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Shi W, Wasson LK, Dorr KM, Robbe ZL, Wilczewski CM, Hepperla AJ, Davis IJ, Seidman CE, Seidman JG, Conlon FL. CHD4 and SMYD1 repress common transcriptional programs in the developing heart. Development 2024; 151:dev202505. [PMID: 38619323 DOI: 10.1242/dev.202505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
Regulation of chromatin states is essential for proper temporal and spatial gene expression. Chromatin states are modulated by remodeling complexes composed of components that have enzymatic activities. CHD4 is the catalytic core of the nucleosome remodeling and deacetylase (NuRD) complex, which represses gene transcription. However, it remains to be determined how CHD4, a ubiquitous enzyme that remodels chromatin structure, functions in cardiomyocytes to maintain heart development. In particular, whether other proteins besides the NuRD components interact with CHD4 in the heart is controversial. Using quantitative proteomics, we identified that CHD4 interacts with SMYD1, a striated muscle-restricted histone methyltransferase that is essential for cardiomyocyte differentiation and cardiac morphogenesis. Comprehensive transcriptomic and chromatin accessibility studies of Smyd1 and Chd4 null embryonic mouse hearts revealed that SMYD1 and CHD4 repress a group of common genes and pathways involved in glycolysis, response to hypoxia, and angiogenesis. Our study reveals a mechanism by which CHD4 functions during heart development, and a previously uncharacterized mechanism regarding how SMYD1 represses cardiac transcription in the developing heart.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kerry M Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary L Robbe
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Barish S, Berg K, Drozd J, Berglund-Brown I, Khizir L, Wasson LK, Seidman CE, Seidman JG, Chen S, Brueckner M. The H2Bub1-deposition complex is required for human and mouse cardiogenesis. Development 2023; 150:dev201899. [PMID: 38038666 PMCID: PMC10730087 DOI: 10.1242/dev.201899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023]
Abstract
De novo variants affecting monoubiquitylation of histone H2B (H2Bub1) are enriched in human congenital heart disease. H2Bub1 is required in stem cell differentiation, cilia function, post-natal cardiomyocyte maturation and transcriptional elongation. However, how H2Bub1 affects cardiogenesis is unknown. We show that the H2Bub1-deposition complex (RNF20-RNF40-UBE2B) is required for mouse cardiogenesis and for differentiation of human iPSCs into cardiomyocytes. Mice with cardiac-specific Rnf20 deletion are embryonic lethal and have abnormal myocardium. We then analyzed H2Bub1 marks during differentiation of human iPSCs into cardiomyocytes. H2Bub1 is erased from most genes at the transition from cardiac mesoderm to cardiac progenitor cells but is preserved on a subset of long cardiac-specific genes. When H2Bub1 is reduced in iPSC-derived cardiomyocytes, long cardiac-specific genes have fewer full-length transcripts. This correlates with H2Bub1 accumulation near the center of these genes. H2Bub1 accumulation near the center of tissue-specific genes was also observed in embryonic fibroblasts and fetal osteoblasts. In summary, we show that normal H2Bub1 distribution is required for cardiogenesis and cardiomyocyte differentiation, and suggest that H2Bub1 regulates tissue-specific gene expression by increasing the amount of full-length transcripts.
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Affiliation(s)
- Syndi Barish
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Kathryn Berg
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Jeffrey Drozd
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Isabella Berglund-Brown
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Labeeqa Khizir
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard University, Boston, MA 02115, USA
| | | | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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Shi W, Scialdone AP, Emerson JI, Mei L, Wasson LK, Davies HA, Seidman CE, Seidman JG, Cook JG, Conlon FL. Missense Mutation in Human CHD4 Causes Ventricular Noncompaction by Repressing ADAMTS1. Circ Res 2023; 133:48-67. [PMID: 37254794 PMCID: PMC10284140 DOI: 10.1161/circresaha.122.322223] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Left ventricular noncompaction (LVNC) is a prevalent cardiomyopathy associated with excessive trabeculation and thin compact myocardium. Patients with LVNC are vulnerable to cardiac dysfunction and at high risk of sudden death. Although sporadic and inherited mutations in cardiac genes are implicated in LVNC, understanding of the mechanisms responsible for human LVNC is limited. METHODS We screened the complete exome sequence database of the Pediatrics Cardiac Genomics Consortium and identified a cohort with a de novo CHD4 (chromodomain helicase DNA-binding protein 4) proband, CHD4M202I, with congenital heart defects. We engineered a humanized mouse model of CHD4M202I (mouse CHD4M195I). Histological analysis, immunohistochemistry, flow cytometry, transmission electron microscopy, and echocardiography were used to analyze cardiac anatomy and function. Ex vivo culture, immunopurification coupled with mass spectrometry, transcriptional profiling, and chromatin immunoprecipitation were performed to deduce the mechanism of CHD4M195I-mediated ventricular wall defects. RESULTS CHD4M195I/M195I mice developed biventricular hypertrabeculation and noncompaction and died at birth. Proliferation of cardiomyocytes was significantly increased in CHD4M195I hearts, and the excessive trabeculation was associated with accumulation of ECM (extracellular matrix) proteins and a reduction of ADAMTS1 (ADAM metallopeptidase with thrombospondin type 1 motif 1), an ECM protease. We rescued the hyperproliferation and hypertrabeculation defects in CHD4M195I hearts by administration of ADAMTS1. Mechanistically, the CHD4M195I protein showed augmented affinity to endocardial BRG1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4). This enhanced affinity resulted in the failure of derepression of Adamts1 transcription such that ADAMTS1-mediated trabeculation termination was impaired. CONCLUSIONS Our study reveals how a single mutation in the chromatin remodeler CHD4, in mice or humans, modulates ventricular chamber maturation and that cardiac defects associated with the missense mutation CHD4M195I can be attenuated by the administration of ADAMTS1.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Angel P. Scialdone
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - James I. Emerson
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Liu Mei
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
| | - Haley A. Davies
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Jonathan G. Seidman
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
| | - Jeanette G. Cook
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Department of Biochemistry & Biophysics (L.M., J.G.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
- Department of Genetics, Harvard Medical School, Boston, MA (L.K.W., C.E.S., J.G.S.)
- Howard Hughes Medical Institute, Chevy Chase, MD (L.K.W., C.E.S.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (C.E.S.)
| | - Frank L. Conlon
- Department of Biology and Genetics, McAllister Heart Institute (W.S., A.P.S., J.I.E., H.A.D., F.L.C.), the University of North Carolina at Chapel Hill
- Lineberger Comprehensive Cancer Center (F.L.C.), the University of North Carolina at Chapel Hill
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4
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Venturini G, Alvim JM, Padilha K, Toepfer CN, Gorham JM, Wasson LK, Biagi D, Schenkman S, Carvalho VM, Salgueiro JS, Cardozo KHM, Krieger JE, Pereira AC, Seidman JG, Seidman CE. Cardiomyocyte infection by Trypanosoma cruzi promotes innate immune response and glycolysis activation. Front Cell Infect Microbiol 2023; 13:1098457. [PMID: 36814444 PMCID: PMC9940271 DOI: 10.3389/fcimb.2023.1098457] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Introduction Chagas cardiomyopathy, a disease caused by Trypanosoma cruzi (T. cruzi) infection, is a major contributor to heart failure in Latin America. There are significant gaps in our understanding of the mechanism for infection of human cardiomyocytes, the pathways activated during the acute phase of the disease, and the molecular changes that lead to the progression of cardiomyopathy. Methods To investigate the effects of T. cruzi on human cardiomyocytes during infection, we infected induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) with the parasite and analyzed cellular, molecular, and metabolic responses at 3 hours, 24 hours, and 48 hours post infection (hpi) using transcriptomics (RNAseq), proteomics (LC-MS), and metabolomics (GC-MS and Seahorse) analyses. Results Analyses of multiomic data revealed that cardiomyocyte infection caused a rapid increase in genes and proteins related to activation innate and adaptive immune systems and pathways, including alpha and gamma interferons, HIF-1α signaling, and glycolysis. These responses resemble prototypic responses observed in pathogen-activated immune cells. Infection also caused an activation of glycolysis that was dependent on HIF-1α signaling. Using gene editing and pharmacological inhibitors, we found that T. cruzi uptake was mediated in part by the glucose-facilitated transporter GLUT4 and that the attenuation of glycolysis, HIF-1α activation, or GLUT4 expression decreased T. cruzi infection. In contrast, pre-activation of pro-inflammatory immune responses with LPS resulted in increased infection rates. Conclusion These findings suggest that T. cruzi exploits a HIF-1α-dependent, cardiomyocyte-intrinsic stress-response activation of glycolysis to promote intracellular infection and replication. These chronic immuno-metabolic responses by cardiomyocytes promote dysfunction, cell death, and the emergence of cardiomyopathy.
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Affiliation(s)
- Gabriela Venturini
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Juliana M. Alvim
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Kallyandra Padilha
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Christopher N. Toepfer
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Lauren K. Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | | | - Sergio Schenkman
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, São Paulo, Brazil
| | | | | | | | - Jose E. Krieger
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States,Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States,Howard Hughes Medical Institute, Chevy Chase, MD, United States,*Correspondence: Christine E. Seidman,
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5
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Shi W, Sheng X, Dorr KM, Hutton JE, Emerson JI, Davies HA, Andrade TD, Wasson LK, Greco TM, Hashimoto Y, Federspiel JD, Robbe ZL, Chen X, Arnold AP, Cristea IM, Conlon FL. Cardiac proteomics reveals sex chromosome-dependent differences between males and females that arise prior to gonad formation. Dev Cell 2021; 56:3019-3034.e7. [PMID: 34655525 PMCID: PMC9290207 DOI: 10.1016/j.devcel.2021.09.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023]
Abstract
Sex disparities in cardiac homeostasis and heart disease are well documented, with differences attributed to actions of sex hormones. However, studies have indicated sex chromosomes act outside of the gonads to function without mediation by gonadal hormones. Here, we performed transcriptional and proteomics profiling to define differences between male and female mouse hearts. We demonstrate, contrary to current dogma, cardiac sex disparities are controlled not only by sex hormones but also through a sex-chromosome mechanism. Using Turner syndrome (XO) and Klinefelter (XXY) models, we find the sex-chromosome pathway is established by X-linked gene dosage. We demonstrate cardiac sex disparities occur at the earliest stages of heart formation, a period before gonad formation. Using these datasets, we identify and define a role for alpha-1B-glycoprotein (A1BG), showing loss of A1BG leads to cardiac defects in females, but not males. These studies provide resources for studying sex-biased cardiac disease states.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Kerry M Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Josiah E Hutton
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - James I Emerson
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haley A Davies
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tia D Andrade
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lauren K Wasson
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Yutaka Hashimoto
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Zachary L Robbe
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xuqi Chen
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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6
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Kathiriya IS, Rao KS, Iacono G, Devine WP, Blair AP, Hota SK, Lai MH, Garay BI, Thomas R, Gong HZ, Wasson LK, Goyal P, Sukonnik T, Hu KM, Akgun GA, Bernard LD, Akerberg BN, Gu F, Li K, Speir ML, Haeussler M, Pu WT, Stuart JM, Seidman CE, Seidman JG, Heyn H, Bruneau BG. Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease. Dev Cell 2021; 56:292-309.e9. [PMID: 33321106 PMCID: PMC7878434 DOI: 10.1016/j.devcel.2020.11.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 01/10/2023]
Abstract
Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.
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Affiliation(s)
- Irfan S Kathiriya
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Kavitha S Rao
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Giovanni Iacono
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - W Patrick Devine
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Andrew P Blair
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Swetansu K Hota
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Michael H Lai
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Bayardo I Garay
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | | | - Henry Z Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Piyush Goyal
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Tatyana Sukonnik
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevin M Hu
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Gunes A Akgun
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Laure D Bernard
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02115, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94158, USA.
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7
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Sharma A, Wasson LK, Willcox JA, Morton SU, Gorham JM, DeLaughter DM, Neyazi M, Schmid M, Agarwal R, Jang MY, Toepfer CN, Ward T, Kim Y, Pereira AC, DePalma SR, Tai A, Kim S, Conner D, Bernstein D, Gelb BD, Chung WK, Goldmuntz E, Porter G, Tristani-Firouzi M, Srivastava D, Seidman JG, Seidman CE. GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm. eLife 2020; 9:53278. [PMID: 33054971 PMCID: PMC7593088 DOI: 10.7554/elife.53278] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Damaging GATA6 variants cause cardiac outflow tract defects, sometimes with pancreatic and diaphragmic malformations. To define molecular mechanisms for these diverse developmental defects, we studied transcriptional and epigenetic responses to GATA6 loss of function (LoF) and missense variants during cardiomyocyte differentiation of isogenic human induced pluripotent stem cells. We show that GATA6 is a pioneer factor in cardiac development, regulating SMYD1 that activates HAND2, and KDR that with HAND2 orchestrates outflow tract formation. LoF variants perturbed cardiac genes and also endoderm lineage genes that direct PDX1 expression and pancreatic development. Remarkably, an exon 4 GATA6 missense variant, highly associated with extra-cardiac malformations, caused ectopic pioneer activities, profoundly diminishing GATA4, FOXA1/2, and PDX1 expression and increasing normal retinoic acid signaling that promotes diaphragm development. These aberrant epigenetic and transcriptional signatures illuminate the molecular mechanisms for cardiovascular malformations, pancreas and diaphragm dysgenesis that arise in patients with distinct GATA6 variants.
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Affiliation(s)
- Arun Sharma
- Department of Genetics, Harvard Medical School, Boston, United States.,Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, United States.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, United States
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Jon Al Willcox
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Sarah U Morton
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Newborn Medicine, Boston Children's Hospital, Boston, United States
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, United States
| | | | - Meraj Neyazi
- Department of Genetics, Harvard Medical School, Boston, United States.,Hannover Medical School, Hannover, Germany
| | - Manuel Schmid
- Department of Genetics, Harvard Medical School, Boston, United States.,Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Radhika Agarwal
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Min Young Jang
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Christopher N Toepfer
- Department of Genetics, Harvard Medical School, Boston, United States.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tarsha Ward
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Alexandre C Pereira
- Department of Genetics, Harvard Medical School, Boston, United States.,Laboratory of Genetics and Molecular Cardiology, Heart Institute, Medical School of University of Sao Paulo, Sao Paulo, Brazil
| | - Steven R DePalma
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Angela Tai
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Seongwon Kim
- Department of Genetics, Harvard Medical School, Boston, United States
| | - David Conner
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, United States
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wendy K Chung
- Department of Medicine, Columbia University Medical Center, New York, United States
| | - Elizabeth Goldmuntz
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, United States
| | | | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, United States
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8
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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: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Neyazi M, Schmid M, Sharma A, Toepfer CN, Kim Y, Wasson LK, Kim SW, DeLaughter DM, Willcox JA, Agarwal R, Tai A, Gorham JM, DePalma S, Seidman JG, Seidman CE. Abstract 104: Identification and Characterization of a
Titin
Enhancer using CRISPR/Cas9 Genome Editing and hiPSC-Derived Cardiomyocytes. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Dilated cardiomyopathy (DCM) is a leading cause for heart failure and is associated with a rate of mortality of 20% within 5 years of diagnosis. The most common genetic causes for DCM are mutations of the sarcomere protein titin (encoded by
TTN
), which occurs in 10-20% of DCM cases. Dominant DCM mutations truncate titin (TTNtv) and result in haploinsufficiency. Thus, strategies to increase the expression of the wild type
TTN
allele could attenuate damaging effects of TTNtv. Utilizing bioinformatic tools, we identified a putative enhancer for
TTN
in its intron 1. We deleted a 658 bp region from intron 1 which encompasses the region of interest in human induced pluripotent stem cells (hiPSCs) using CRISPR/Cas9 genome editing to validate its function. Utilizing RNA sequencing and qPCR of RNA harvested from hiPSC-derived cardiomyocytes (hiPSC-CMs), we demonstrated that a homozygous deletion in this region leads to a drop in
TTN
expression compared to the wild type (WT) control (0.344-fold change, p < 0.001). To further characterize this region, we subdivided it into three parts which we called E1 (296 bp), E2 (206 bp), and E3 (139 bp). E1 includes a highly conserved region and a region of open chromatin as identified by the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) performed on hiPSC-CMs. A homozygous E1 deletion resulted in a decreased
TTN
expression of 0.63-fold compared to the WT control (p < 0.001) when performing RNA sequencing on hiPSC-CMs. Both homozygous E2 and E3 deletions resulted in an increased
TTN
expression (1.56-fold change, p < 0.001; 1.19 fold change, p < 0.001). Utilizing a published sarcomere tracking platform, SarcTrack, to investigate hiPSC-CM physiology, we saw a decreased contractility of 6.6% in hiPSC-CMs carrying a homozygous E1 deletion compared to 10.1% in the WT control (p < 0.001). Cells carrying homozygous E2 or E3 deletions were hypercontractile (13.8%, p < 0.001; 13.7%, p < 0.001). Given our results, we hypothesize that
TTN
expression depends on the E1 region. If confirmed, we expect that increasing the activity of this enhancer using small molecules may provide a novel therapeutic target for DCM caused by TTNtv.
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10
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Neyazi M, Schmid M, Sharma A, Wasson LK, Gorham JM, DePalma S, Kim SW, Seidman JG, Seidman CE. Abstract 231: Identification of a
Titin
Enhancer using hiPSC-Derived Cardiomyocytes and CRISPR/Cas9 Genome Editing. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Dilated cardiomyopathy (DCM), a disorder that occurs in 1:250 individuals, is associated with rates of mortality of 20% within 5 years of diagnosis and is a leading cause for heart failure and cardiac transplantation. Mutations in the massive sarcomere protein titin (encoded by
TTN
) are the most common genetic cause of DCM, occurring in 10-20% of cases. As dominant DCM mutations truncate titin (TTNtv) and result in haploinsufficiency, we predict that strategies to increase the expression of the wild type (WT)
TTN
allele might attenuate the damaging effects of TTNtv. We used bioinformatic analyses to identify a putative
TTN
enhancer within intron 1. To confirm its function, we deleted 658 bp from intron 1 that encompasses the putative
TTN
enhancer in human induced pluripotent stem cells (hiPSCs) using CRISPR/Cas9 genome editing. We used qPCR and RNA sequencing of RNA harvested from hiPSC-derived cardiomyocytes (hiPSC-CMs) and demonstrated that a homozygous deletion in this region leads to decreased
TTN
gene expression compared to the WT control (0.344 fold change, p < 0.001), and also to decreased expression of other sarcomeric genes such as
TNNT2
(0.074 fold change, p < 0.001),
MYH6
(0.18 fold change, p < 0.001),
MYH7
(0.008 fold change, p < 0.001), and
ACTN2
(0.118 fold change, p < 0.001). The expression of transcription factors (TF) that have binding sites in this region is also affected, such as
MEIS2
(0.4 fold change, p < 0.001) and
KLF6
(0.33 fold change, p < 0.001), both of which are known to be involved in cardiogenesis. These TF may act as a link between the deletion in
TTN
Intron 1 and a decreased transcription of other cardiac-relevant genes. We also utilized Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) on WT hiPSC-CMs to identify open regions of chromatin that are accessible for TF binding. This provided additional evidence that this 658 bp region in
TTN
intron 1 has enhancer activity. Ongoing studies are aiming to refine the
TTN
Intron 1 enhancer by further studies using CRISPR/Cas9, CRISPR droplet sequencing (CROP-Seq), and luciferase-based enhancer activity assays. If confirmed, we expect that increasing the activity of this 658 bp region with small molecules may provide a novel therapeutic target for DCM caused by TTNtv.
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Affiliation(s)
| | | | - Arun Sharma
- Dept of Genetics, Harvard Med Sch, Boston, MA
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