1
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Emerson JI, Shi W, Conlon FL. Sex-Specific Response to A1BG Loss Results in Female Dilated Cardiomyopathy. RESEARCH SQUARE 2024:rs.3.rs-4631369. [PMID: 39070637 PMCID: PMC11276010 DOI: 10.21203/rs.3.rs-4631369/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background Cardiac disease often manifests differently in terms of frequency and pathology between men and women. However, the mechanisms underlying these differences are not fully understood. The glycoprotein A1BG is necessary for proper cardiac function in females but not males. Despite this, the role of A1BG in the female heart remains poorly studied. Methods To determine the sex differential function of A1BG, we generated a novel conditional A1bg allele and a novel conditional A1bg Rosa26 knockin allele. Histology, electrocardiography, transcriptional profiling (RNA-seq), transmission electron microscopy, western blot analyses, mass spectrometry, and immunohistochemistry were used to assess cardiac structure and function. Results The study reveals that the absence of A1BG results in significant cardiac dysfunction in female but not male mice. Gene expression underscores that A1BG plays a critical role in metabolic processes and the integrity of intercalated discs in female cardiomyocytes. This dysfunction may be related to sex-specific A1BG cardiac interactomes and manifests as structural and functional alterations in the left ventricle indicative of dilated cardiomyopathy, thus suggesting a sex-specific requirement for A1BG in cardiac health. Conclusion The loss of A1BG in cardiomyocytes leads to dilated cardiomyopathy in females, not males.
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Affiliation(s)
| | - Wei Shi
- University of North Carolina at Chapel Hill
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2
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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 PMCID: PMC11112163 DOI: 10.1242/dev.202505] [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: 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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3
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Broman MT, Nadadur RD, Perez-Cervantes C, Burnicka-Turek O, Lazarevic S, Gams A, Laforest B, Steimle JD, Iddir S, Wang Z, Smith L, Mazurek SR, Olivey HE, Zhou P, Gadek M, Shen KM, Khan Z, Theisen JW, Yang XH, Ikegami K, Efimov IR, Pu WT, Weber CR, McNally EM, Svensson EC, Moskowitz IP. A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network. Circulation 2024; 149:1205-1230. [PMID: 38189150 PMCID: PMC11152454 DOI: 10.1161/circulationaha.123.066804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.
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Affiliation(s)
- Michael T. Broman
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Rangarajan D. Nadadur
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Carlos Perez-Cervantes
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sonja Lazarevic
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Anna Gams
- Department of Biomedical Engineering, George Washington University
| | - Brigitte Laforest
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Jeffrey D. Steimle
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sabrina Iddir
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zhezhen Wang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Linsin Smith
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Stefan R. Mazurek
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Harold E. Olivey
- Department of Biology, Indiana University Northwest, Gary, IN 46408
| | | | - Margaret Gadek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kaitlyn M. Shen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zoheb Khan
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Joshua W.M. Theisen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Xinan H. Yang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kohta Ikegami
- Division of Molecular and Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Igor R. Efimov
- Department of Biomedical Engineering, George Washington University
| | - William T. Pu
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, 02115
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University, 303 E. Superior, SQ5-516, Chicago, IL 60611
| | | | - Ivan P. Moskowitz
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
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Grunert M, Dorn C, Dopazo A, Sánchez-Cabo F, Vázquez J, Rickert-Sperling S, Lara-Pezzi E. Technologies to Study Genetics and Molecular Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:435-458. [PMID: 38884724 DOI: 10.1007/978-3-031-44087-8_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Over the last few decades, the study of congenital heart disease (CHD) has benefited from various model systems and the development of molecular biological techniques enabling the analysis of single gene as well as global effects. In this chapter, we first describe different models including CHD patients and their families, animal models ranging from invertebrates to mammals, and various cell culture systems. Moreover, techniques to experimentally manipulate these models are discussed. Second, we introduce cardiac phenotyping technologies comprising the analysis of mouse and cell culture models, live imaging of cardiogenesis, and histological methods for fixed hearts. Finally, the most important and latest molecular biotechniques are described. These include genotyping technologies, different applications of next-generation sequencing, and the analysis of transcriptome, epigenome, proteome, and metabolome. In summary, the models and technologies presented in this chapter are essential to study the function and development of the heart and to understand the molecular pathways underlying CHD.
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Affiliation(s)
- Marcel Grunert
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- DiNAQOR AG, Schlieren, Switzerland
| | - Cornelia Dorn
- Cardiovascular Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Jésus Vázquez
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | - Enrique Lara-Pezzi
- Myocardial Homeostasis and Cardiac Injury Programme, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
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5
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Lenz J, Brehm A. Conserved mechanisms of NuRD function in hematopoetic gene expression. Enzymes 2023; 53:7-32. [PMID: 37748838 DOI: 10.1016/bs.enz.2023.07.006] [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: 09/27/2023]
Abstract
The Nucleosome Remodeling and Deacetylating Complex (NuRD) is ubiquitously expressed in all metazoans. It combines nucleosome remodeling and histone deacetylating activities to generate inaccessible chromatin structures and to repress gene transcription. NuRD is involved in the generation and maintenance of a wide variety of lineage-specific gene expression programs during differentiation and in differentiated cells. A close cooperation with a large number of lineage-specific transcription factors is key to allow NuRD to function in many distinct differentiation contexts. The molecular nature of this interplay between transcription factors and NuRD is complex and not well understood. This review uses hematopoiesis as a paradigm to highlight recent advances in our understanding of how transcription factors and NuRD cooperate at the molecular level during differentiation. A comparison of vertebrate and invertebrate systems serves to identify the conserved and fundamental concepts guiding functional interactions between transcription factors and NuRD. We also discuss how the transcription factor-NuRD axis constitutes a potential therapeutic target for the treatment of hemoglobinopathies.
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Affiliation(s)
- Jonathan Lenz
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University Marburg, Marburg, Germany.
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6
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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7
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Cao Y, Zhang X, Akerberg BN, Yuan H, Sakamoto T, Xiao F, VanDusen NJ, Zhou P, Sweat ME, Wang Y, Prondzynski M, Chen J, Zhang Y, Wang P, Kelly DP, Pu WT. In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity. Circulation 2023; 147:881-896. [PMID: 36705030 PMCID: PMC10010668 DOI: 10.1161/circulationaha.122.061955] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cardiac chamber-selective transcriptional programs underpin the structural and functional differences between atrial and ventricular cardiomyocytes (aCMs and vCMs). The mechanisms responsible for these chamber-selective transcriptional programs remain largely undefined. METHODS We nominated candidate chamber-selective enhancers (CSEs) by determining the genome-wide occupancy of 7 key cardiac transcription factors (GATA4, MEF2A, MEF2C, NKX2-5, SRF, TBX5, TEAD1) and transcriptional coactivator P300 in atria and ventricles. Candidate enhancers were tested using an adeno-associated virus-mediated massively parallel reporter assay. Chromatin features of CSEs were evaluated by performing assay of transposase accessible chromatin sequencing and acetylation of histone H3 at lysine 27-HiChIP on aCMs and vCMs. CSE sequence requirements were determined by systematic tiling mutagenesis of 29 CSEs at 5 bp resolution. Estrogen-related receptor (ERR) function in cardiomyocytes was evaluated by Cre-loxP-mediated inactivation of ERRα and ERRγ in cardiomyocytes. RESULTS We identified 134 066 and 97 506 regions reproducibly occupied by at least 1 transcription factor or P300, in atria or ventricles, respectively. Enhancer activities of 2639 regions bound by transcription factors or P300 were tested in aCMs and vCMs by adeno-associated virus-mediated massively parallel reporter assay. This identified 1092 active enhancers in aCMs or vCMs. Several overlapped loci associated with cardiovascular disease through genome-wide association studies, and 229 exhibited chamber-selective activity in aCMs or vCMs. Many CSEs exhibited differential chromatin accessibility between aCMs and vCMs, and CSEs were enriched for aCM- or vCM-selective acetylation of histone H3 at lysine 27-anchored loops. Tiling mutagenesis of 29 CSEs identified the binding motif of ERRα/γ as important for ventricular enhancer activity. The requirement of ERRα/γ to activate ventricular CSEs and promote vCM identity was confirmed by loss of the vCM gene profile in ERRα/γ knockout vCMs. CONCLUSIONS We identified 229 CSEs that could be useful research tools or direct therapeutic gene expression. We showed that chamber-selective multi-transcription factor, P300 occupancy, open chromatin, and chromatin looping are predictive features of CSEs. We found that ERRα/γ are essential for maintenance of ventricular identity. Finally, our gene expression, epigenetic, 3-dimensional genome, and enhancer activity atlas provide key resources for future studies of chamber-selective gene regulation.
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Affiliation(s)
- Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Haiyun Yuan
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangzhou, China (H.Y.)
| | - Tomoya Sakamoto
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - Feng Xiao
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Nathan J VanDusen
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis (N.J.V.)
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yi Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Maksymilian Prondzynski
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Jian Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Yan Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Peizhe Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.)
| | - Daniel P Kelly
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (T.S., D.P.K.)
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA (Y.C., X.Z., B.N.A., F.X., P.Z., M.E.S., Y.W., M.P., J.C., Y.Z., P.W., W.T.P.).,Harvard Stem Cell Institute, Cambridge, MA (W.T.P.)
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8
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Bersell KR, Yang T, Mosley JD, Glazer AM, Hale AT, Kryshtal DO, Kim K, Steimle JD, Brown JD, Salem JE, Campbell CC, Hong CC, Wells QS, Johnson AN, Short L, Blair MA, Behr ER, Petropoulou E, Jamshidi Y, Benson MD, Keyes MJ, Ngo D, Vasan RS, Yang Q, Gerszten RE, Shaffer C, Parikh S, Sheng Q, Kannankeril PJ, Moskowitz IP, York JD, Wang TJ, Knollmann BC, Roden DM. Transcriptional Dysregulation Underlies Both Monogenic Arrhythmia Syndrome and Common Modifiers of Cardiac Repolarization. Circulation 2023; 147:824-840. [PMID: 36524479 PMCID: PMC9992308 DOI: 10.1161/circulationaha.122.062193] [Citation(s) in RCA: 4] [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] [Received: 09/01/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Brugada syndrome (BrS) is an inherited arrhythmia syndrome caused by loss-of-function variants in the cardiac sodium channel gene SCN5A (sodium voltage-gated channel alpha subunit 5) in ≈20% of subjects. We identified a family with 4 individuals diagnosed with BrS harboring the rare G145R missense variant in the cardiac transcription factor TBX5 (T-box transcription factor 5) and no SCN5A variant. METHODS We generated induced pluripotent stem cells (iPSCs) from 2 members of a family carrying TBX5-G145R and diagnosed with Brugada syndrome. After differentiation to iPSC-derived cardiomyocytes (iPSC-CMs), electrophysiologic characteristics were assessed by voltage- and current-clamp experiments (n=9 to 21 cells per group) and transcriptional differences by RNA sequencing (n=3 samples per group), and compared with iPSC-CMs in which G145R was corrected by CRISPR/Cas9 approaches. The role of platelet-derived growth factor (PDGF)/phosphoinositide 3-kinase (PI3K) pathway was elucidated by small molecule perturbation. The rate-corrected QT (QTc) interval association with serum PDGF was tested in the Framingham Heart Study cohort (n=1893 individuals). RESULTS TBX5-G145R reduced transcriptional activity and caused multiple electrophysiologic abnormalities, including decreased peak and enhanced "late" cardiac sodium current (INa), which were entirely corrected by editing G145R to wild-type. Transcriptional profiling and functional assays in genome-unedited and -edited iPSC-CMs showed direct SCN5A down-regulation caused decreased peak INa, and that reduced PDGF receptor (PDGFRA [platelet-derived growth factor receptor α]) expression and blunted signal transduction to PI3K was implicated in enhanced late INa. Tbx5 regulation of the PDGF axis increased arrhythmia risk due to disruption of PDGF signaling and was conserved in murine model systems. PDGF receptor blockade markedly prolonged normal iPSC-CM action potentials and plasma levels of PDGF in the Framingham Heart Study were inversely correlated with the QTc interval (P<0.001). CONCLUSIONS These results not only establish decreased SCN5A transcription by the TBX5 variant as a cause of BrS, but also reveal a new general transcriptional mechanism of arrhythmogenesis of enhanced late sodium current caused by reduced PDGF receptor-mediated PI3K signaling.
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Affiliation(s)
- Kevin R Bersell
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Tao Yang
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Jonathan D Mosley
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Andrew M Glazer
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Andrew T Hale
- Biochemistry (A.T.H., J.D.Y.), Vanderbilt University, Nashville, TN
| | - Dmytro O Kryshtal
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Kyungsoo Kim
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, IL (J.D.S., I.P.M.)
| | - Jonathan D Brown
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Joe-Elie Salem
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Assistance Publique - Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Pharmacology, CIC-1901, Sorbonne University, Paris, France (J-E.S.)
- Sorbonne Universités, UPMC Univ Paris 06, Faculty of Medicine, France (J-E.S.)
| | - Courtney C Campbell
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore (C.C.H.)
| | - Quinn S Wells
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Biomedical Informatics (Q.S.W., D.M.R.), Vanderbilt University, Nashville, TN
| | - Amanda N Johnson
- Molecular Physiology and Biophysics (A.N.J.), Vanderbilt University, Nashville, TN
| | - Laura Short
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Marcia A Blair
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | | | - Evmorfia Petropoulou
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London and St George's University Hospitals National Health Service Foundation Trust, London, UK (E.P., Y.J.)
| | - Yalda Jamshidi
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Institute, St George's, University of London and St George's University Hospitals National Health Service Foundation Trust, London, UK (E.P., Y.J.)
| | - Mark D Benson
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (M.D.B.)
| | - Michelle J Keyes
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | - Debby Ngo
- Division of Pulmonary and Cardiovascular Medicine (D.N., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | | | - Qiong Yang
- Boston University School of Medicine, MA (R.S.V., Q.Y.)
| | - Robert E Gerszten
- Cardiovascular Research Center (E.J.B., M.D.B., M.J.K., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
- Division of Pulmonary and Cardiovascular Medicine (D.N., R.E.G.), Beth Israel Deaconess Hospital, Boston, MA
| | - Christian Shaffer
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Shan Parikh
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | | | | | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, IL (J.D.S., I.P.M.)
| | - John D York
- Biochemistry (A.T.H., J.D.Y.), Vanderbilt University, Nashville, TN
| | - Thomas J Wang
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Bjorn C Knollmann
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
| | - Dan M Roden
- Departments of Pharmacology (K.R.B., A.M.G., D.O.K., K.K., J-E.S., C.C.C., Q.S.W., S.P., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Medicine (T.Y., J.D.M., J.D.B., J-E.S., Q.S.W., L.S., M.A.B., C.S., T.J.W., B.C.K., D.M.R.), Vanderbilt University, Nashville, TN
- Biomedical Informatics (Q.S.W., D.M.R.), Vanderbilt University, Nashville, TN
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9
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Siatra P, Vatsellas G, Chatzianastasiou A, Balafas E, Manolakou T, Papapetropoulos A, Agapaki A, Mouchtouri ET, Ruchaya PJ, Korovesi AG, Mavroidis M, Thanos D, Beis D, Kokkinopoulos I. Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart. NPJ Regen Med 2023; 8:13. [PMID: 36869039 PMCID: PMC9984483 DOI: 10.1038/s41536-023-00280-9] [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: 03/03/2022] [Accepted: 01/25/2023] [Indexed: 03/05/2023] Open
Abstract
The single curative measure for heart failure patients is a heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have identified a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes, in vivo, in vitro and ex vivo. Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the center of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues. The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.
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Affiliation(s)
- Panagiota Siatra
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Giannis Vatsellas
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Greek Genome Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Athanasia Chatzianastasiou
- Department of Pharmacy, Laboratory of Pharmacology, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Balafas
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Andreas Papapetropoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Department of Pharmacy, Laboratory of Pharmacology, National and Kapodistrian University of Athens, Athens, Greece
| | - Anna Agapaki
- Histochemistry Facility, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Prashant J Ruchaya
- School of Health, Sport and Biosciences, University of East London, London, UK
| | - Artemis G Korovesi
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Greek Genome Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Manolis Mavroidis
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Dimitrios Thanos
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Greek Genome Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Dimitris Beis
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Ioannis Kokkinopoulos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.
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10
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Al-Khindi T, Sherman MB, Kodama T, Gopal P, Pan Z, Kiraly JK, Zhang H, Goff LA, du Lac S, Kolodkin AL. The transcription factor Tbx5 regulates direction-selective retinal ganglion cell development and image stabilization. Curr Biol 2022; 32:4286-4298.e5. [PMID: 35998637 PMCID: PMC9560999 DOI: 10.1016/j.cub.2022.07.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
The diversity of visual input processed by the mammalian visual system requires the generation of many distinct retinal ganglion cell (RGC) types, each tuned to a particular feature. The molecular code needed to generate this cell-type diversity is poorly understood. Here, we focus on the molecules needed to specify one type of retinal cell: the upward-preferring ON direction-selective ganglion cell (up-oDSGC) of the mouse visual system. Single-cell transcriptomic profiling of up- and down-oDSGCs shows that the transcription factor Tbx5 is selectively expressed in up-oDSGCs. The loss of Tbx5 in up-oDSGCs results in a selective defect in the formation of up-oDSGCs and a corresponding inability to detect vertical motion. A downstream effector of Tbx5, Sfrp1, is also critical for vertical motion detection but not up-oDSGC formation. These results advance our understanding of the molecular mechanisms that specify a rare retinal cell type and show how disrupting this specification leads to a corresponding defect in neural circuitry and behavior.
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Affiliation(s)
- Timour Al-Khindi
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael B Sherman
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Takashi Kodama
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Otolaryngology & Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Preethi Gopal
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhiwei Pan
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James K Kiraly
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hao Zhang
- Department of Microbiology and Immunology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sascha du Lac
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Otolaryngology & Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alex L Kolodkin
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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11
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Leighton GO, Irvin EM, Kaur P, Liu M, You C, Bhattaram D, Piehler J, Riehn R, Wang H, Pan H, Williams DC. Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3. J Biol Chem 2022; 298:102428. [PMID: 36037972 PMCID: PMC9520026 DOI: 10.1016/j.jbc.2022.102428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 10/29/2022] Open
Abstract
The methyl-CpG-binding domain 2 and 3 proteins (MBD2 and MBD3) provide structural and DNA-binding function for the Nucleosome Remodeling and Deacetylase (NuRD) complex. The two proteins form distinct NuRD complexes and show different binding affinity and selectivity for methylated DNA. Previous studies have shown that MBD2 binds with high affinity and selectivity for a single methylated CpG dinucleotide while MBD3 does not. However, the NuRD complex functions in regions of the genome that contain many CpG dinucleotides (CpG islands). Therefore, in this work, we investigate the binding and diffusion of MBD2 and MBD3 on more biologically relevant DNA templates that contain a large CpG island or limited CpG sites. Using a combination of single-molecule and biophysical analyses, we show that both MBD2 and MBD3 diffuse freely and rapidly across unmethylated CpG-rich DNA. In contrast, we found methylation of large CpG islands traps MBD2 leading to stable and apparently static binding on the CpG island while MBD3 continues to diffuse freely. In addition, we demonstrate both proteins bend DNA, which is augmented by methylation. Together, these studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NuRD can freely mobilize nucleosomes independent of methylation status.
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Affiliation(s)
- Gage O Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Ming Liu
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Dhruv Bhattaram
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University of Medicine, Atlanta, Georgia, USA
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, North Carolina, USA; Department of Physics, North Carolina State University, Raleigh, North Carolina, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, USA
| | - Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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12
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Zhang X, Liu L, Chen W, Wang F, Cheng Y, Liu Y, Lai Y, Zhang R, Qiao Y, Yuan Y, Lin Y, Xu W, Cao J, Gui Y, Zhao J. Gestational Leucylation Suppresses Embryonic T-Box Transcription Factor 5 Signal and Causes Congenital Heart Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201034. [PMID: 35320615 PMCID: PMC9130917 DOI: 10.1002/advs.202201034] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 06/01/2023]
Abstract
Dysregulated maternal nutrition, such as vitamin deficiencies and excessive levels of glucose and fatty acids, increases the risk for congenital heart disease (CHD) in the offspring. However, the association between maternal amino-acid levels and CHD is unclear. Here, it is shown that increased leucine levels in maternal plasma during the first trimester are associated with elevated CHD risk in the offspring. High levels of maternal leucine increase embryonic lysine-leucylation (K-Leu), which is catalyzed by leucyl-tRNA synthetase (LARS). LARS preferentially binds to and catalyzes K-Leu modification of lysine 339 within T-box transcription factor TBX5, whereas SIRT3 removes K-Leu from TBX5. Reversible leucylation retains TBX5 in the cytoplasm and inhibits its transcriptional activity. Increasing embryonic K-Leu levels in high-leucine-diet fed or Sirt3 knockout mice causes CHD in the offspring. Targeting K-Leu using the leucine analogue leucinol can inhibit LARS activity, reverse TBX5 K-Leu modification, and decrease the occurrence of CHD in high-leucine-diet fed mice. This study reveals that increased maternal leucine levels increases CHD risk in the offspring through inhibition of embryonic TBX5 signaling, indicating that leucylation exerts teratogenic effects during heart development and may be an intervening target of CHD.
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Affiliation(s)
- Xuan Zhang
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Lian Liu
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Wei‐Cheng Chen
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Feng Wang
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Yi‐Rong Cheng
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Yi‐Meng Liu
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Yang‐Fan Lai
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Rui‐Jia Zhang
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Ya‐Nan Qiao
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Yi‐Yuan Yuan
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Yan Lin
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
- Key Laboratory of Reproduction Regulation of NPFPC and Institutes of Biomedical SciencesFudan UniversityShanghai200438P. R. China
| | - Wei Xu
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
- Key Laboratory of Reproduction Regulation of NPFPC and Institutes of Biomedical SciencesFudan UniversityShanghai200438P. R. China
| | - Jing Cao
- School of Basic Medical SciencesZhengzhou UniversityZhengzhou450001China
| | - Yong‐Hao Gui
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
| | - Jian‐Yuan Zhao
- Children's Hospital of Fudan UniversityObstetrics & Gynecology Hospital of Fudan UniversityFudan University Shanghai Cancer CenterState Key Laboratory of Genetic Engineeringand School of Life SciencesShanghai200438P. R. China
- School of Basic Medical SciencesZhengzhou UniversityZhengzhou450001China
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13
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Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, Hepperla AJ, Akerberg BN, Pu WT, Cristea IM, Davis IJ, Conlon FL. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev 2022; 36:468-482. [PMID: 35450884 PMCID: PMC9067406 DOI: 10.1101/gad.349154.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.
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Affiliation(s)
- Zachary L Robbe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei Shi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lauren K Wasson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Angel P Scialdone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - 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
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Frank L Conlon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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14
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Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell 2022; 185:794-814.e30. [PMID: 35182466 PMCID: PMC8923057 DOI: 10.1016/j.cell.2022.01.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/20/2021] [Accepted: 01/25/2022] [Indexed: 02/08/2023]
Abstract
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA4 and TBX5, within human cardiac progenitors, and integrating the results with nearly 9,000 exomes from proband-parent trios revealed an enrichment of de novo missense variants associated with CHD within the interactomes. Scoring variants of interactome members based on residue, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the identified GLYR1 missense variant disrupted interaction with GATA4, impairing in vitro and in vivo function in mice. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating genetic variants in heart disease.
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Affiliation(s)
- Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Maureen Pittman
- Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Franco Felix
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Desmond Richmond-Buccola
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Mauro W Costa
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Bonnie E J Maven
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Kaitlen Samse-Knapp
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael McGregor
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Casey A Gifford
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Cardiovascular Division, 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
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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15
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DNA Methylation Levels of the TBX5 Gene Promoter Are Associated with Congenital Septal Defects in Mexican Paediatric Patients. BIOLOGY 2022; 11:biology11010096. [PMID: 35053095 PMCID: PMC8773106 DOI: 10.3390/biology11010096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/07/2022] [Indexed: 11/17/2022]
Abstract
The TBX5 gene regulates morphological changes during heart development, and it has been associated with epigenetic abnormalities observed in congenital heart defects (CHD). The aim of this research was to evaluate the association between DNA methylation levels of the TBX5 gene promoter and congenital septal defects. DNA methylation levels of six CpG sites in the TBX5 gene promoter were evaluated using pyrosequencing analysis in 35 patients with congenital septal defects and 48 controls. Average methylation levels were higher in individuals with congenital septal defects than in the controls (p < 0.004). In five CpG sites, we also found higher methylation levels in patients than in the controls (p < 0.05). High methylation levels were associated with congenital septal defects (OR = 3.91; 95% CI = 1.02–14.8; p = 0.045). The analysis of Receiver Operating Characteristic (ROC) showed that the methylation levels of the TBX5 gene could be used as a risk marker for congenital septal defects (AUC = 0.68, 95% CI = 0.56–0.80; p = 0.004). Finally, an analysis of environmental factors indicated that maternal infections increased the risk (OR = 2.90; 95% CI = 1.01–8.33; p = 0.048) of congenital septal defects. Our data suggest that a high DNA methylation of the TBX5 gene could be associated with congenital septal defects.
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16
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Proteomic analysis identifies ZMYM2 as endogenous binding partner of TBX18 protein in 293 and A549 cells. Biochem J 2021; 479:91-109. [PMID: 34935912 DOI: 10.1042/bcj20210642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
The TBX18 transcription factor regulates patterning and differentiation programs in the primordia of many organs yet the molecular complexes in which TBX18 resides to exert its crucial transcriptional function in these embryonic contexts have remained elusive. Here, we used 293 and A549 cells as an accessible cell source to search for endogenous protein interaction partners of TBX18 by an unbiased proteomic approach. We tagged endogenous TBX18 by CRISPR/Cas9 targeted genome editing with a triple FLAG peptide, and identified by anti-FLAG affinity purification and subsequent LC-MS analysis the ZMYM2 protein to be statistically enriched together with TBX18 in both 293 and A549 nuclear extracts. Using a variety of assays, we confirmed binding of TBX18 to ZMYM2, a component of the CoREST transcriptional corepressor complex. Tbx18 is coexpressed with Zmym2 in the mesenchymal compartment of the developing ureter of the mouse, and mutations in TBX18and in ZMYM2 were recently linked to congenital anomalies in the kidney and urinary tract (CAKUT) in line with a possible in vivo relevance of TBX18-ZMYM2 protein interaction in ureter development.
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17
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Ison HE, Griffin EL, Parrott A, Shikany AR, Meyers L, Thomas MJ, Syverson E, Demo EM, Fitzgerald KK, Fitzgerald-Butt S, Ziegler KL, Schartman AF, Stone KM, Helm BM. Genetic counseling for congenital heart disease - Practice resource of the national society of genetic counselors. J Genet Couns 2021; 31:9-33. [PMID: 34510635 DOI: 10.1002/jgc4.1498] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 12/11/2022]
Abstract
Congenital heart disease (CHD) is an indication which spans multiple specialties across various genetic counseling practices. This practice resource aims to provide guidance on key considerations when approaching counseling for this particular indication while recognizing the rapidly changing landscape of knowledge within this domain. This resource was developed with consensus from a diverse group of certified genetic counselors utilizing literature relevant for CHD genetic counseling practice and is aimed at supporting genetic counselors who encounter this indication in their practice both pre- and postnatally.
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Affiliation(s)
- Hannah E Ison
- Stanford Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, California, USA
| | - Emily L Griffin
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Amy R Shikany
- Cincinnati Children's Hospital Medical Center, The Heart Institute, Cincinnati, Ohio, USA
| | | | - Matthew J Thomas
- Department of Pediatrics, Division of Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Erin Syverson
- Department of Pediatrics, Division of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Erin M Demo
- Sibley Heart Center Cardiology at Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kristi K Fitzgerald
- Nemours Cardiac Center, Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Sara Fitzgerald-Butt
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Allison F Schartman
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, Indiana University Health, Indianapolis, Indiana, USA
| | - Kristyne M Stone
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, Indiana University Health, Indianapolis, Indiana, USA
| | - Benjamin M Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, Indiana, USA
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18
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Bian H, Zhu T, Liang Y, Hei R, Zhang X, Li X, Chen J, Lu Y, Gu J, Qiao L, Zheng Q. Expression Profiling and Functional Analysis of Candidate Col10a1 Regulators Identified by the TRAP Program. Front Genet 2021; 12:683939. [PMID: 34276786 PMCID: PMC8283764 DOI: 10.3389/fgene.2021.683939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Hypertrophic chondrocytes and their specific marker, the type X collagen gene (Col10a1), are critical components of endochondral bone formation during skeletal development. We previously found that Runx2 is an indispensable mouse Col10a1 gene regulator and identified many other transcription factors (TFs) that potentially interact with the 150-bp Col10a1 cis-enhancer. However, the roles of these candidate TFs in Col10a1 expression and chondrocyte hypertrophy have not been elucidated. Here, we focus on 32 candidate TFs recently identified by analyzing the 150-bp Col10a1 enhancer using the transcription factor affinity prediction (TRAP) program. We found that 12 TFs (Hoxa3, Lsx, Evx2, Dlx5, S8, Pax2, Egr2, Mef2a, Barhl2, GKlf, Sox17, and Crx) were significantly upregulated and four TFs (Lhx4, Tbx5, Mef2c, and Hb9) were significantly downregulated in hypertrophic MCT cells, which show upregulation of Col10a1 expression. Most of the differential expression pattern of these TFs conformed with the results obtained from ATDC5 cell model and primary mouse chondrocytes. Notably, Tbx5 was downregulated upon Col10a1 upregulation, overexpression of Tbx5 decreased Col10a1 expression, and knock-down of Tbx5 increased Col10a1 expression in hypertrophic chondrocytes, suggesting that Tbx5 is a negative regulator of Col10a1. We further generated a stable Tbx5-overexpressing ATDC5 cell line and ColX-Tbx5 transgenic mice driven by Col10a1-specific enhancers and promoters. Tbx5 overexpression decreased Col10a1 expression in ATDC5 cells cultured as early as day 7 and in limb tissue on post-natal day 1. Slightly weaker alkaline phosphatase staining was also observed in cell culture on day 7 and in limb digits on embryonic day 17.5, indicating mildly delayed ossification. Further characterization of these candidate Col10a1 transcriptional regulators could help identify novel therapeutic targets for skeletal diseases associated with abnormal chondrocyte hypertrophy.
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Affiliation(s)
- Huiqin Bian
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ting Zhu
- Laboratory of Clinical Medicine, Huai'an Women & Children Hospital, Affiliated to Yangzhou University, Huai'an, China
| | - Yuting Liang
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ruoxuan Hei
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaojing Zhang
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaochen Li
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jinnan Chen
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yaojuan Lu
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.,Shenzhen Academy of Peptide Targeting Technology at Pingshan and Shenzhen Tyercan Bio-Pharm Co., Ltd., Shenzhen, China
| | - Junxia Gu
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Longwei Qiao
- Suzhou Affiliated to State Key Laboratory of Reproductive Medicine, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Suzhou, China
| | - Qiping Zheng
- Department of Hematology and Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.,Shenzhen Academy of Peptide Targeting Technology at Pingshan and Shenzhen Tyercan Bio-Pharm Co., Ltd., Shenzhen, China
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19
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Zhang C, Li Y, Cao J, Yu B, Zhang K, Li K, Xu X, Guo Z, Liang Y, Yang X, Yang Z, Sun Y, Kaartinen V, Ding K, Wang J. Hedgehog signalling controls sinoatrial node development and atrioventricular cushion formation. Open Biol 2021; 11:210020. [PMID: 34062094 PMCID: PMC8169207 DOI: 10.1098/rsob.210020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Smoothened is a key receptor of the hedgehog pathway, but the roles of Smoothened in cardiac development remain incompletely understood. In this study, we found that the conditional knockout of Smoothened from the mesoderm impaired the development of the venous pole of the heart and resulted in hypoplasia of the atrium/inflow tract (IFT) and a low heart rate. The blockage of Smoothened led to reduced expression of genes critical for sinoatrial node (SAN) development in the IFT. In a cardiac cell culture model, we identified a Gli2–Tbx5–Hcn4 pathway that controls SAN development. In the mutant embryos, the endocardial-to-mesenchymal transition (EndMT) in the atrioventricular cushion failed, and Bmp signalling was downregulated. The addition of Bmp2 rescued the EndMT in mutant explant cultures. Furthermore, we analysed Gli2+ scRNAseq and Tbx5−/− RNAseq data and explored the potential genes downstream of hedgehog signalling in posterior second heart field derivatives. In conclusion, our study reveals that Smoothened-mediated hedgehog signalling controls posterior cardiac progenitor commitment, which suggests that the mutation of Smoothened might be involved in the aetiology of congenital heart diseases related to the cardiac conduction system and heart valves.
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Affiliation(s)
- Chaohui Zhang
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Yuxin Li
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Jiaheng Cao
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Beibei Yu
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Kaiyue Zhang
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Ke Li
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Xinhui Xu
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Zhikun Guo
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Yinming Liang
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing 102206, People's Republic of China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing 210061, People's Republic of China
| | - Yunfu Sun
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai 200120, People's Republic of China
| | - Vesa Kaartinen
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital of Henan University, Zhengzhou 450003, People's Republic of China
| | - Jikui Wang
- Henan Key Laboratory for Medical Tissue Regeneration, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, People's Republic of China
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20
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Turunen T, Hernández de Sande A, Pölönen P, Heinäniemi M. Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. Comput Struct Biotechnol J 2021; 19:1944-1955. [PMID: 33995896 PMCID: PMC8082160 DOI: 10.1016/j.csbj.2021.03.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 10/29/2022] Open
Abstract
MicroRNAs are key players in gene regulatory networks controlling cell homeostasis. Their altered expression has been previously linked to disease outcomes and microRNAs thus serve as biomarkers for disease diagnostics. However, their synthesis and its transcriptional regulation have been challenging to investigate. In this study, we validated the use of H3K36me3 histone modification for the quantification of microRNA transcription levels using data from the ENCODE Consortium and then applied this approach to provide new insight into the cell-type-specific regulation in tissues, cell line models and cardiac disease. In cardiomyocytes derived from patients suffering from septal defects, carrying a G296S mutation in the transcription factor GATA4, we show that microRNA gene transcription is altered in cardiomyocytes carrying this mutation and coincides with novel super-enhancers formed within regulatory domains defined using chromatin interaction profiles. The most prominently elevated primary transcript encodes for let-7a and miR-100 that may target genes in the Hippo signaling pathway. Collectively, our work presents a methodology to quantify microRNA gene expression using histone marker data and paves the way for functional studies of cell-type-specific transcriptional regulation occurring in disease pathology.
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Affiliation(s)
- Tanja Turunen
- School of Medicine, University of Eastern Finland, Kuopio FI-70200, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu FI-80101, Finland
| | | | - Petri Pölönen
- School of Medicine, University of Eastern Finland, Kuopio FI-70200, Finland
| | - Merja Heinäniemi
- School of Medicine, University of Eastern Finland, Kuopio FI-70200, Finland
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21
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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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22
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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: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [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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23
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Cai Y, Yan L, Kielt MJ, Cogan JD, Hedges LK, Nunley B, West J, Austin ED, Hamid R. TBX4 Transcription Factor Is a Positive Feedback Regulator of Itself and Phospho-SMAD1/5. Am J Respir Cell Mol Biol 2021; 64:140-143. [PMID: 33385213 DOI: 10.1165/rcmb.2020-0331le] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ying Cai
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Ling Yan
- Vanderbilt University Medical Center Nashville, Tennessee and
| | | | - Joy D Cogan
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Lora K Hedges
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Bethany Nunley
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - James West
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Eric D Austin
- Vanderbilt University Medical Center Nashville, Tennessee and
| | - Rizwan Hamid
- Vanderbilt University Medical Center Nashville, Tennessee and
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24
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Leigh RS, Ruskoaho HJ, Kaynak BL. Cholecystokinin peptide signaling is regulated by a TBX5-MEF2 axis in the heart. Peptides 2021; 136:170459. [PMID: 33249116 DOI: 10.1016/j.peptides.2020.170459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 11/15/2022]
Abstract
The procholecystokinin (proCCK) gene encodes a secreted peptide known to regulate the digestive, endocrine, and nervous systems. Though recently proposed as a biomarker for heart dysfunction, its physiological role in both the embryonic and adult heart is poorly understood, and there are no reports of tissue-specific regulators of cholecystokinin signaling in the heart or other tissues. In the present study, mRNA of proCCK was observed in cardiac tissues during mouse embryonic development, establishing proCCK as an early marker of differentiated cardiomyocytes which is later restricted to anatomical subdomains of the neonatal heart. Three-dimensional analysis of the expression of proCCK and CCKAR/CCKBR receptors was performed using in situ hybridization and optical projection tomography, illustrating chamber-specific expression patterns in the postnatal heart. Transcription factor motif analyses indicated developmental cardiac transcription factors TBX5 and MEF2C as upstream regulators of proCCK, and this regulatory activity was confirmed in reporter gene assays. proCCK mRNA levels were also measured in the infarcted heart and in response to cyclic mechanical stretch and endothelin-1, indicating dynamic transcriptional regulation which might be leveraged for improved biomarker development. Functional analyses of exogenous cholecystokinin octapeptide (CCK-8) administration were performed in differentiating mouse embryonic stem cells (mESCs), and the results suggest that CCK-8 does not act as a differentiation modulator of cardiomyocyte subtypes. Collectively, these findings indicate that proCCK is regulated at the transcriptional level by TBX5-MEF2 and neurohormonal signaling, informing use of proCCK as a biomarker and future strategies for upstream manipulation of cholecystokinin signaling in the heart and other tissues.
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Affiliation(s)
- Robert S Leigh
- Drug Research Programme, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Heikki J Ruskoaho
- Drug Research Programme, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Bogac L Kaynak
- Drug Research Programme, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
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25
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Anterior lateral plate mesoderm gives rise to multiple tissues and requires tbx5a function in left-right asymmetry, migration dynamics, and cell specification of late-addition cardiac cells. Dev Biol 2021; 472:52-66. [PMID: 33482174 DOI: 10.1016/j.ydbio.2021.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 01/23/2023]
Abstract
In this study, we elucidate a single cell resolution fate map in the zebrafish in a sub-section of the anterior Lateral Plate Mesoderm (aLPM) at 18 hpf. Our results show that this tissue is not organized into segregated regions but gives rise to intermingled pericardial sac, peritoneum, pharyngeal arch and cardiac precursors. We further report upon asymmetrical contributions of lateral aLPM-derived heart precursors-specifically that twice as many heart precursors arise from the right side versus the left side of the embryo. Cell tracking analyses and large-scale cell labeling of the lateral aLPM corroborate these differences and show that the observed asymmetries are dependent upon Tbx5a expression. Previously, it was shown that cardiac looping was affected in Tbx5a knock-down and knock-out zebrafish (Garrity et al., 2002; Parrie et al., 2013); our present data also implicate tbx5a function in cell specification, establishment and maintenance of cardiac left-right asymmetry.
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26
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Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol 2021; 17:e8792. [PMID: 33434350 PMCID: PMC7803364 DOI: 10.15252/msb.20188792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/23/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
A better understanding of the molecular mechanisms underlying disease is key for expediting the development of novel therapeutic interventions. Disease mechanisms are often mediated by interactions between proteins. Insights into the physical rewiring of protein-protein interactions in response to mutations, pathological conditions, or pathogen infection can advance our understanding of disease etiology, progression, and pathogenesis and can lead to the identification of potential druggable targets. Advances in quantitative mass spectrometry (MS)-based approaches have allowed unbiased mapping of these disease-mediated changes in protein-protein interactions on a global scale. Here, we review MS techniques that have been instrumental for the identification of protein-protein interactions at a system-level, and we discuss the challenges associated with these methodologies as well as novel MS advancements that aim to address these challenges. An overview of examples from diverse disease contexts illustrates the potential of MS-based protein-protein interaction mapping approaches for revealing disease mechanisms, pinpointing new therapeutic targets, and eventually moving toward personalized applications.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI)University of California San FranciscoSan FranciscoCAUSA
- J. David Gladstone InstitutesSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoCAUSA
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27
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Varshney A, Chahal G, Santos L, Stolper J, Hallab JC, Nim HT, Nikolov M, Yip A, Ramialison M. Human Cardiac Transcription Factor Networks. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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28
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Markunas AM, Manivannan PKR, Ezekian JE, Agarwal A, Eisner W, Alsina K, Allen HD, Wray GA, Kim JJ, Wehrens XHT, Landstrom AP. TBX5-encoded T-box transcription factor 5 variant T223M is associated with long QT syndrome and pediatric sudden cardiac death. Am J Med Genet A 2020; 185:923-929. [PMID: 33369127 DOI: 10.1002/ajmg.a.62037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/14/2022]
Abstract
Long QT syndrome (LQTS) is a genetic disease resulting in a prolonged QT interval on a resting electrocardiogram, predisposing affected individuals to polymorphic ventricular tachycardia and sudden death. Although a number of genes have been implicated in this disease, nearly one in four individuals exhibiting the LQTS phenotype are genotype-negative. Whole-exome sequencing identified a missense T223M variant in TBX5 that cosegregates with prolonged QT interval in a family with otherwise genotype-negative LQTS and sudden death. The TBX5-T223M variant was absent among large ostensibly healthy populations (gnomAD) and predicted to be pathogenic by in silico modeling based on Panther, PolyPhen-2, Provean, SIFT, SNAP2, and PredictSNP prediction tools. The variant was located in a highly conserved region of TBX5 predicted to be part of the DNA-binding interface. A luciferase assay identified a 57.5% reduction in the ability of TBX5-T223M to drive expression at the atrial natriuretic factor promotor compared to wildtype TBX5 in vitro. We conclude that the variant is pathogenic in this family, and we put TBX5 forward as a disease susceptibility allele for genotype-negative LQTS. The identification of this familial variant may serve as a basis for the identification of previously unknown mechanisms of LQTS with broader implications for cardiac electrophysiology.
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Affiliation(s)
- Alexandra M Markunas
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Perathu K R Manivannan
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jordan E Ezekian
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Agnim Agarwal
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - William Eisner
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Katherina Alsina
- Departments of Molecular Physiology & Biophysics and Medicine (Cardiology), Baylor College of Medicine, Houston, Texas, USA
| | - Hugh D Allen
- Department of Pediatrics, Section of Cardiology, Baylor College of Medicine, Houston, Texas, USA
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jeffrey J Kim
- Department of Pediatrics, Section of Cardiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xander H T Wehrens
- Departments of Molecular Physiology & Biophysics and Medicine (Cardiology), Baylor College of Medicine, Houston, Texas, USA
| | - Andrew P Landstrom
- Department of Pediatrics, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
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29
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Guzzolino E, Pellegrino M, Ahuja N, Garrity D, D'Aurizio R, Groth M, Baumgart M, Hatcher CJ, Mercatanti A, Evangelista M, Ippolito C, Tognoni E, Fukuda R, Lionetti V, Pellegrini M, Cremisi F, Pitto L. miR-182-5p is an evolutionarily conserved Tbx5 effector that impacts cardiac development and electrical activity in zebrafish. Cell Mol Life Sci 2020; 77:3215-3229. [PMID: 31686119 PMCID: PMC11104936 DOI: 10.1007/s00018-019-03343-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
To dissect the TBX5 regulatory circuit, we focused on microRNAs (miRNAs) that collectively contribute to make TBX5 a pivotal cardiac regulator. We profiled miRNAs in hearts isolated from wild-type, CRE, Tbx5lox/+and Tbx5del/+ mice using a Next Generation Sequencing (NGS) approach. TBX5 deficiency in cardiomyocytes increased the expression of the miR-183 cluster family that is controlled by Kruppel-like factor 4, a transcription factor repressed by TBX5. MiR-182-5p, the most highly expressed miRNA of this family, was functionally analyzed in zebrafish. Transient overexpression of miR-182-5p affected heart morphology, calcium handling and the onset of arrhythmias as detected by ECG tracings. Accordingly, several calcium channel proteins identified as putative miR-182-5p targets were downregulated in miR-182-5p overexpressing hearts. In stable zebrafish transgenic lines, we demonstrated that selective miRNA-182-5p upregulation contributes to arrhythmias. Moreover, cardiac-specific down-regulation of miR-182-5p rescued cardiac defects in a zebrafish model of Holt-Oram syndrome. In conclusion, miR-182-5p exerts an evolutionarily conserved role as a TBX5 effector in the onset of cardiac propensity for arrhythmia, and constitutes a relevant target for mediating the relationship between TBX5, arrhythmia and heart development.
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Affiliation(s)
- Elena Guzzolino
- Institute of Clinical Physiology, National Research Council, IFC via Moruzzi 1, 56124, Pisa, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | - Neha Ahuja
- Department of Biology, Colorado State University (CSU), Fort Collins, CO, USA
| | - Deborah Garrity
- Department of Biology, Colorado State University (CSU), Fort Collins, CO, USA
| | | | - Marco Groth
- The Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Mario Baumgart
- The Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Cathy J Hatcher
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA, USA
| | - Alberto Mercatanti
- Institute of Clinical Physiology, National Research Council, IFC via Moruzzi 1, 56124, Pisa, Italy
| | - Monica Evangelista
- Institute of Clinical Physiology, National Research Council, IFC via Moruzzi 1, 56124, Pisa, Italy
| | - Chiara Ippolito
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | | | - Ryuichi Fukuda
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vincenzo Lionetti
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- UOS Anesthesiology, Fondazione Toscana "G.Monasterio", Pisa, Italy
| | | | | | - Letizia Pitto
- Institute of Clinical Physiology, National Research Council, IFC via Moruzzi 1, 56124, Pisa, Italy.
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30
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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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31
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Ma J, Chen S, Hao L, Sheng W, Chen W, Ma X, Zhang B, Ma D, Huang G. Hypermethylation-mediated down-regulation of lncRNA TBX5-AS1:2 in Tetralogy of Fallot inhibits cell proliferation by reducing TBX5 expression. J Cell Mol Med 2020; 24:6472-6484. [PMID: 32368852 PMCID: PMC7294119 DOI: 10.1111/jcmm.15298] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/06/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common complex congenital heart disease (CHD) with uncertain cause. Although long non‐coding RNAs (lncRNAs) have been implicated in heart development and several CHDs, their role in TOF is not well understood. This study aimed to investigate how dysregulated lncRNAs contribute to TOF. Using Gene Expression Omnibus data mining, bioinformatics analysis and clinical heart tissue sample detecting, we identified a novel antisense lncRNA TBX5‐AS1:2 with unknown function that was significantly down‐regulated in injured cardiac tissues from TOF patients. LncRNA TBX5‐AS1:2 was mainly located in the nucleus of the human embryonic kidney 293 (HEK293T) cells and formed an RNA‐RNA double‐stranded structure in the overlapping region with its sense mRNA T‐box transcription factor 5 (TBX5), which is an important regulator in heart development. Knock‐down of lncRNA TBX5‐AS1:2 via promoter hypermethylation reduced TBX5 expression at both the mRNA and protein levels by affecting its mRNA stability through RNA‐RNA interaction. Moreover, lncRNA TBX5‐AS1:2 knock‐down inhibited the proliferation of HEK293T cells. In conclusion, these results indicated that lncRNA TBX5‐AS1:2 may be involved in TOF by affecting cell proliferation by targeting TBX5.
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Affiliation(s)
- Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, ENT Institute, Eye & ENT Hospital, Fudan University, Shanghai, China.,Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shiyu Chen
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lili Hao
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wei Sheng
- Children's Hospital of Fudan University, Shanghai, China
| | - WeiCheng Chen
- Children's Hospital of Fudan University, Shanghai, China
| | - Xiaojing Ma
- Children's Hospital of Fudan University, Shanghai, China
| | - Bowen Zhang
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
| | - Guoying Huang
- Children's Hospital of Fudan University, Shanghai, China
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TBX5 R264K acts as a modifier to develop dilated cardiomyopathy in mice independently of T-box pathway. PLoS One 2020; 15:e0227393. [PMID: 32236096 PMCID: PMC7112173 DOI: 10.1371/journal.pone.0227393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/05/2020] [Indexed: 11/28/2022] Open
Abstract
Background TBX5 is a transcription factor that has an important role in development of heart. TBX5 variants in the region encoding the T-box domain have been shown to cause cardiac defects, such as atrial septal defect or ventricular septal defect, while TBX5 variants have also been identified in a few cardiomyopathy patients and considered causative. We identified a TBX5 variant (c.791G>A, p.Arg264Lys), that is over-represented in cardiomyopathy patients. This variant is located outside of the T-box domain, and its pathogenicity has not been confirmed by functional analyses. Objective To investigate whether the TBX5 R264K is deleterious and could contribute to the pathogenesis of cardiomyopathy. Methods and results We developed mice expressing Tbx5 R264K. Mice homozygous for this variant displayed compensated dilated cardiomyopathy; mild decreased fractional shortening, dilatation of the left ventricle, left ventricular wall thinning and increased heart weight without major heart structural disorders. There was no difference in activation of the ANF promotor, a transcriptional target of Tbx5, compared to wild-type. However, analysis of RNA isolated from left ventricular samples showed significant increases in the expression of Acta1 in left ventricle with concomitant increases in the protein level of ACTA1. Conclusions Mice homozygous for Tbx5 R264K showed compensated dilated cardiomyopathy. Thus, TBX5 R264K may have a significant pathogenic role in some cardiomyopathy patients independently of T-box domain pathway.
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Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state. Nat Cell Biol 2019; 21:1518-1531. [PMID: 31792383 DOI: 10.1038/s41556-019-0423-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022]
Abstract
The first lineage specification of pluripotent mouse epiblast segregates neuroectoderm (NE) from mesoderm and definitive endoderm (ME) by mechanisms that are not well understood. Here we demonstrate that the induction of ME gene programs critically relies on the T-box transcription factors Eomesodermin (also known as Eomes) and Brachyury, which concomitantly repress pluripotency and NE gene programs. Cells deficient in these T-box transcription factors retain pluripotency and differentiate to NE lineages despite the presence of ME-inducing signals transforming growth factor β (TGF-β)/Nodal and Wnt. Pluripotency and NE gene networks are additionally repressed by ME factors downstream of T-box factor induction, demonstrating a redundancy in program regulation to safeguard mutually exclusive lineage specification. Analyses of chromatin revealed that accessibility of ME enhancers depends on T-box factor binding, whereas NE enhancers are accessible and already activation primed at pluripotency. This asymmetry of the chromatin landscape thus explains the default differentiation of pluripotent cells to NE in the absence of ME induction that depends on activating and repressive functions of Eomes and Brachyury.
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34
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Ghosh TK, Aparicio-Sánchez JJ, Buxton S, Brook JD. HDAC4 and 5 repression of TBX5 is relieved by protein kinase D1. Sci Rep 2019; 9:17992. [PMID: 31784580 PMCID: PMC6884511 DOI: 10.1038/s41598-019-54312-w] [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: 04/05/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
TBX5 is a T-box family transcription factor that regulates heart and forelimb development in vertebrates and functional deficiencies in this protein result in Holt-Oram syndrome. Recently, we have shown that acetylation of TBX5 potentiates its activity and is important for heart and limb development. Here we report that class II histone deacetylases HDAC4 and HDAC5 associate with TBX5 and repress its role in cardiac gene transcription. Both HDAC4 and HDAC5 deacetylate TBX5, which promotes its relocation to the cytoplasm and HDAC4 antagonizes the physical association and functional cooperation between TBX5 and MEF2C. We also show that protein kinase D1 (PRKD1) relieves the HDAC4/5-mediated repression of TBX5. Thus, this study reveals a novel interaction of HDAC4/5 and PRKD1 in the regulation of TBX5 transcriptional activity.
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Affiliation(s)
- Tushar K Ghosh
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - José J Aparicio-Sánchez
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sarah Buxton
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - J David Brook
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
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35
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Akerberg BN, Gu F, VanDusen NJ, Zhang X, Dong R, Li K, Zhang B, Zhou B, Sethi I, Ma Q, Wasson L, Wen T, Liu J, Dong K, Conlon FL, Zhou J, Yuan GC, Zhou P, Pu WT. A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers. Nat Commun 2019; 10:4907. [PMID: 31659164 PMCID: PMC6817842 DOI: 10.1038/s41467-019-12812-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/27/2019] [Indexed: 01/09/2023] Open
Abstract
Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. These maps show that TF occupancy is dynamic between developmental stages and that multiple TFs often collaboratively occupy the same chromatin region through indirect cooperativity. Multi-TF regions exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. H3K27ac, a feature of many enhancers, incompletely overlaps multi-TF regions, and multi-TF regions lacking H3K27ac retain conservation and enhancer activity. TEAD1 is a core component of the cardiac transcriptional network, co-occupying cardiac regulatory regions and controlling cardiomyocyte-specific gene functions. Our study provides a resource for deciphering the cardiac transcriptional regulatory network and gaining insights into the molecular mechanisms governing heart development.
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Affiliation(s)
- Brynn N. Akerberg
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Fei Gu
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA ,grid.481558.5Alibaba Cloud Intelligence Business Group, Alibaba Group, 311121 Hangzhou, China
| | - Nathan J. VanDusen
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Xiaoran Zhang
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Rui Dong
- 0000 0001 2106 9910grid.65499.37Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 USA
| | - Kai Li
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Bing Zhang
- 0000 0004 0368 8293grid.16821.3cXin Hua Hospital, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Bin Zhou
- 0000 0004 0467 2285grid.419092.7Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, 200031 Shanghai, China
| | - Isha Sethi
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Qing Ma
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Lauren Wasson
- 0000000122483208grid.10698.36Biology Department, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599 USA
| | - Tong Wen
- 0000 0004 1758 4073grid.412604.5Department of Cardiology, The First Affiliated Hospital of Nanchang University, 330006 Nanchang, China
| | - Jinhua Liu
- 0000 0004 1758 4073grid.412604.5Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, 330006 Nanchang, China
| | - Kunzhe Dong
- 0000 0001 2284 9329grid.410427.4Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, 1459 Laney Walker Boulevard, Augusta, GA 30912 USA
| | - Frank L. Conlon
- 0000000122483208grid.10698.36Biology Department, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599 USA
| | - Jiliang Zhou
- 0000 0001 2284 9329grid.410427.4Department of Pharmacology & Toxicology, Medical College of Georgia, Augusta University, 1459 Laney Walker Boulevard, Augusta, GA 30912 USA
| | - Guo-Cheng Yuan
- 0000 0001 2106 9910grid.65499.37Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215 USA ,000000041936754Xgrid.38142.3cDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Pingzhu Zhou
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA
| | - William T. Pu
- 0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138 USA
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Leighton G, Williams DC. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex. J Mol Biol 2019:S0022-2836(19)30599-6. [PMID: 31626804 DOI: 10.1016/j.jmb.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex uniquely combines both deacetylase and remodeling enzymatic activities in a single macromolecular complex. The methyl-CpG-binding domain 2 and 3 (MBD2 and MBD3) proteins provide a critical structural link between the deacetylase and remodeling components, while MBD2 endows the complex with the ability to selectively recognize methylated DNA. Hence, NuRD combines three major arms of epigenetic gene regulation. Research over the past few decades has revealed much of the structural basis driving formation of this complex and started to uncover the functional roles of NuRD in epigenetic gene regulation. However, we have yet to fully understand the molecular and biophysical basis for methylation-dependent chromatin remodeling and transcription regulation by NuRD. In this review, we discuss the structural information currently available for the complex, the role MBD2 and MBD3 play in forming and recruiting the complex to methylated DNA, and the biological functions of NuRD.
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Affiliation(s)
- Gage Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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37
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Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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38
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Federspiel JD, Tandon P, Wilczewski CM, Wasson L, Herring LE, Venkatesh SS, Cristea IM, Conlon FL. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol 2019; 17:e3000437. [PMID: 31490923 PMCID: PMC6750614 DOI: 10.1371/journal.pbio.3000437] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/18/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
Heart disease is the leading cause of death in the western world. Attaining a mechanistic understanding of human heart development and homeostasis and the molecular basis of associated disease states relies on the use of animal models. Here, we present the cardiac proteomes of 4 model vertebrates with dual circulatory systems: the pig (Sus scrofa), the mouse (Mus musculus), and 2 frogs (Xenopus laevis and Xenopus tropicalis). Determination of which proteins and protein pathways are conserved and which have diverged within these species will aid in our ability to choose the appropriate models for determining protein function and to model human disease. We uncover mammalian- and amphibian-specific, as well as species-specific, enriched proteins and protein pathways. Among these, we find and validate an enrichment in cell-cycle-associated proteins within Xenopus laevis. To further investigate functional units within cardiac proteomes, we develop a computational approach to profile the abundance of protein complexes across species. Finally, we demonstrate the utility of these data sets for predicting appropriate model systems for studying given cardiac conditions by testing the role of Kielin/chordin-like protein (Kcp), a protein found as enriched in frog hearts compared to mammals. We establish that germ-line mutations in Kcp in Xenopus lead to valve defects and, ultimately, cardiac failure and death. Thus, integrating these findings with data on proteins responsible for cardiac disease should lead to the development of refined, species-specific models for protein function and disease states.
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Affiliation(s)
| | - Panna Tandon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caralynn M. Wilczewski
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lauren Wasson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laura E. Herring
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Ileana M. Cristea
- Princeton University, Princeton, New Jersey, United States of America
| | - Frank L. Conlon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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39
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Liu Y, Lu P, Wang Y, Morrow BE, Zhou B, Zheng D. Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis. J Am Heart Assoc 2019; 8:e012941. [PMID: 31322043 PMCID: PMC6761639 DOI: 10.1161/jaha.119.012941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Background Heart tube looping to form a 4-chambered heart is a critical stage of embryonic heart development, but the gene drivers and their regulatory targets have not been extensively characterized at the cell-type level. Methods and Results To study the interaction of signaling pathways, transcription factors (TFs), and genetic networks in the process, we constructed gene co-expression networks and identified gene modules highly activated in individual cardiomyocytes at multiple anatomical regions and developmental stages using previously published single-cell RNA-seq data. Function analyses of the modules uncovered major pathways important for spatiotemporal cardiomyocyte differentiation. Interestingly, about half of the pathways were highly active in cardiomyocytes at the outflow tract (OFT) and atrioventricular canal, including well-known pathways for cardiac development and many newly identified ones. We predicted that these OFT-atrioventricular canal pathways were regulated by a large number of TFs actively expressed at the OFT-atrioventricular canal cardiomyocytes, with the prediction supported by motif enrichment analysis, including 10 TFs that have not been previously associated with cardiac development (eg, Etv5, Rbpms, and Baz2b). Furthermore, we found that TF targets in the OFT-atrioventricular canal modules were most significantly enriched with genes associated with mouse heart developmental abnormalities and human congenital heart defects, in comparison with TF targets in other modules, consistent with the critical developmental roles of OFT. Conclusions By analyzing gene co-expression at single cardiomyocytes, our systematic study has uncovered many known and additional new important TFs and their regulated molecular signaling pathways that are spatiotemporally active during heart looping.
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Affiliation(s)
- Yang Liu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Pengfei Lu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Yidong Wang
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Bernice E. Morrow
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
| | - Bin Zhou
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
- Department of MedicineAlbert Einstein College of MedicineBronxNY
| | - Deyou Zheng
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of NeurologyAlbert Einstein College of MedicineBronxNY
- Department of NeuroscienceAlbert Einstein College of MedicineBronxNY
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40
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Xiong H, Luo Y, Yue Y, Zhang J, Ai S, Li X, Wang X, Zhang YL, Wei Y, Li HH, Hu X, Li C, He A. Single-Cell Transcriptomics Reveals Chemotaxis-Mediated Intraorgan Crosstalk During Cardiogenesis. Circ Res 2019; 125:398-410. [PMID: 31221018 DOI: 10.1161/circresaha.119.315243] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RATIONALE We hypothesized that the differentiation processes of cardiac progenitor cell (CP) from first and second heart fields (FHF and SHF) may undergo the unique instructive gene regulatory networks or signaling pathways, and the precise SHF progression is contingent on the FHF signaling developmental cues. OBJECTIVE We investigated how the intraorgan communications control sequential building of discrete anatomic regions of the heart at single-cell resolution. METHODS AND RESULTS By single-cell transcriptomic analysis of Nkx2-5 (NK2 homeobox 5) and Isl1 (ISL LIM homeobox 1) lineages at embryonic day 7.75, embryonic day 8.25, embryonic day 8.75, and embryonic day 9.25, we present a panoramic view of distinct CP differentiation hierarchies. Computational identifications of FHF- and SHF-CP descendants revealed that SHF differentiation toward cardiomyocytes underwent numerous step-like transitions, whereas earlier FHF progressed toward cardiomyocytes in a wave-like manner. Importantly, single-cell pairing analysis demonstrated that SHF-CPs were attracted to and expanded FHF-populated heart tube region through interlineage communications mediated by the chemotactic guidance (MIF [macrophage migration inhibitory factor]-CXCR2 [C-X-C motif chemokine receptor 2]). This finding was verified by pharmacological blockade of this chemotaxis in embryos manifesting limited SHF cell migration and contribution to the growth of the outflow tract and right ventricle but undetectable effects on the left ventricle or heart tube initiation. Genetic loss-of-function assay of Cxcr2 showed that the expression domain of CXCR4 was expanded predominantly at SHF. Furthermore, double knockout of Cxcr2/Cxcr4 exhibited defective SHF development, corroborating the redundant function. Mechanistically, NKX2-5 directly bound the Cxcr2 and Cxcr4 genomic loci and activated their transcription in SHF. CONCLUSIONS Collectively, we propose a model in which the chemotaxis-mediated intraorgan crosstalk spatiotemporally guides the successive process of positioning SHF-CP and promoting primary heart expansion and patterning upon FHF-derived heart tube initiation.
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Affiliation(s)
- Haiqing Xiong
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China.,Academy for Advanced Interdisciplinary Studies (H.X., Y.L.), Peking University, China
| | - Yingjie Luo
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China.,Academy for Advanced Interdisciplinary Studies (H.X., Y.L.), Peking University, China
| | - Yanzhu Yue
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Jiejie Zhang
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Shanshan Ai
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Xin Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Xuelian Wang
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Yun-Long Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, China (Y.-L.Z., H.-H.L.)
| | - Yusheng Wei
- School of Life Sciences (Y.W., C.L.), Peking University, China
| | - Hui-Hua Li
- Department of Cardiology, Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, China (Y.-L.Z., H.-H.L.)
| | - Xinli Hu
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Cheng Li
- School of Life Sciences (Y.W., C.L.), Peking University, China.,Center for Statistical Science, Center for Bioinformatics (C.L.), Peking University, China
| | - Aibin He
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China
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Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming. Cell Stem Cell 2019; 25:149-164.e9. [PMID: 31230860 DOI: 10.1016/j.stem.2019.05.020] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/21/2019] [Accepted: 05/22/2019] [Indexed: 12/11/2022]
Abstract
Direct cellular reprogramming provides a powerful platform to study cell plasticity and dissect mechanisms underlying cell fate determination. Here, we report a single-cell transcriptomic study of human cardiac (hiCM) reprogramming that utilizes an analysis pipeline incorporating current data normalization methods, multiple trajectory prediction algorithms, and a cell fate index calculation we developed to measure reprogramming progression. These analyses revealed hiCM reprogramming-specific features and a decision point at which cells either embark on reprogramming or regress toward their original fibroblast state. In combination with functional screening, we found that immune-response-associated DNA methylation is required for hiCM induction and validated several downstream targets of reprogramming factors as necessary for productive hiCM reprograming. Collectively, this single-cell transcriptomics study provides detailed datasets that reveal molecular features underlying hiCM determination and rigorous analytical pipelines for predicting cell fate conversion.
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42
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Poelmann RE, Gittenberger-de Groot AC. Development and evolution of the metazoan heart. Dev Dyn 2019; 248:634-656. [PMID: 31063648 PMCID: PMC6767493 DOI: 10.1002/dvdy.45] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of the evolution and development of the heart in metazoans are highlighted, starting with the evolutionary origin of the contractile cell, supposedly the precursor of cardiomyocytes. The last eukaryotic common ancestor is likely a combination of several cellular organisms containing their specific metabolic pathways and genetic signaling networks. During evolution, these tool kits diversified. Shared parts of these conserved tool kits act in the development and functioning of pumping hearts and open or closed circulations in such diverse species as arthropods, mollusks, and chordates. The genetic tool kits became more complex by gene duplications, addition of epigenetic modifications, influence of environmental factors, incorporation of viral genomes, cardiac changes necessitated by air‐breathing, and many others. We evaluate mechanisms involved in mollusks in the formation of three separate hearts and in arthropods in the formation of a tubular heart. A tubular heart is also present in embryonic stages of chordates, providing the septated four‐chambered heart, in birds and mammals passing through stages with first and second heart fields. The four‐chambered heart permits the formation of high‐pressure systemic and low‐pressure pulmonary circulation in birds and mammals, allowing for high metabolic rates and maintenance of body temperature. Crocodiles also have a (nearly) separated circulation, but their resting temperature conforms with the environment. We argue that endothermic ancestors lost the capacity to elevate their body temperature during evolution, resulting in ectothermic modern crocodilians. Finally, a clinically relevant paragraph reviews the occurrence of congenital cardiac malformations in humans as derailments of signaling pathways during embryonic development. The cardiac regulatory toolkit contains many factors including epigenetic, genetic, viral, hemodynamic, and environmental factors, but also transcriptional activators, repressors, duplicated genes, redundancies and dose‐dependancies. Numerous toolkits regulate mechanisms including cell‐cell interactions, EMT, mitosis patterns, cell migration and differentiation and left/right sidedness involved in the development of endocardial cushions, looping, septum complexes, pharyngeal arch arteries, chamber and valve formation and conduction system. Evolutionary development of the yolk sac circulation likely preceded the advent of endothermy in amniotes. Parallel evolutionary traits regulate the development of contractile pumps in various taxa often in conjunction with the gut, lungs and excretory organs.
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Affiliation(s)
- Robert E Poelmann
- Institute of Biology, Department of Animal Sciences and Health, Leiden University, Leiden, The Netherlands.,Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
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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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De Bono C, Thellier C, Bertrand N, Sturny R, Jullian E, Cortes C, Stefanovic S, Zaffran S, Théveniau-Ruissy M, Kelly RG. T-box genes and retinoic acid signaling regulate the segregation of arterial and venous pole progenitor cells in the murine second heart field. Hum Mol Genet 2019; 27:3747-3760. [PMID: 30016433 DOI: 10.1093/hmg/ddy266] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/11/2018] [Indexed: 01/10/2023] Open
Abstract
The arterial and venous poles of the mammalian heart are hotspots of congenital heart defects (CHD) such as those observed in 22q11.2 deletion (or DiGeorge) and Holt-Oram syndromes. These regions of the heart are derived from late differentiating cardiac progenitor cells of the Second Heart Field (SHF) located in pharyngeal mesoderm contiguous with the elongating heart tube. The T-box transcription factor Tbx1, encoded by the major 22q11.2 deletion syndrome gene, regulates SHF addition to both cardiac poles from a common progenitor population. Despite the significance of this cellular addition the mechanisms regulating the deployment of common progenitor cells to alternate cardiac poles remain poorly understood. Here we demonstrate that Tbx5, mutated in Holt-Oram syndrome and essential for venous pole development, is activated in Tbx1 expressing cells in the posterior region of the SHF at early stages of heart tube elongation. A subset of the SHF transcriptional program, including Tbx1 expression, is subsequently downregulated in Tbx5 expressing cells, generating a transcriptional boundary between Tbx1-positive arterial pole and Tbx5-positive venous pole progenitor cell populations. We show that normal downregulation of the definitive arterial pole progenitor cell program in the posterior SHF is dependent on both Tbx1 and Tbx5. Furthermore, retinoic acid (RA) signaling is required for Tbx5 activation in Tbx1-positive cells and blocking RA signaling at the time of Tbx5 activation results in atrioventricular septal defects at fetal stages. Our results reveal sequential steps of cardiac progenitor cell patterning and provide mechanistic insights into the origin of common forms of CHD.
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Affiliation(s)
| | | | | | - Rachel Sturny
- Aix-Marseille Univ, CNRS UMR 7288, IBDM, Marseille, France
| | | | - Claudio Cortes
- Aix-Marseille Univ, CNRS UMR 7288, IBDM, Marseille, France
| | | | | | | | - Robert G Kelly
- Aix-Marseille Univ, CNRS UMR 7288, IBDM, Marseille, France
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Dorr KM, Conlon FL. Proteomic-based approaches to cardiac development and disease. Curr Opin Chem Biol 2019; 48:150-157. [PMID: 30711722 DOI: 10.1016/j.cbpa.2019.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 01/14/2023]
Abstract
Congenital malformations, or structural birth defects, are now the leading cause of infant mortality in the United States and Europe (Dolk et al., 2010; Heron et al., 2009). Of the congenital malformations, congenital heart disease (CHD) is the most common (Dolk et al., 2010; Heron et al., 2009). Thus, a molecular understanding of heart development is an essential goal for improving clinical approaches to CHD. However, CHDs are commonly a result of genetic defects that manifest themselves in a spatial and temporal manner during the early stages of embryogenesis, leaving them mostly intractable to mass spectrometry-based analysis. Here, we describe the technologies and advancements in the field of mass spectrometry over the past few years that have begun to provide insights into the molecular and cellular basis of CHD and prospects for these types of approaches in the future.
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Affiliation(s)
- Kerry M Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA.
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Evolutionarily conserved Tbx5- Wnt2/2b pathway orchestrates cardiopulmonary development. Proc Natl Acad Sci U S A 2018; 115:E10615-E10624. [PMID: 30352852 DOI: 10.1073/pnas.1811624115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Codevelopment of the lungs and heart underlies key evolutionary innovations in the transition to terrestrial life. Cardiac specializations that support pulmonary circulation, including the atrial septum, are generated by second heart field (SHF) cardiopulmonary progenitors (CPPs). It has been presumed that transcription factors required in the SHF for cardiac septation, e.g., Tbx5, directly drive a cardiac morphogenesis gene-regulatory network. Here, we report instead that TBX5 directly drives Wnt ligands to initiate a bidirectional signaling loop between cardiopulmonary mesoderm and the foregut endoderm for endodermal pulmonary specification and, subsequently, atrial septation. We show that Tbx5 is required for pulmonary specification in mice and amphibians but not for swim bladder development in zebrafish. TBX5 is non-cell-autonomously required for pulmonary endoderm specification by directly driving Wnt2 and Wnt2b expression in cardiopulmonary mesoderm. TBX5 ChIP-sequencing identified cis-regulatory elements at Wnt2 sufficient for endogenous Wnt2 expression domains in vivo and required for Wnt2 expression in precardiac mesoderm in vitro. Tbx5 cooperated with Shh signaling to drive Wnt2b expression for lung morphogenesis. Tbx5 haploinsufficiency in mice, a model of Holt-Oram syndrome, caused a quantitative decrement of mesodermal-to-endodermal Wnt signaling and subsequent endodermal-to-mesodermal Shh signaling required for cardiac morphogenesis. Thus, Tbx5 initiates a mesoderm-endoderm-mesoderm signaling loop in lunged vertebrates that provides a molecular basis for the coevolution of pulmonary and cardiac structures required for terrestrial life.
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Spiridon MR, Petris AO, Gorduza EV, Petras AS, Popescu R, Caba L. Holt-Oram Syndrome With Multiple Cardiac Abnormalities. Cardiol Res 2018; 9:324-329. [PMID: 30344832 PMCID: PMC6188042 DOI: 10.14740/cr767w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022] Open
Abstract
Holt-Oram syndrome (HOS) is a rare monogenic disorder characterized by upper limb abnormalities, congenital heart defects and/or conduction abnormalities. It is determined by mutations of TBX5 gene and is inherited in an autosomal dominant manner. Penetrance is complete, but variable expressivity is present, which gives sometimes diagnostic difficulties. Our case is a young adult with a personal history of preaxial polydactyly operated in infancy, multiple cardiac malformations (atrial septal defect, bicuspid aortic valve, left ventricular non-compaction) and radiologic findings consistent with HOS. Family history is negative for HOS. In conclusion, we present a case of HOS diagnosed in the adult period to highlight the diagnostic problems for the proband and the family and the importance of an early diagnostic.
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Affiliation(s)
| | - Antoniu Octavian Petris
- Cardiology Department, "St. Spiridon" Emergency Hospital, Iasi, Romania.,Cardiology Department, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania
| | - Eusebiu Vlad Gorduza
- Medical Genetics Department, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania
| | | | - Roxana Popescu
- Medical Genetics Department, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania
| | - Lavinia Caba
- Medical Genetics Department, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania
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48
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Abstract
Cardiac development relies on proper cardiomyocyte differentiation, including expression and assembly of cell-type-specific actomyosin subunits into a functional cardiac sarcomere. Control of this process involves not only promoting expression of cardiac sarcomere subunits but also repressing expression of noncardiac myofibril paralogs. This level of transcriptional control requires broadly expressed multiprotein machines that modify and remodel the chromatin landscape to restrict transcription machinery access. Prominent among these is the nucleosome remodeling and deacetylase (NuRD) complex, which includes the catalytic core subunit CHD4. Here, we demonstrate that direct CHD4-mediated repression of skeletal and smooth muscle myofibril isoforms is required for normal cardiac sarcomere formation, function, and embryonic survival early in gestation. Through transcriptomic and genome-wide analyses of CHD4 localization, we identified unique CHD4 binding sites in smooth muscle myosin heavy chain, fast skeletal α-actin, and the fast skeletal troponin complex genes. We further demonstrate that in the absence of CHD4, cardiomyocytes in the developing heart form a hybrid muscle cell that contains cardiac, skeletal, and smooth muscle myofibril components. These misexpressed paralogs intercalate into the nascent cardiac sarcomere to disrupt sarcomere formation and cause impaired cardiac function in utero. These results demonstrate the genomic and physiological requirements for CHD4 in mammalian cardiac development.
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Liu Z, Wang L, Welch JD, Ma H, Zhou Y, Vaseghi HR, Yu S, Wall JB, Alimohamadi S, Zheng M, Yin C, Shen W, Prins JF, Liu J, Qian L. Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte. Nature 2017; 551:100-104. [PMID: 29072293 PMCID: PMC5954984 DOI: 10.1038/nature24454] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/22/2017] [Indexed: 12/18/2022]
Abstract
Direct lineage conversion offers a new strategy for tissue regeneration and disease modelling. Despite recent success in directly reprogramming fibroblasts into various cell types, the precise changes that occur as fibroblasts progressively convert to the target cell fates remain unclear. The inherent heterogeneity and asynchronous nature of the reprogramming process renders it difficult to study this process using bulk genomic techniques. Here we used single-cell RNA sequencing to overcome this limitation and analysed global transcriptome changes at early stages during the reprogramming of mouse fibroblasts into induced cardiomyocytes (iCMs). Using unsupervised dimensionality reduction and clustering algorithms, we identified molecularly distinct subpopulations of cells during reprogramming. We also constructed routes of iCM formation, and delineated the relationship between cell proliferation and iCM induction. Further analysis of global gene expression changes during reprogramming revealed unexpected downregulation of factors involved in mRNA processing and splicing. Detailed functional analysis of the top candidate splicing factor, Ptbp1, revealed that it is a critical barrier for the acquisition of cardiomyocyte-specific splicing patterns in fibroblasts. Concomitantly, Ptbp1 depletion promoted cardiac transcriptome acquisition and increased iCM reprogramming efficiency. Additional quantitative analysis of our dataset revealed a strong correlation between the expression of each reprogramming factor and the progress of individual cells through the reprogramming process, and led to the discovery of new surface markers for the enrichment of iCMs. In summary, our single-cell transcriptomics approaches enabled us to reconstruct the reprogramming trajectory and to uncover intermediate cell populations, gene pathways and regulators involved in iCM induction.
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Affiliation(s)
- Ziqing Liu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Li Wang
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Joshua D. Welch
- Department of Computer Science, University of North Carolina at Chapel Hill
| | - Hong Ma
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Yang Zhou
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Haley Ruth Vaseghi
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Shuo Yu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Joseph Blake Wall
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Sahar Alimohamadi
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Michael Zheng
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Chaoying Yin
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Weining Shen
- Department of Statistics, University of California at Irvine
| | - Jan F. Prins
- Department of Computer Science, University of North Carolina at Chapel Hill
| | - Jiandong Liu
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
| | - Li Qian
- McAllister Heart Institute, University of North Carolina at Chapel Hill
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill
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50
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Kennedy L, Kaltenbrun E, Greco TM, Temple B, Herring LE, Cristea IM, Conlon FL. Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis. PLoS Genet 2017; 13:e1007011. [PMID: 28945738 PMCID: PMC5629033 DOI: 10.1371/journal.pgen.1007011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/05/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
By the age of 40, one in five adults without symptoms of cardiovascular disease are at risk for developing congestive heart failure. Within this population, dilated cardiomyopathy (DCM) remains one of the leading causes of disease and death, with nearly half of cases genetically determined. Though genetic and high throughput sequencing-based approaches have identified sporadic and inherited mutations in a multitude of genes implicated in cardiomyopathy, how combinations of asymptomatic mutations lead to cardiac failure remains a mystery. Since a number of studies have implicated mutations of the transcription factor TBX20 in congenital heart diseases, we investigated the underlying mechanisms, using an unbiased systems-based screen to identify novel, cardiac-specific binding partners. We demonstrated that TBX20 physically and genetically interacts with the essential transcription factor CASZ1. This interaction is required for survival, as mice heterozygous for both Tbx20 and Casz1 die post-natally as a result of DCM. A Tbx20 mutation associated with human familial DCM sterically interferes with the TBX20-CASZ1 interaction and provides a physical basis for how this human mutation disrupts normal cardiac function. Finally, we employed quantitative proteomic analyses to define the molecular pathways mis-regulated upon disruption of this novel complex. Collectively, our proteomic, biochemical, genetic, and structural studies suggest that the physical interaction between TBX20 and CASZ1 is required for cardiac homeostasis, and further, that reduction or loss of this critical interaction leads to DCM. This work provides strong evidence that DCM can be inherited through a digenic mechanism. A molecular understanding of cardiomyocyte development is an essential goal for improving clinical approaches to CHD. While TBX20 is an essential transcription factor for heart development and its disease relevance is well established, many fundamental questions remain about the mechanism of TBX20 function. Principle among these is how TBX20 mutations associated with adult dilated cardiomyopathy circumvent (DCM) the essential embryonic requirement for TBX20 in heart development. Here we report using an integrated approach that TBX20 complexes with the cardiac transcription factor CASZ1 in vivo. We confirmed TBX20 and CASZ1 interact biochemically and genetically, and show mice heterozygous for both Tbx20 and Casz1 die, beginning at 4 to 8 weeks post birth, exhibiting hallmarks of DCM. Interestingly, the human mutant TBX20F256I bypasses the early essential requirement for TBX20 but leads to DCM. We report here that TBX20F256I disrupts the TBX20-CASZ1 interaction, ascribing clinical relevance to this protein complex. Further, by using quantitative proteomics we have identified the molecular pathways altered in TBX20-CASZ1-mediated DCM. Together, these results identify a novel interaction between TBX20 and CASZ1 that is essential for maintaining cardiac homeostasis and imply that DCM can be inherited through a digenic mechanism.
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Affiliation(s)
- Leslie Kennedy
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Erin Kaltenbrun
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Todd M. Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Brenda Temple
- R.L. Juliano Structural Bioinformatics Core, Department of Biochemistry and Biophysics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Laura E. Herring
- UNC Proteomics Core Facility, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Frank L. Conlon
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- Department of Biology, UNC-Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
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