1
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Kosicki M, Baltoumas FA, Kelman G, Boverhof J, Ong Y, Cook LE, Dickel DE, Pavlopoulos GA, Pennacchio LA, Visel A. VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers. Nucleic Acids Res 2024:gkae940. [PMID: 39470740 DOI: 10.1093/nar/gkae940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 10/14/2024] [Indexed: 11/01/2024] Open
Abstract
Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.
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Affiliation(s)
- Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Fotis A Baltoumas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, 16672, Greece
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Joshua Boverhof
- Scientific Data Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Yeongshnn Ong
- Scientific Data Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Vari, 16672, Greece
| | - Len A Pennacchio
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
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2
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Abassah-Oppong S, Zoia M, Mannion BJ, Rouco R, Tissières V, Spurrell CH, Roland V, Darbellay F, Itum A, Gamart J, Festa-Daroux TA, Sullivan CS, Kosicki M, Rodríguez-Carballo E, Fukuda-Yuzawa Y, Hunter RD, Novak CS, Plajzer-Frick I, Tran S, Akiyama JA, Dickel DE, Lopez-Rios J, Barozzi I, Andrey G, Visel A, Pennacchio LA, Cobb J, Osterwalder M. A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival. Nat Commun 2024; 15:8793. [PMID: 39389973 PMCID: PMC11467299 DOI: 10.1038/s41467-024-53009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 09/26/2024] [Indexed: 10/12/2024] Open
Abstract
Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.
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Affiliation(s)
- Samuel Abassah-Oppong
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
| | - Matteo Zoia
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Raquel Rouco
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Virginie Tissières
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013, Seville, Spain
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Virginia Roland
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anja Itum
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Julie Gamart
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland
| | - Tabitha A Festa-Daroux
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Carly S Sullivan
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eddie Rodríguez-Carballo
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Guillaume Andrey
- Department of Genetic Medicine and Development and iGE3, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, T2N 1N4, Canada.
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Department of Cardiology, Bern University Hospital, 3010, Bern, Switzerland.
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3
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Mansoorshahi S, Yetman AT, Bissell MM, Kim YY, Michelena HI, De Backer J, Mosquera LM, Hui DS, Caffarelli A, Andreassi MG, Foffa I, Guo D, Citro R, De Marco M, Tretter JT, Morris SA, Body SC, Chong JX, Bamshad MJ, Milewicz DM, Prakash SK. Whole-exome sequencing uncovers the genetic complexity of bicuspid aortic valve in families with early-onset complications. Am J Hum Genet 2024; 111:2219-2231. [PMID: 39226896 PMCID: PMC11480851 DOI: 10.1016/j.ajhg.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart lesion with an estimated population prevalence of 1%. We hypothesize that specific gene variants predispose to early-onset complications of BAV (EBAV). We analyzed whole-exome sequences (WESs) to identify rare coding variants that contribute to BAV disease in 215 EBAV-affected families. Predicted damaging variants in candidate genes with moderate or strong supportive evidence to cause developmental cardiac phenotypes were present in 107 EBAV-affected families (50% of total), including genes that cause BAV (9%) or heritable thoracic aortic disease (HTAD, 19%). After appropriate filtration, we also identified 129 variants in 54 candidate genes that are associated with autosomal-dominant congenital heart phenotypes, including recurrent deleterious variation of FBN2, MYH6, channelopathy genes, and type 1 and 5 collagen genes. These findings confirm our hypothesis that unique rare genetic variants drive early-onset presentations of BAV disease.
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Affiliation(s)
- Sara Mansoorshahi
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Anji T Yetman
- Children's Hospital and Medical Center, University of Nebraska, Omaha, NE, USA
| | - Malenka M Bissell
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Yuli Y Kim
- Division of Cardiovascular Medicine, The Hospital of the University of Pennsylvania, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Julie De Backer
- Department of Cardiology and Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Laura Muiño Mosquera
- Department of Cardiology and Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Dawn S Hui
- Department of Cardiothoracic Surgery, University of Texas Health Science Center, San Antonio, TX, USA
| | - Anthony Caffarelli
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria G Andreassi
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Ilenia Foffa
- Consiglio Nazionale delle Richerche (CNR), Instituto di Fisiologia Clinica, Pisa, Italy
| | - Dongchuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rodolfo Citro
- Cardiothoracic and Vascular Department, University Hospital "San Giovanni di Dio e Ruggi d'Aragona," Salerno, Italy
| | - Margot De Marco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy
| | | | - Shaine A Morris
- Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Simon C Body
- Department of Anesthesiology, Boston University School of Medicine, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
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4
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Kosicki M, Zhang B, Pampari A, Akiyama JA, Plajzer-Frick I, Novak CS, Tran S, Zhu Y, Kato M, Hunter RD, von Maydell K, Barton S, Beckman E, Kundaje A, Dickel DE, Visel A, Pennacchio LA. Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611737. [PMID: 39282388 PMCID: PMC11398460 DOI: 10.1101/2024.09.06.611737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Distant-acting enhancers are central to human development. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease. Here, we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers active in the developing brain, heart, limb and face, we created over 1700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-basepair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modeling, we annotated critical nucleotides at base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes to in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.
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Affiliation(s)
- Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Boyang Zhang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anusri Pampari
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Sarah Barton
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Erik Beckman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Diane E. Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
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5
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 PMCID: PMC11203181 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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6
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Xiao F, Zhang X, Morton SU, Kim SW, Fan Y, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao Y, Chen J, Hagen J, Liu X, Zhou P, Richter F, Shen Y, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nat Genet 2024; 56:420-430. [PMID: 38378865 PMCID: PMC11218660 DOI: 10.1038/s41588-024-01669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
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Affiliation(s)
- Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Youfei Fan
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Huan Zhang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Berkson
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Neil Mazumdar
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Jacob Hagen
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Xujie Liu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Felix Richter
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York City, NY, USA
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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7
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Narayan P, Richter F, Morton S. Genetics and etiology of congenital heart disease. Curr Top Dev Biol 2024; 156:297-331. [PMID: 38556426 DOI: 10.1016/bs.ctdb.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common severe birth anomaly, affecting almost 1% of infants. Most CHD is genetic, but only 40% of patients have an identifiable genetic risk factor for CHD. Chromosomal variation contributes significantly to CHD but is not readily amenable to biological follow-up due to the number of affected genes and lack of evolutionary synteny. The first CHD genes were implicated in extended families with syndromic CHD based on the segregation of risk alleles in affected family members. These have been complemented by more CHD gene discoveries in large-scale cohort studies. However, fewer than half of the 440 estimated human CHD risk genes have been identified, and the molecular mechanisms underlying CHD genetics remains incompletely understood. Therefore, model organisms and cell-based models are essential tools for improving our understanding of cardiac development and CHD genetic risk. Recent advances in genome editing, cell-specific genetic manipulation of model organisms, and differentiation of human induced pluripotent stem cells have recently enabled the characterization of developmental stages. In this chapter, we will summarize the latest studies in CHD genetics and the strengths of various study methodologies. We identify opportunities for future work that will continue to further CHD knowledge and ultimately enable better diagnosis, prognosis, treatment, and prevention of CHD.
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Affiliation(s)
| | - Felix Richter
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sarah Morton
- Boston Children's Hospital and Harvard Medical School, Boston, MA, United States.
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8
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Peña-Martínez EG, Pomales-Matos DA, Rivera-Madera A, Messon-Bird JL, Medina-Feliciano JG, Sanabria-Alberto L, Barreiro-Rosario AC, Rivera-Del Valle J, Rodríguez-Ríos JM, Rodríguez-Martínez JA. Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach. J Biol Chem 2023; 299:105423. [PMID: 37926287 PMCID: PMC10750078 DOI: 10.1016/j.jbc.2023.105423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies have mapped >90% of CVD-associated variants within the noncoding genome, which can alter the function of regulatory proteins, such as transcription factors (TFs). However, due to the overwhelming number of single-nucleotide polymorphisms (SNPs) (>500,000) in genome-wide association studies, prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1535 CVD-associated SNPs within TF footprints and putative cardiac enhancers plus 14,218 variants in linkage disequilibrium with genotype-dependent gene expression in cardiac tissues. Using ChIP-seq data from two cardiac TFs (NKX2-5 and TBX5) in human-induced pluripotent stem cell-derived cardiomyocytes, we trained a large-scale gapped k-mer SVM model to identify CVD-associated SNPs that altered NKX2-5 and TBX5 binding. The model was tested by scoring human heart TF genomic footprints within putative enhancers and measuring in vitro binding through electrophoretic mobility shift assay. Five variants predicted to alter NKX2-5 (rs59310144, rs6715570, and rs61872084) and TBX5 (rs7612445 and rs7790964) binding were prioritized for in vitro validation based on the magnitude of the predicted change in binding and are in cardiac tissue eQTLs. All five variants altered NKX2-5 and TBX5 DNA binding. We present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro analysis.
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Affiliation(s)
- Edwin G Peña-Martínez
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | - Diego A Pomales-Matos
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | | | - Jean L Messon-Bird
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
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9
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Serio S, Pagiatakis C, Musolino E, Felicetta A, Carullo P, Laura Frances J, Papa L, Rozzi G, Salvarani N, Miragoli M, Gornati R, Bernardini G, Condorelli G, Papait R. Cardiac Aging Is Promoted by Pseudohypoxia Increasing p300-Induced Glycolysis. Circ Res 2023; 133:687-703. [PMID: 37681309 DOI: 10.1161/circresaha.123.322676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Heart failure is typical in the elderly. Metabolic remodeling of cardiomyocytes underlies inexorable deterioration of cardiac function with aging: glycolysis increases at the expense of oxidative phosphorylation, causing an energy deficit contributing to impaired contractility. Better understanding of the mechanisms of this metabolic switching could be critical for reversing the condition. METHODS To investigate the role of 3 histone modifications (H3K27ac, H3K27me3, and H3K4me1) in the metabolic remodeling occurring in the aging heart, we cross-compared epigenomic, transcriptomic, and metabolomic data from mice of different ages. In addition, the role of the transcriptional coactivator p300 (E1A-associated binding protein p300)/CBP (CREB binding protein) in cardiac aging was investigated using a specific inhibitor of this histone acetyltransferase enzyme. RESULTS We report a set of species-conserved enhancers associated with transcriptional changes underlying age-related metabolic remodeling in cardiomyocytes. Activation of the enhancer region of Hk2-a key glycolysis pathway gene-was fostered in old age-onset mouse heart by pseudohypoxia, wherein hypoxia-related genes are expressed under normal O2 levels, via increased activity of P300/CBP. Pharmacological inhibition of this transcriptional coactivator before the onset of cardiac aging led to a more aerobic, less glycolytic, metabolic state, improved heart contractility, and overall blunting of cardiac decline. CONCLUSIONS Taken together, our results suggest how epigenetic dysregulation of glycolysis pathway enhancers could potentially be targeted to treat heart failure in the elderly.
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Affiliation(s)
- Simone Serio
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy (S.S., G.C.)
| | - Christina Pagiatakis
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy (C.P., E.M., R.G., G.B., R.P.)
| | - Elettra Musolino
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy (C.P., E.M., R.G., G.B., R.P.)
| | - Arianna Felicetta
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
| | - Pierluigi Carullo
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
| | - Javier Laura Frances
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
| | - Laura Papa
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
| | - Giacomo Rozzi
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
| | - Nicolò Salvarani
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Institute of Genetic and Biomedical Research, UOS of Milan, National Research Council of Italy (N.S.)
| | - Michele Miragoli
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Department of Medicine and Surgery, University of Parma, Italy (M.M.)
| | - Rosalba Gornati
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy (C.P., E.M., R.G., G.B., R.P.)
| | - Giovanni Bernardini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy (C.P., E.M., R.G., G.B., R.P.)
| | - Gianluigi Condorelli
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy (S.S., G.C.)
| | - Roberto Papait
- Department of Cardiovascular Medicine, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano (MI), Italy (S.S., C.P., A.F., P.C., J.L.F., L.P., G.R., N.S., M.M., G.C., R.P.)
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100, Varese, Italy (C.P., E.M., R.G., G.B., R.P.)
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10
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Htet M, Lei S, Bajpayi S, Zoitou A, Chamakioti M, Tampakakis E. The role of noncoding genetic variants in cardiomyopathy. Front Cardiovasc Med 2023; 10:1116925. [PMID: 37283586 PMCID: PMC10239966 DOI: 10.3389/fcvm.2023.1116925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Cardiomyopathies remain one of the leading causes of morbidity and mortality worldwide. Environmental risk factors and genetic predisposition account for most cardiomyopathy cases. As with all complex diseases, there are significant challenges in the interpretation of the molecular mechanisms underlying cardiomyopathy-associated genetic variants. Given the technical improvements and reduced costs of DNA sequence technologies, an increasing number of patients are now undergoing genetic testing, resulting in a continuously expanding list of novel mutations. However, many patients carry noncoding genetic variants, and although emerging evidence supports their contribution to cardiac disease, their role in cardiomyopathies remains largely understudied. In this review, we summarize published studies reporting on the association of different types of noncoding variants with various types of cardiomyopathies. We focus on variants within transcriptional enhancers, promoters, intronic sites, and untranslated regions that are likely associated with cardiac disease. Given the broad nature of this topic, we provide an overview of studies that are relatively recent and have sufficient evidence to support a significant degree of causality. We believe that more research with additional validation of noncoding genetic variants will provide further mechanistic insights on the development of cardiac disease, and noncoding variants will be increasingly incorporated in future genetic screening tests.
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Affiliation(s)
- Myo Htet
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Shunyao Lei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Sheetal Bajpayi
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Asimina Zoitou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | - Emmanouil Tampakakis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
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11
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Bhattacharyya S, Kollipara RK, Orquera-Tornakian G, Goetsch S, Zhang M, Perry C, Li B, Shelton JM, Bhakta M, Duan J, Xie Y, Xiao G, Evers BM, Hon GC, Kittler R, Munshi NV. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm. J Clin Invest 2023; 133:e153635. [PMID: 36454649 PMCID: PMC9888383 DOI: 10.1172/jci153635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.
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Affiliation(s)
| | | | | | - Sean Goetsch
- Department of Internal Medicine, Division of Cardiology
| | - Minzhe Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Cameron Perry
- Department of Internal Medicine, Division of Cardiology
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | | | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Bret M. Evers
- Department of Internal Medicine, Division of Cardiology
| | - Gary C. Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
- Department of Bioinformatics
- Hamon Center for Regenerative Science and Medicine, and
| | - Ralf Kittler
- McDermott Center for Human Growth and Development
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology
- McDermott Center for Human Growth and Development
- Hamon Center for Regenerative Science and Medicine, and
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
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12
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Deviatiiarov RM, Gams A, Kulakovskiy IV, Buyan A, Meshcheryakov G, Syunyaev R, Singh R, Shah P, Tatarinova TV, Gusev O, Efimov IR. An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure. NATURE CARDIOVASCULAR RESEARCH 2023; 2:58-75. [PMID: 39196209 DOI: 10.1038/s44161-022-00182-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/02/2022] [Indexed: 08/29/2024]
Abstract
A deeper knowledge of the dynamic transcriptional activity of promoters and enhancers is needed to improve mechanistic understanding of the pathogenesis of heart failure and heart diseases. In this study, we used cap analysis of gene expression (CAGE) to identify and quantify the activity of transcribed regulatory elements (TREs) in the four cardiac chambers of 21 healthy and ten failing adult human hearts. We identified 17,668 promoters and 14,920 enhancers associated with the expression of 14,519 genes. We showed how these regulatory elements are alternatively transcribed in different heart regions, in healthy versus failing hearts and in ischemic versus non-ischemic heart failure samples. Cardiac-disease-related single-nucleotide polymorphisms (SNPs) appeared to be enriched in TREs, potentially affecting the allele-specific transcription factor binding. To conclude, our open-source heart CAGE atlas will serve the cardiovascular community in improving the understanding of the role of the cardiac gene regulatory networks in cardiovascular disease and therapy.
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Affiliation(s)
- Ruslan M Deviatiiarov
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Anna Gams
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - Ivan V Kulakovskiy
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Buyan
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | | | - Roman Syunyaev
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ramesh Singh
- Inova Heart and Vascular Institute, Falls Church, VA, USA
| | - Palak Shah
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
- Inova Heart and Vascular Institute, Falls Church, VA, USA
| | - Tatiana V Tatarinova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Department of Biology, University of La Verne, La Verne, CA, USA.
| | - Oleg Gusev
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
- Graduate School of Medicine, Juntendo University, Tokyo, Japan.
- RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan.
- Endocrinology Research Center, Moscow, Russia.
| | - Igor R Efimov
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA.
- Department of Biomedical Engineering, Northwestern University, Chicago, IL, USA.
- Department of Medicine, Northwestern University, Chicago, IL, USA.
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13
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Begeman IJ, Emery B, Kurth A, Kang J. Regeneration and developmental enhancers are differentially compatible with minimal promoters. Dev Biol 2022; 492:47-58. [PMID: 36167150 PMCID: PMC10211259 DOI: 10.1016/j.ydbio.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/01/2022]
Abstract
Enhancers and promoters are cis-regulatory elements that control gene expression. Enhancers are activated in a cell type-, tissue-, and condition-specific manner to stimulate promoter function and transcription. Zebrafish have emerged as a powerful animal model for examining the activities of enhancers derived from various species through transgenic enhancer assays, in which an enhancer is coupled with a minimal promoter. However, the efficiency of minimal promoters and their compatibility with multiple developmental and regeneration enhancers have not been systematically tested in zebrafish. Thus, we assessed the efficiency of six minimal promoters and comprehensively interrogated the compatibility of the promoters with developmental and regeneration enhancers. We found that the fos minimal promoter and Drosophila synthetic core promoter (DSCP) yielded high rates of leaky expression that may complicate the interpretation of enhancer assays. Notably, the adenovirus E1b promoter, the zebrafish lepb 0.8-kb (P0.8) and lepb 2-kb (P2) promoters, and a new zebrafish synthetic promoter (ZSP) that combines elements of the E1b and P0.8 promoters drove little or no ectopic expression, making them suitable for transgenic assays. We also found significant differences in compatibility among specific combinations of promoters and enhancers, indicating the importance of promoters as key regulatory elements determining the specificity of gene expression. Our study provides guidelines for transgenic enhancer assays in zebrafish to aid in the discovery of functional enhancers regulating development and regeneration.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Benjamin Emery
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA; UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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14
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Wang F, Zhang Y, Wu F, Gui Y, Chen X, Wang Y, Wang X, Gui Y, Li Q. Functional assessment of heart-specific enhancers by integrating ChIP-seq data. Pediatr Res 2022; 92:1332-1340. [PMID: 35173300 DOI: 10.1038/s41390-022-01981-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Identification and functional annotations of regulatory sequences play a pivotal role in heart development and function. METHODS To generate a map of human heart-specific enhancers, we performed an integrative analysis of 148 chromatin immunoprecipitation coupled to massively parallel sequencing (ChIP-seq) samples with enhancer-associated epigenetic marks from the heart, liver, brain, and kidney. Functional validation of heart-specific enhancer activity was then performed using cultured cells. RESULTS A 144.6-Mb candidate heart-specific enhancer compendium was generated by integrating the analysis of 148 epigenomic data sets from human and mouse hearts and control tissues. To validate in vivo enhancer activity, we tested 12 of these sequences around 45 CHD-related genes in cultured cells and found that 8 (67%) have reproducible heart-specific enhancer activity. A functional analysis demonstrated that the identified human heart-specific enhancer wf1 regulates the FBN1 gene which is involved in heart disease. CONCLUSIONS Our study provides an integrative analysis pipeline for ChIP-seq data and identified a comprehensive catalog of human heart-specific enhancers for clinical CHD-related studies. IMPACT Establishing an efficient way to analyze regulatory regions in CHD is very important. A highly qualified heart-specific enhancer compendium was generated by integrating 148 online ChIP-seq samples. Sixty-seven percent of predicted regulatory sequences have reproducible heart-specific enhancer activity in vivo. Human heart-specific enhancer wf1 regulates the CHD-related FBN1 gene.
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Affiliation(s)
- Feng Wang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.,Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yawen Zhang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.,Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Fang Wu
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.,Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yiting Gui
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.,Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Xudong Chen
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Youhua Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Xu Wang
- Cancer Metabolism Laboratory, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yonghao Gui
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Key Laboratory of Birth Defects Prevention and Control, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
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15
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Spurrell CH, Barozzi I, Kosicki M, Mannion BJ, Blow MJ, Fukuda-Yuzawa Y, Slaven N, Afzal SY, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Lee EA, Garvin TH, Pham QT, Kronshage AN, Lisgo S, Bristow J, Cappola TP, Morley MP, Margulies KB, Pennacchio LA, Dickel DE, Visel A. Genome-wide fetalization of enhancer architecture in heart disease. Cell Rep 2022; 40:111400. [PMID: 36130500 PMCID: PMC9534044 DOI: 10.1016/j.celrep.2022.111400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart. However, the impact of this reactivation on the regulatory landscape in heart disease is unclear. Here, we use RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from up to 26 healthy controls, 18 individuals with idiopathic dilated cardiomyopathy (DCM), and five fetal hearts. Healthy individuals have a highly reproducible epigenomic landscape, consisting of more than 33,000 predicted heart enhancers. In contrast, we observe reproducible disease-associated changes in activity at 6,850 predicted heart enhancers. Combined analysis of adult and fetal samples reveals that the heart disease epigenome and transcriptome both acquire fetal-like characteristics, with 3,400 individual enhancers sharing fetal regulatory properties. We also provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of DCM etiology.
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Affiliation(s)
- Cailyn H Spurrell
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Neil Slaven
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah Y Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elizabeth A Lee
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan T Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Kronshage
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - James Bristow
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas P Cappola
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael P Morley
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kenneth B Margulies
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA.
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16
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Bennett JS, Gordon DM, Majumdar U, Lawrence PJ, Matos-Nieves A, Myers K, Kamp AN, Leonard JC, McBride KL, White P, Garg V. Use of machine learning to classify high-risk variants of uncertain significance in lamin A/C cardiac disease. Heart Rhythm 2022; 19:676-685. [PMID: 34958940 PMCID: PMC10082443 DOI: 10.1016/j.hrthm.2021.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Variation in lamin A/C results in a spectrum of clinical disease, including arrhythmias and cardiomyopathy. Benign variation is rare, and classification of LMNA missense variants via in silico prediction tools results in a high rate of variants of uncertain significance (VUSs). OBJECTIVE The goal of this study was to use a machine learning (ML) approach for in silico prediction of LMNA pathogenic variation. METHODS Genetic sequencing was performed on family members with conduction system disease, and patient cell lines were examined for LMNA expression. In silico predictions of conservation and pathogenicity of published LMNA variants were visualized with uniform manifold approximation and projection. K-means clustering was used to identify variant groups with similarly projected scores, allowing the generation of statistically supported risk categories. RESULTS We discovered a novel LMNA variant (c.408C>A:p.Asp136Glu) segregating with conduction system disease in a multigeneration pedigree, which was reported as a VUS by a commercial testing company. Additional familial analysis and in vitro testing found it to be pathogenic, which prompted the development of an ML algorithm that used in silico predictions of pathogenicity for known LMNA missense variants. This identified 3 clusters of variation, each with a significantly different incidence of known pathogenic variants (38.8%, 15.0%, and 6.1%). Three hundred thirty-nine of 415 head/rod domain variants (81.7%), including p.Asp136Glu, were in clusters with highest proportions of pathogenic variants. CONCLUSION An unsupervised ML method successfully identified clusters enriched for pathogenic LMNA variants including a novel variant associated with conduction system disease. Our ML method may assist in identifying high-risk VUS when familial testing is unavailable.
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Affiliation(s)
- Jeffrey S Bennett
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - David M Gordon
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Uddalak Majumdar
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio
| | - Patrick J Lawrence
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Adrianna Matos-Nieves
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio
| | - Katherine Myers
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio
| | - Anna N Kamp
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Julie C Leonard
- Department of Pediatrics, Ohio State University, Columbus, Ohio; Center for Injury Research and Policy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio
| | - Kim L McBride
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Peter White
- Department of Pediatrics, Ohio State University, Columbus, Ohio; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Vidu Garg
- Center for Cardiovascular Research and Heart Center, Nationwide Children's Hospital, Columbus, Ohio; Department of Pediatrics, Ohio State University, Columbus, Ohio; Department of Molecular Genetics, Ohio State University, Columbus, Ohio.
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17
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Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Yue MCS, Sung WWL, Thiruvahindrapuram B, Lougheed J, Oechslin E, Mondal T, Bergin L, Smythe J, Jayappa S, Rao VJ, Shenthar J, Dhandapany PS, Semsarian C, Weintraub RG, Bagnall RD, Ingles J, Melé M, Maass PG, Ellis J, Scherer SW, Mital S. Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genom Med 2022; 7:18. [PMID: 35288587 PMCID: PMC8921194 DOI: 10.1038/s41525-022-00288-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.
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Affiliation(s)
- Robert Lesurf
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Abdelrahman Said
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Oyediran Akinrinade
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- St. George's University School of Medicine, Grenada, Grenada
| | | | - Kathleen Delfosse
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ting Liu
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roderick Yao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabrielle Persad
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Fintan McKenna
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ramil R Noche
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Zebrafish Genetics and Disease Models Core, The Hospital for Sick Children, Toronto, ON, Canada
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shreya Shah
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anastasia Miron
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qian Yang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Erwin Oechslin
- Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Tapas Mondal
- Department of Pediatrics, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Lynn Bergin
- Division of Cardiology, London Health Sciences Centre, London, ON, Canada
| | - John Smythe
- Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Robert G Weintraub
- Cardiology Department, Royal Children's Hospital, Melbourne, Australia
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard D Bagnall
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Philipp G Maass
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada.
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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18
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Nim HT, Dang L, Thiyagarajah H, Bakopoulos D, See M, Charitakis N, Sibbritt T, Eichenlaub MP, Archer SK, Fossat N, Burke RE, Tam PPL, Warr CG, Johnson TK, Ramialison M. A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biol 2021; 22:335. [PMID: 34906219 PMCID: PMC8672579 DOI: 10.1186/s13059-021-02539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
| | - Louis Dang
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Harshini Thiyagarajah
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Daniel Bakopoulos
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Michael See
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Natalie Charitakis
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Michael P. Eichenlaub
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Nicolas Fossat
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
- Present address: Copenhagen Hepatitis C Program, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Present address: Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Richard E. Burke
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Coral G. Warr
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
- School of Molecular Sciences, La Trobe University, Bundoora, Victoria 3083 Australia
| | - Travis K. Johnson
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
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19
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Laber S, Forcisi S, Bentley L, Petzold J, Moritz F, Smirnov KS, Al Sadat L, Williamson I, Strobel S, Agnew T, Sengupta S, Nicol T, Grallert H, Heier M, Honecker J, Mianne J, Teboul L, Dumbell R, Long H, Simon M, Lindgren C, Bickmore WA, Hauner H, Schmitt-Kopplin P, Claussnitzer M, Cox RD. Linking the FTO obesity rs1421085 variant circuitry to cellular, metabolic, and organismal phenotypes in vivo. SCIENCE ADVANCES 2021; 7:eabg0108. [PMID: 34290091 PMCID: PMC8294759 DOI: 10.1126/sciadv.abg0108] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/04/2021] [Indexed: 05/09/2023]
Abstract
Variants in FTO have the strongest association with obesity; however, it is still unclear how those noncoding variants mechanistically affect whole-body physiology. We engineered a deletion of the rs1421085 conserved cis-regulatory module (CRM) in mice and confirmed in vivo that the CRM modulates Irx3 and Irx5 gene expression and mitochondrial function in adipocytes. The CRM affects molecular and cellular phenotypes in an adipose depot-dependent manner and affects organismal phenotypes that are relevant for obesity, including decreased high-fat diet-induced weight gain, decreased whole-body fat mass, and decreased skin fat thickness. Last, we connected the CRM to a genetically determined effect on steroid patterns in males that was dependent on nutritional challenge and conserved across mice and humans. Together, our data establish cross-species conservation of the rs1421085 regulatory circuitry at the molecular, cellular, metabolic, and organismal level, revealing previously unknown contextual dependence of the variant's action.
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Affiliation(s)
- Samantha Laber
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Liz Bentley
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Julia Petzold
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Franco Moritz
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kirill S Smirnov
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Loubna Al Sadat
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Sophie Strobel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Thomas Agnew
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Shahana Sengupta
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Tom Nicol
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Center Munich, Germany
| | - Margit Heier
- KORA Study Center Augsburg, University Hospital of Augsburg, Augsburg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, Munich, Germany
| | - Julius Honecker
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Joffrey Mianne
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Rebecca Dumbell
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Helen Long
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
- Nuffield Department of Medicine, University of Oxford, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Michelle Simon
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK
| | - Cecilia Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Hans Hauner
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Analytical Food Chemistry, Technical University of Munich, Freising, Germany
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Institute for Aging Research, Hebrew SeniorLife and Harvard Medical School, Boston, MA, USA
| | - Roger D Cox
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.
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20
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Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, Ren B, Chi NC, Preissl S. Cardiac cell type-specific gene regulatory programs and disease risk association. SCIENCE ADVANCES 2021; 7:eabf1444. [PMID: 33990324 PMCID: PMC8121433 DOI: 10.1126/sciadv.abf1444] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/25/2021] [Indexed: 05/07/2023]
Abstract
Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.
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Affiliation(s)
- James D Hocker
- Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Fugui Zhu
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Tsui-Min Wang
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingquan Zhang
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Elie N Farah
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Andrew D McCulloch
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
- Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
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21
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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22
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Gacita AM, Fullenkamp DE, Ohiri J, Pottinger T, Puckelwartz MJ, Nobrega MA, McNally EM. Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression. Circulation 2021; 143:1302-1316. [PMID: 33478249 PMCID: PMC8009836 DOI: 10.1161/circulationaha.120.050432] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Inherited cardiomyopathy associates with a range of phenotypes, mediated by genetic and nongenetic factors. Noninherited cardiomyopathy also displays varying progression and outcomes. Expression of cardiomyopathy genes is under the regulatory control of promoters and enhancers, and human genetic variation in promoters and enhancers may contribute to this variability. METHODS We superimposed epigenomic profiling from hearts and cardiomyocytes, including promoter-capture chromatin conformation information, to identify enhancers for 2 cardiomyopathy genes, MYH7 and LMNA. Enhancer function was validated in human cardiomyocytes derived from induced pluripotent stem cells. We also conducted a genome-wide search to ascertain genomic variation in enhancers positioned to alter cardiac expression and correlated one of these variants to cardiomyopathy progression using biobank data. RESULTS Multiple enhancers were identified and validated for LMNA and MYH7, including a key enhancer that regulates the switch from MYH6 expression to MYH7 expression. Deletion of this enhancer resulted in a dose-dependent increase in MYH6 and faster contractile rate in engineered heart tissues. We searched for genomic variation in enhancer sequences across the genome, with a focus on nucleotide changes that create or interrupt transcription factor binding sites. The sequence variant, rs875908, disrupts a T-Box Transcription Factor 5 binding motif and maps to an enhancer region 2 kilobases from the transcriptional start site of MYH7. Gene editing to remove the enhancer that harbors this variant markedly reduced MYH7 expression in human cardiomyocytes. Using biobank-derived data, rs875908 associated with longitudinal echocardiographic features of cardiomyopathy. CONCLUSIONS Enhancers regulate cardiomyopathy gene expression, and genomic variation within these enhancer regions associates with cardiomyopathic progression over time. This integrated approach identified noncoding modifiers of cardiomyopathy and is applicable to other cardiac genes.
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Affiliation(s)
- Anthony M. Gacita
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Dominic E. Fullenkamp
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Joyce Ohiri
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Tess Pottinger
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
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23
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Transcriptional Regulation of Postnatal Cardiomyocyte Maturation and Regeneration. Int J Mol Sci 2021; 22:ijms22063288. [PMID: 33807107 PMCID: PMC8004589 DOI: 10.3390/ijms22063288] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
During the postnatal period, mammalian cardiomyocytes undergo numerous maturational changes associated with increased cardiac function and output, including hypertrophic growth, cell cycle exit, sarcomeric protein isoform switching, and mitochondrial maturation. These changes come at the expense of loss of regenerative capacity of the heart, contributing to heart failure after cardiac injury in adults. While most studies focus on the transcriptional regulation of embryonic or adult cardiomyocytes, the transcriptional changes that occur during the postnatal period are relatively unknown. In this review, we focus on the transcriptional regulators responsible for these aspects of cardiomyocyte maturation during the postnatal period in mammals. By specifically highlighting this transitional period, we draw attention to critical processes in cardiomyocyte maturation with potential therapeutic implications in cardiovascular disease.
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24
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Feng Y, Xu H, Liu J, Xie N, Gao L, He Y, Yao Y, Lv F, Zhang Y, Lu J, Zhang W, Li CY, Hu X, Yang Z, Xiao RP. Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates. Mol Biol Evol 2021; 38:2930-2945. [PMID: 33744959 PMCID: PMC8233513 DOI: 10.1093/molbev/msab083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cis-regulatory elements play important roles in tissue-specific gene expression and in the evolution of various phenotypes, and mutations in promoters and enhancers may be responsible for adaptations of species to environments. TRIM72 is a highly conserved protein that is involved in energy metabolism. Its expression in the heart varies considerably in primates, with high levels of expression in Old World monkeys and near absence in hominids. Here, we combine phylogenetic hypothesis testing and experimentation to demonstrate that mutations in promoter are responsible for the differences among primate species in the heart-specific expression of TRIM72. Maximum likelihood estimates of lineage-specific substitution rates under local-clock models show that relative to the evolutionary rate of introns, the rate of promoter was accelerated by 78% in the common ancestor of Old World monkeys, suggesting a role for positive selection in the evolution of the TRIM72 promoter, possibly driven by selective pressure due to changes in cardiac physiology after species divergence. We demonstrate that mutations in the TRIM72 promoter account for the differential myocardial TRIM72 expression of the human and the rhesus macaque. Furthermore, changes in TRIM72 expression alter the expression of genes involved in oxidative phosphorylation, which in turn affects mitochondrial respiration and cardiac energy capacity. On a broader timescale, phylogenetic regression analyses of data from 29 mammalian species show that mammals with high cardiac expression of TRIM72 have high heart rate, suggesting that the expression changes of TRIM72 may be related to differences in the heart physiology of those species.
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Affiliation(s)
- Yuanqing Feng
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Hongzhan Xu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jinghao Liu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ning Xie
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lei Gao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanyun He
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yuan Yao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fengxiang Lv
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yan Zhang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian Lu
- Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Gene Research, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Wei Zhang
- Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Protein and Plant Gene Research, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Chuan-Yun Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinli Hu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Rui-Ping Xiao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Biomembrane and Membrane Biotechnology, Beijing, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
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25
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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26
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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: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [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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27
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Mulvey B, Lagunas T, Dougherty JD. Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts. Biol Psychiatry 2021; 89:76-89. [PMID: 32843144 PMCID: PMC7938388 DOI: 10.1016/j.biopsych.2020.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/18/2022]
Abstract
Neuropsychiatric phenotypes have long been known to be influenced by heritable risk factors, directly confirmed by the past decade of genetic studies that have revealed specific genetic variants enriched in disease cohorts. However, the initial hope that a small set of genes would be responsible for a given disorder proved false. The more complex reality is that a given disorder may be influenced by myriad small-effect noncoding variants and/or by rare but severe coding variants, many de novo. Noncoding genomic sequences-for which molecular functions cannot usually be inferred-harbor a large portion of these variants, creating a substantial barrier to understanding higher-order molecular and biological systems of disease. Fortunately, novel genetic technologies-scalable oligonucleotide synthesis, RNA sequencing, and CRISPR (clustered regularly interspaced short palindromic repeats)-have opened novel avenues to experimentally identify biologically significant variants en masse. Massively parallel reporter assays (MPRAs) are an especially versatile technique resulting from such innovations. MPRAs are powerful molecular genetics tools that can be used to screen thousands of untranscribed or untranslated sequences and their variants for functional effects in a single experiment. This approach, though underutilized in psychiatric genetics, has several useful features for the field. We review methods for assaying putatively functional genetic variants and regions, emphasizing MPRAs and the opportunities they hold for dissection of psychiatric polygenicity. We discuss literature applying functional assays in neurogenetics, highlighting strengths, caveats, and design considerations-especially regarding disease-relevant variables (cell type, neurodevelopment, and sex), and we ultimately propose applications of MPRA to both computational and experimental neurogenetics of polygenic disease risk.
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Affiliation(s)
- Bernard Mulvey
- Division of Biology and Biomedical Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Tomás Lagunas
- Division of Biology and Biomedical Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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28
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van Eif VW, Protze S, Bosada FM, Yuan X, Sinha T, van Duijvenboden K, Ernault AC, Mohan RA, Wakker V, de Gier-de Vries C, Hooijkaas IB, Wilson MD, Verkerk AO, Bakkers J, Boukens BJ, Black BL, Scott IC, Christoffels VM. Genome-Wide Analysis Identifies an Essential Human TBX3 Pacemaker Enhancer. Circ Res 2020; 127:1522-1535. [PMID: 33040635 PMCID: PMC8153223 DOI: 10.1161/circresaha.120.317054] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
RATIONALE The development and function of the pacemaker cardiomyocytes of the sinoatrial node (SAN), the leading pacemaker of the heart, are tightly controlled by a conserved network of transcription factors, including TBX3 (T-box transcription factor 3), ISL1 (ISL LIM homeobox 1), and SHOX2 (short stature homeobox 2). Yet, the regulatory DNA elements (REs) controlling target gene expression in the SAN pacemaker cells have remained undefined. OBJECTIVE Identification of the regulatory landscape of human SAN-like pacemaker cells and functional assessment of SAN-specific REs potentially involved in pacemaker cell gene regulation. METHODS AND RESULTS We performed Assay for Transposase-Accessible Chromatin using sequencing on human pluripotent stem cell-derived SAN-like pacemaker cells and ventricle-like cells and identified thousands of putative REs specific for either human cell type. We validated pacemaker cell-specific elements in the SHOX2 and TBX3 loci. CRISPR-mediated homozygous deletion of the mouse ortholog of a noncoding region with candidate pacemaker-specific REs in the SHOX2 locus resulted in selective loss of Shox2 expression from the developing SAN and embryonic lethality. Putative pacemaker-specific REs were identified up to 1 Mbp upstream of TBX3 in a region close to MED13L harboring variants associated with heart rate recovery after exercise. The orthologous region was deleted in mice, which resulted in selective loss of expression of Tbx3 from the SAN and (cardiac) ganglia and in neonatal lethality. Expression of Tbx3 was maintained in other tissues including the atrioventricular conduction system, lungs, and liver. Heterozygous adult mice showed increased SAN recovery times after pacing. The human REs harboring the associated variants robustly drove expression in the SAN of transgenic mouse embryos. CONCLUSIONS We provided a genome-wide collection of candidate human pacemaker-specific REs, including the loci of SHOX2, TBX3, and ISL1, and identified a link between human genetic variants influencing heart rate recovery after exercise and a variant RE with highly conserved function, driving SAN expression of TBX3.
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Affiliation(s)
- Vincent W.W. van Eif
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Stephanie Protze
- McEwen Stem Cell Institute, University Health Network and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Fernanda M. Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Xuefei Yuan
- The Hospital for Sick Children; and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Canada
| | - Tanvi Sinha
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, United States
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Auriane C. Ernault
- Department of Experimental Cardiology, University of Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Aix-Marseille Université, INSERM, MMG - U1251, Marseille, France
| | - Rajiv A. Mohan
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Corrie de Gier-de Vries
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ingeborg B. Hooijkaas
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael D. Wilson
- The Hospital for Sick Children; and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Canada
| | - Arie O. Verkerk
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Cardiology, University of Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute and University Medical Center Utrecht, 3584 CT Utrecht, Netherlands
| | - Bastiaan J. Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Cardiology, University of Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Brian L. Black
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California, San Francisco, United States
| | - Ian C. Scott
- The Hospital for Sick Children; and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Canada
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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29
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Hall AW, Chaffin M, Roselli C, Lin H, Lubitz SA, Bianchi V, Geeven G, Bedi K, Margulies KB, de Laat W, Tucker NR, Ellinor PT. Epigenetic Analyses of Human Left Atrial Tissue Identifies Gene Networks Underlying Atrial Fibrillation. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2020; 13:e003085. [PMID: 33155827 PMCID: PMC8240092 DOI: 10.1161/circgen.120.003085] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Atrial fibrillation (AF) often arises from structural abnormalities in the left atria (LA). Annotation of the noncoding genome in human LA is limited, as are effects on gene expression and chromatin architecture. Many AF-associated genetic variants reside in noncoding regions; this knowledge gap impairs efforts to understand the molecular mechanisms of AF and cardiac conduction phenotypes. METHODS We generated a model of the LA noncoding genome by profiling 7 histone post-translational modifications (active: H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K36me3; repressive: H3K27me3, H3K9me3), CTCF binding, and gene expression in samples from 5 individuals without structural heart disease or AF. We used MACS2 to identify peak regions (P<0.01), applied a Markov model to classify regulatory elements, and annotated this model with matched gene expression data. We intersected chromatin states with expression quantitative trait locus, DNA methylation, and HiC chromatin interaction data from LA and left ventricle. Finally, we integrated genome-wide association data for AF and electrocardiographic traits to link disease-related variants to genes. RESULTS Our model identified 21 epigenetic states, encompassing regulatory motifs, such as promoters, enhancers, and repressed regions. Genes were regulated by proximal chromatin states; repressive states were associated with a significant reduction in gene expression (P<2×10-16). Chromatin states were differentially methylated, promoters were less methylated than repressed regions (P<2×10-16). We identified over 15 000 LA-specific enhancers, defined by homeobox family motifs, and annotated several cardiovascular disease susceptibility loci. Intersecting AF and PR genome-wide association studies loci with long-range chromatin conformation data identified a gene interaction network dominated by NKX2-5, TBX3, ZFHX3, and SYNPO2L. CONCLUSIONS Profiling the noncoding genome provides new insights into the gene expression and chromatin regulation in human LA tissue. These findings enabled identification of a gene network underlying AF; our experimental and analytic approach can be extended to identify molecular mechanisms for other cardiac diseases and traits.
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Affiliation(s)
- Amelia Weber Hall
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Mark Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Steven A. Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Geert Geeven
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kenneth Bedi
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kenneth B. Margulies
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nathan R. Tucker
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
- Masonic Medical Research Institute, Utica, NY
| | - Patrick T. Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge, MA
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30
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Abstract
RATIONALE There is growing evidence that common variants and rare sequence alterations in regulatory sequences can result in birth defects or predisposition to disease. Congenital heart defects are the most common birth defect and have a clear genetic component, yet only a third of cases can be attributed to structural variation in the genome or a mutation in a gene. The remaining unknown cases could be caused by alterations in regulatory sequences. OBJECTIVE Identify regulatory sequences and gene expression networks that are active during organogenesis of the human heart. Determine whether these sites and networks are enriched for disease-relevant genes and associated genetic variation. METHODS AND RESULTS We characterized ChromHMM (chromatin state) and gene expression dynamics during human heart organogenesis. We profiled 7 histone modifications in embryonic hearts from each of 9 distinct Carnegie stages (13-14, 16-21, and 23), annotated chromatin states, and compared these maps to over 100 human tissues and cell types. We also generated RNA-sequencing data, performed differential expression, and constructed weighted gene coexpression networks. We identified 177 412 heart enhancers; 12 395 had not been previously annotated as strong enhancers. We identified 92% of all functionally validated heart-positive enhancers (n=281; 7.5× enrichment; P<2.2×10-16). Integration of these data demonstrated novel heart enhancers are enriched near genes expressed more strongly in cardiac tissue and are enriched for variants associated with ECG measures and atrial fibrillation. Our gene expression network analysis identified gene modules strongly enriched for heart-related functions, regulatory control by heart-specific enhancers, and putative disease genes. CONCLUSIONS Well-connected hub genes with heart-specific expression targeted by embryonic heart-specific enhancers are likely disease candidates. Our functional annotations will allow for better interpretation of whole genome sequencing data in the large number of patients affected by congenital heart defects.
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Affiliation(s)
- Jennifer VanOudenhove
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
| | - Tara N. Yankee
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Andrea Wilderman
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Justin Cotney
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Institute for Systems Genomics, UConn, Storrs CT, USA
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31
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Gacita AM, Dellefave-Castillo L, Page PGT, Barefield DY, Wasserstrom JA, Puckelwartz MJ, Nobrega MA, McNally EM. Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart. Circ Heart Fail 2020; 13:e006926. [PMID: 32993371 PMCID: PMC7577963 DOI: 10.1161/circheartfailure.120.006926] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND The failing heart is characterized by changes in gene expression. However, the regulatory regions of the genome that drive these gene expression changes have not been well defined in human hearts. METHODS To define genome-wide enhancer and promoter use in heart failure, cap analysis of gene expression sequencing was applied to 3 healthy and 4 failed human hearts to identify promoter and enhancer regions used in left ventricles. Healthy hearts were derived from donors unused for transplantation and failed hearts were obtained as discarded tissue after transplantation. RESULTS Cap analysis of gene expression sequencing identified a combined potential for ≈23 000 promoters and ≈5000 enhancers active in human left ventricles. Of these, 17 000 promoters and 1800 enhancers had additional support for their regulatory function. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered aminoterminal protein sequences. Enhancer usage between healthy and failed hearts identified a majority of differentially used heart failure enhancers were intronic and primarily localized within the first intron, revealing this position as a common feature associated with tissue-specific gene expression changes in the heart. CONCLUSIONS This data set defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction. Additionally, regulatory changes contributing to heart failure are attractive therapeutic targets for controlling ventricular remodeling and clinical progression.
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Affiliation(s)
- Anthony M Gacita
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Patrick G T Page
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - David Y Barefield
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - J Andrew Wasserstrom
- Department of Medicine (Cardiology) (J.A.W.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Megan J Puckelwartz
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | | | - Elizabeth M McNally
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
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32
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Salamon I, Serio S, Bianco S, Pagiatakis C, Crasto S, Chiariello AM, Conte M, Cattaneo P, Fiorillo L, Felicetta A, di Pasquale E, Kunderfranco P, Nicodemi M, Papait R, Condorelli G. Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions. iScience 2020; 23:101539. [PMID: 33083767 PMCID: PMC7509214 DOI: 10.1016/j.isci.2020.101539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/09/2020] [Accepted: 09/03/2020] [Indexed: 01/12/2023] Open
Abstract
Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5—a gene specifying a master cardiomyogenic lineage transcription factor (TF)—which we call Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs). The IRENEs are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5: IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. Two eRNAs (IRENE-SS, IRENE-div) with opposing functions are found upstream of Nkx2-5 IRENE-SS works as a classical eRNA, acting as a transcriptional activator IRENE-div acts unconventionally, functioning as a transcriptional repressor IRENEs epigenetically control enhancer status and, subsequently, locus architecture
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Affiliation(s)
- Irene Salamon
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy
| | - Simone Serio
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele (MI), Italy
| | - Simona Bianco
- Department of Physics, Federico II University, 80126 Naples, Italy
| | | | - Silvia Crasto
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, 20189 Rozzano (MI), Italy
| | | | - Mattia Conte
- Department of Physics, Federico II University, 80126 Naples, Italy
| | - Paola Cattaneo
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, 20189 Rozzano (MI), Italy
| | - Luca Fiorillo
- Department of Physics, Federico II University, 80126 Naples, Italy
| | - Arianna Felicetta
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele (MI), Italy
| | - Elisa di Pasquale
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, 20189 Rozzano (MI), Italy
| | | | - Mario Nicodemi
- Department of Physics, Federico II University, 80126 Naples, Italy.,Berlin Institute of Health, Max Delbrück Center, 13125 Berlin, Germany
| | - Roberto Papait
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Gianluigi Condorelli
- Humanitas Clinical and Research Center-IRCCS, 20189 Rozzano (MI), Italy.,Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele (MI), Italy.,Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, 20189 Rozzano (MI), Italy
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33
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Conjugated activation of myocardial-specific transcription of Gja5 by a pair of Nkx2-5-Shox2 co-responsive elements. Dev Biol 2020; 465:79-87. [PMID: 32687896 DOI: 10.1016/j.ydbio.2020.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
The sinoatrial node (SAN) is the primary pacemaker in the heart. During cardiogenesis, Shox2 and Nkx2-5 are co-expressed in the junction domain of the SAN and regulate pacemaker cell fate through a Shox2-Nkx2-5 antagonism. Cx40 is a marker of working myocardium and an Nkx2-5 transcriptional output antagonized by Shox2, but the underlying regulatory mechanisms remain elusive. Here we characterized a bona fide myocardial-specific Gja5 (coding gene of Cx40) distal enhancer consisting of a pair of Nkx2-5 and Shox2 co-bound elements in the regulatory region of Gja5. Transgenic reporter assays revealed that neither element alone, but the conjugation of both elements together, drives myocardial-specific transcription. Genetic analyses confirmed that the activation of this enhancer depends on Nkx2-5 but is inhibited by Shox2 in vivo, and its presence is essential for Gja5 expression in the myocardium but not the endothelial cells of the heart. Furthermore, chromatin conformation analysis showed an Nkx2-5-dependent loop formation between these two elements and the Gja5 promoter in vivo, indicating that Nkx2-5 bridges the conjugated activation of this enhancer by pairing the two elements to the Gja5 promoter.
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34
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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] [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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35
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Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet 2020; 52:769-777. [PMID: 32601476 PMCID: PMC7415662 DOI: 10.1038/s41588-020-0652-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.
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Affiliation(s)
- Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander Kitaygorodsky
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongjian Qi
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Center for External Innovation, Takeda Pharmaceuticals USA, Cambridge, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kathryn B Manheimer
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Matthew Velinder
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD, USA
| | | | | | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martina Brueckner
- Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Kim
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California San Francisco, San Francisco, CA, USA
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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36
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Akerberg BN, Pu WT. Genetic and Epigenetic Control of Heart Development. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036756. [PMID: 31818853 DOI: 10.1101/cshperspect.a036756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A transcriptional program implemented by transcription factors and epigenetic regulators governs cardiac development and disease. Mutations in these factors are important causes of congenital heart disease. Here, we review selected recent advances in our understanding of the transcriptional and epigenetic control of heart development, including determinants of cardiac transcription factor chromatin occupancy, the gene regulatory network that regulates atrial septation, the chromatin landscape and cardiac gene regulation, and the role of Brg/Brahma-associated factor (BAF), nucleosome remodeling and histone deacetylation (NuRD), and Polycomb epigenetic regulatory complexes in heart development.
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Affiliation(s)
- Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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37
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Villar D, Frost S, Deloukas P, Tinker A. The contribution of non-coding regulatory elements to cardiovascular disease. Open Biol 2020; 10:200088. [PMID: 32603637 PMCID: PMC7574544 DOI: 10.1098/rsob.200088] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular disease collectively accounts for a quarter of deaths worldwide. Genome-wide association studies across a range of cardiovascular traits and pathologies have highlighted the prevalence of common non-coding genetic variants within candidate loci. Here, we review genetic, epigenomic and molecular approaches to investigate the contribution of non-coding regulatory elements in cardiovascular biology. We then discuss recent insights on the emerging role of non-coding variation in predisposition to cardiovascular disease, with a focus on novel mechanistic examples from functional genomics studies. Lastly, we consider the clinical significance of these findings at present, and some of the current challenges facing the field.
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Affiliation(s)
- Diego Villar
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Stephanie Frost
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Panos Deloukas
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Andrew Tinker
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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38
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Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, Morton SU, DePalma S, Gorham J, Kitaygorodksy A, Porter GA, Giardini A, Shen Y, Chung WK, Seidman JG, Seidman CE, Schadt EE, Gelb BD. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics 2020; 35:3906-3912. [PMID: 30903145 DOI: 10.1093/bioinformatics/btz202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 01/13/2019] [Accepted: 03/20/2019] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying outlier definitions were employed and no comprehensive open-source software was developed. RESULTS We developed Outlier-RV Enrichment (ORE) to identify biologically-meaningful non-coding RVs. We implemented ORE combining whole-genome sequencing and cardiac RNAseq from congenital heart defect patients from the Pediatric Cardiac Genomics Consortium and deceased adults from Genotype-Tissue Expression. Use of rank-based outliers maximized sensitivity while a most extreme outlier approach maximized specificity. Rarer variants had stronger associations, suggesting they are under negative selective pressure and providing a basis for investigating their contribution to Mendelian disorders. AVAILABILITY AND IMPLEMENTATION ORE, source code, and documentation are available at https://pypi.python.org/pypi/ore under the MIT license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- F Richter
- Graduate School of Biomedical Sciences
| | - G E Hoffman
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - N Patel
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D McKean
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S U Morton
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S DePalma
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - J Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - A Kitaygorodksy
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - G A Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - A Giardini
- Cardiorespiratory Unit, Great Ormond Street Hospital and University College London, London, UK
| | - Y Shen
- Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - W K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - E E Schadt
- Icahn Institute for Genomics and Multiscale Biology.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, A Mount Sinai Venture, Stamford, CT, USA
| | - B D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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39
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van Ouwerkerk AF, Hall AW, Kadow ZA, Lazarevic S, Reyat JS, Tucker NR, Nadadur RD, Bosada FM, Bianchi V, Ellinor PT, Fabritz L, Martin J, de Laat W, Kirchhof P, Moskowitz I, Christoffels VM. Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation. Circ Res 2020; 127:34-50. [PMID: 32717170 PMCID: PMC8315291 DOI: 10.1161/circresaha.120.316574] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies have uncovered over a 100 genetic loci associated with atrial fibrillation (AF), the most common arrhythmia. Many of the top AF-associated loci harbor key cardiac transcription factors, including PITX2, TBX5, PRRX1, and ZFHX3. Moreover, the vast majority of the AF-associated variants lie within noncoding regions of the genome where causal variants affect gene expression by altering the activity of transcription factors and the epigenetic state of chromatin. In this review, we discuss a transcriptional regulatory network model for AF defined by effector genes in Genome-wide association studies loci. We describe the current state of the field regarding the identification and function of AF-relevant gene regulatory networks, including variant regulatory elements, dose-sensitive transcription factor functionality, target genes, and epigenetic states. We illustrate how altered transcriptional networks may impact cardiomyocyte function and ionic currents that impact AF risk. Last, we identify the need for improved tools to identify and functionally test transcriptional components to define the links between genetic variation, epigenetic gene regulation, and atrial function.
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Affiliation(s)
- Antoinette F. van Ouwerkerk
- Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Amelia W. Hall
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zachary A. Kadow
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sonja Lazarevic
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Jasmeet S. Reyat
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
| | - Nathan R. Tucker
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Masonic Medical Research Institute, Utica, NY, USA
| | - Rangarajan D. Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Fernanda M. Bosada
- Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick T. Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Larissa Fabritz
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- SWBH and UHB NHS Trusts, Birmingham, UK
| | - Jim Martin
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030
- Texas Heart Institute, Houston, Texas, 77030
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paulus Kirchhof
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- SWBH and UHB NHS Trusts, Birmingham, UK
- University Heart and Vascular Center Hamburg, Hamburg, Germany
| | - Ivan Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
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40
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Abstract
Pathological cardiac remodeling is induced through multiple mechanisms that include neurohumoral and biomechanical stress resulting in transcriptional alterations that ultimately become maladaptive and lead to the development of heart failure (HF). Although cardiac transcriptional remodeling is mediated by the activation of numerous signaling pathways that converge on a limited number of transcription factors (TFs) that promote hypertrophy (pro-hypertrophic TFs), the current therapeutic approach to prevent HF utilizes pharmacological inhibitors that largely target specific receptors that are activated in response to pathological stimuli. Thus, there is limited efficacy with the current pharmacological approaches to inhibit transcriptional remodeling associated with the development of HF. Recent evidence suggests that these pro-hypertrophic TFs co-localize at enhancers to cooperatively activate transcription associated with pathological cardiac remodeling. In disease states, including cancer and HF, evidence suggests that the general transcriptional machinery is disproportionately bound at enhancers. Therefore, pharmacological inhibition of transcriptional machinery that integrates pro-hypertrophic TFs may represent a promising alternative therapeutic approach to limit pathological remodeling associated with the development of HF.
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41
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Man JCK, Mohan RA, Boogaard MVD, Hilvering CRE, Jenkins C, Wakker V, Bianchi V, Laat WD, Barnett P, Boukens BJ, Christoffels VM. An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo. Nat Commun 2019; 10:4943. [PMID: 31666509 PMCID: PMC6821807 DOI: 10.1038/s41467-019-12856-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 10/03/2019] [Indexed: 12/19/2022] Open
Abstract
Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia disorders. Here, we identify an evolutionary conserved regulatory cluster with super enhancer characteristics downstream of SCN5A, which drives localized cardiac expression and contains conduction velocity-associated variants. We use genome editing to create a series of deletions in the mouse genome and show that the enhancer cluster controls the conformation of a >0.5 Mb genomic region harboring multiple interacting gene promoters and enhancers. We find that this cluster and its individual components are selectively required for cardiac Scn5a expression, normal cardiac conduction and normal embryonic development. Our studies reveal physiological roles of an enhancer cluster in the SCN5A-SCN10A locus, show that it controls the chromatin architecture of the locus and Scn5a expression, and suggest that genetic variants affecting its activity may influence cardiac function.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Rajiv A Mohan
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Malou van den Boogaard
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Catharina R E Hilvering
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catherine Jenkins
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands.
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42
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Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep 2019; 23:1581-1597. [PMID: 29719267 PMCID: PMC5965702 DOI: 10.1016/j.celrep.2018.03.129] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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Affiliation(s)
- Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | | | - Jeffrey Kron
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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43
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Vervier K, Michaelson JJ. TiSAn: estimating tissue-specific effects of coding and non-coding variants. Bioinformatics 2019; 34:3061-3068. [PMID: 29912365 PMCID: PMC6137979 DOI: 10.1093/bioinformatics/bty301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Motivation Model-based estimates of general deleteriousness, like CADD, DANN or PolyPhen, have become indispensable tools in the interpretation of genetic variants. However, these approaches say little about the tissues in which the effects of deleterious variants will be most meaningful. Tissue-specific annotations have been recently inferred for dozens of tissues/cell types from large collections of cross-tissue epigenomic data, and have demonstrated sensitivity in predicting affected tissues in complex traits. It remains unclear, however, whether including additional genome-scale data specific to the tissue of interest would appreciably improve functional annotations. Results Herein, we introduce TiSAn, a tool that integrates multiple genome-scale data sources, defined by expert knowledge. TiSAn uses machine learning to discriminate variants relevant to a tissue from those with no bearing on the function of that tissue. Predictions are made genome-wide, and can be used to contextualize and filter variants of interest in whole genome sequencing or genome-wide association studies. We demonstrate the accuracy and flexibility of TiSAn by producing predictive models for human heart and brain, and detecting tissue-relevant variations in large cohorts for autism spectrum disorder (TiSAn-brain) and coronary artery disease (TiSAn-heart). We find the multiomics TiSAn model is better able to prioritize genetic variants according to their tissue-specific action than the current state-of-the-art method, GenoSkyLine. Availability and implementation Software and vignettes are available at http://github.com/kevinVervier/TiSAn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kévin Vervier
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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44
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Hoff K, Lemme M, Kahlert AK, Runde K, Audain E, Schuster D, Scheewe J, Attmann T, Pickardt T, Caliebe A, Siebert R, Kramer HH, Milting H, Hansen A, Ammerpohl O, Hitz MP. DNA methylation profiling allows for characterization of atrial and ventricular cardiac tissues and hiPSC-CMs. Clin Epigenetics 2019; 11:89. [PMID: 31186048 PMCID: PMC6560887 DOI: 10.1186/s13148-019-0679-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/03/2019] [Indexed: 02/07/2023] Open
Abstract
Background Cardiac disease modelling using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) requires thorough insight into cardiac cell type differentiation processes. However, current methods to discriminate different cardiac cell types are mostly time-consuming, are costly and often provide imprecise phenotypic evaluation. DNA methylation plays a critical role during early heart development and cardiac cellular specification. We therefore investigated the DNA methylation pattern in different cardiac tissues to identify CpG loci for further cardiac cell type characterization. Results An array-based genome-wide DNA methylation analysis using Illumina Infinium HumanMethylation450 BeadChips led to the identification of 168 differentially methylated CpG loci in atrial and ventricular human heart tissue samples (n = 49) from different patients with congenital heart defects (CHD). Systematic evaluation of atrial-ventricular DNA methylation pattern in cardiac tissues in an independent sample cohort of non-failing donor hearts and cardiac patients using bisulfite pyrosequencing helped us to define a subset of 16 differentially methylated CpG loci enabling precise characterization of human atrial and ventricular cardiac tissue samples. This defined set of reproducible cardiac tissue-specific DNA methylation sites allowed us to consistently detect the cellular identity of hiPSC-CM subtypes. Conclusion Testing DNA methylation of only a small set of defined CpG sites thus makes it possible to distinguish atrial and ventricular cardiac tissues and cardiac atrial and ventricular subtypes of hiPSC-CMs. This method represents a rapid and reliable system for phenotypic characterization of in vitro-generated cardiomyocytes and opens new opportunities for cardiovascular research and patient-specific therapy. Electronic supplementary material The online version of this article (10.1186/s13148-019-0679-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Marta Lemme
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Institute for Clinical Genetics, Carl Gustav Carus Faculty of Medicine, Dresden, Germany
| | - Kerstin Runde
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Dorit Schuster
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jens Scheewe
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tim Attmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Thomas Pickardt
- National Register for Congenital Heart Defects, DZHK (German Centre for Cardiovascular Research), Berlin, Germany.,Competence Network for Congenital Heart Defects, DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute for Cardiovascular Research & Development (EHKI), Heart and Diabetes Center NRW, Ruhr University Bochum, Bad Oeynhausen, Germany
| | - Arne Hansen
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany.,Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany. .,Institute of Human Genetics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany. .,Wellcome Trust Sanger Institute, Cambridge, UK.
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45
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Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers. Cell Stem Cell 2019; 25:69-86.e5. [PMID: 31080136 DOI: 10.1016/j.stem.2019.03.022] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/07/2018] [Accepted: 03/25/2019] [Indexed: 11/21/2022]
Abstract
The cardiogenic transcription factors (TFs) Mef2c, Gata4, and Tbx5 can directly reprogram fibroblasts to induced cardiac-like myocytes (iCLMs), presenting a potential source of cells for cardiac repair. While activity of these TFs is enhanced by Hand2 and Akt1, their genomic targets and interactions during reprogramming are not well studied. We performed genome-wide analyses of cardiogenic TF binding and enhancer profiling during cardiac reprogramming. We found that these TFs synergistically activate enhancers highlighted by Mef2c binding sites and that Hand2 and Akt1 coordinately recruit other TFs to enhancer elements. Intriguingly, these enhancer landscapes collectively resemble patterns of enhancer activation during embryonic cardiogenesis. We further constructed a cardiac reprogramming gene regulatory network and found repression of EGFR signaling pathway genes. Consistently, chemical inhibition of EGFR signaling augmented reprogramming. Thus, by defining epigenetic landscapes these findings reveal synergistic transcriptional activation across a broad landscape of cardiac enhancers and key signaling pathways that govern iCLM reprogramming.
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46
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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47
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Epigenetic therapies in heart failure. J Mol Cell Cardiol 2019; 130:197-204. [PMID: 30991033 DOI: 10.1016/j.yjmcc.2019.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022]
Abstract
Heart failure (HF) is a dominant cause of morbidity and mortality in the developed world, with available pharmacotherapies limited by high rates of residual mortality and a failure to directly target the changes in cell state that drive adverse cardiac remodeling. Pathologic cardiac remodeling is driven by stress-activated cardiac signaling cascades that converge on defined components of the chromatin regulatory apparatus in the nucleus, triggering broad shifts in transcription and cell state. Thus, studies focusing on how cytosolic signaling pathways couple to the nuclear gene control machinery has been an area of therapeutic interest in HF. In this review, we discuss current concepts pertaining to the role of chromatin regulators in HF pathogenesis, with a focus on specific proteins and RNA-containing macromolecular complexes that have shown promise as druggable targets in the experimental setting.
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48
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Begeman IJ, Kang J. Transcriptional Programs and Regeneration Enhancers Underlying Heart Regeneration. J Cardiovasc Dev Dis 2018; 6:jcdd6010002. [PMID: 30583498 PMCID: PMC6463103 DOI: 10.3390/jcdd6010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/31/2022] Open
Abstract
The heart plays the vital role of propelling blood to the entire body, which is essential to life. While maintaining heart function is critical, adult mammalian hearts poorly regenerate damaged cardiac tissue upon injury and form scar tissue instead. Unlike adult mammals, adult zebrafish can regenerate injured hearts with no sign of scarring, making zebrafish an ideal model system with which to study the molecular mechanisms underlying heart regeneration. Investigation of heart regeneration in zebrafish together with mice has revealed multiple cardiac regeneration genes that are induced by injury to facilitate heart regeneration. Altered expression of these regeneration genes in adult mammals is one of the main causes of heart regeneration failure. Previous studies have focused on the roles of these regeneration genes, yet the regulatory mechanisms by which the expression of cardiac regeneration genes is precisely controlled are largely unknown. In this review, we will discuss the importance of differential gene expression for heart regeneration, the recent discovery of cardiac injury or regeneration enhancers, and their impact on heart regeneration.
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Affiliation(s)
- Ian J Begeman
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin⁻Madison, Madison, WI 53705, USA.
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin⁻Madison, Madison, WI 53705, USA.
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49
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Cui M, Wang Z, Bassel-Duby R, Olson EN. Genetic and epigenetic regulation of cardiomyocytes in development, regeneration and disease. Development 2018; 145:145/24/dev171983. [PMID: 30573475 DOI: 10.1242/dev.171983] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Embryonic and postnatal life depend on the uninterrupted function of cardiac muscle cells. These cells, termed cardiomyocytes, display many fascinating behaviors, including complex morphogenic movements, interactions with other cell types of the heart, persistent contractility and quiescence after birth. Each of these behaviors depends on complex interactions between both cardiac-restricted and widely expressed transcription factors, as well as on epigenetic modifications. Here, we review recent advances in our understanding of the genetic and epigenetic control of cardiomyocyte differentiation and proliferation during heart development, regeneration and disease. We focus on those regulators that are required for both heart development and disease, and highlight the regenerative principles that might be manipulated to restore function to the injured adult heart.
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Affiliation(s)
- Miao Cui
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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50
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Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Res 2018; 46:11184-11201. [PMID: 30137428 PMCID: PMC6265487 DOI: 10.1093/nar/gky753] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/15/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks.
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Affiliation(s)
- Shaliu Fu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qin Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael J Purcaro
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kaili Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cuihua Gu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ruixin Zhu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Anshul Kundaje
- Department of Genetics, School of Medicine, Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Aiping Lu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiping Weng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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