomyocytes from ER stress through S100A1-RYR2 axis, and can be applied as a therapeutic target for the treatment of pediatric heart failure in future.
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Affiliation(s)
- Zhu Zeng
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Nina Huang
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Yudan Zhang
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Ying Wang
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Yufei Su
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Huifang Zhang
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003
| | - Yuan An
- Department of Emergency, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China 710003.
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31
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Affiliation(s)
- Roger Sik-Yin Foo
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (R.S.-Y.F., C.G.A.-N.)
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (R.S.-Y.F., C.G.A.-N.).,Genome Institute of Singapore (C.G.A.-N.)
| | - Manuel Rosa-Garrido
- Departments of Anesthesiology, Medicine and Physiology, David Geffen School of Medicine at UCLA (M.R.-G., T.M.V.)
| | - Thomas M Vondriska
- Departments of Anesthesiology, Medicine and Physiology, David Geffen School of Medicine at UCLA (M.R.-G., T.M.V.)
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