1
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Jang J, Bentsen M, Kim YJ, Kim E, Garg V, Cai CL, Looso M, Li D. Endocardial HDAC3 is required for myocardial trabeculation. Nat Commun 2024; 15:4166. [PMID: 38755146 PMCID: PMC11099086 DOI: 10.1038/s41467-024-48362-6] [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: 04/16/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Failure of proper ventricular trabeculation is often associated with congenital heart disease. Support from endocardial cells, including the secretion of extracellular matrix and growth factors is critical for trabeculation. However, it is poorly understood how the secretion of extracellular matrix and growth factors is initiated and regulated by endocardial cells. We find that genetic knockout of histone deacetylase 3 in the endocardium in mice results in early embryo lethality and ventricular hypotrabeculation. Single cell RNA sequencing identifies significant downregulation of extracellular matrix components in histone deacetylase 3 knockout endocardial cells. Secretome from cultured histone deacetylase 3 knockout mouse cardiac endothelial cells lacks transforming growth factor ß3 and shows significantly reduced capacity in stimulating cultured cardiomyocyte proliferation, which is remarkably rescued by transforming growth factor ß3 supplementation. Mechanistically, we identify that histone deacetylase 3 knockout induces transforming growth factor ß3 expression through repressing microRNA-129-5p. Our findings provide insights into the pathogenesis of congenital heart disease and conceptual strategies to promote myocardial regeneration.
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Affiliation(s)
- Jihyun Jang
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA
| | - Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Ye Jun Kim
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Erick Kim
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA
| | - Chen-Leng Cai
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46201, USA
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Deqiang Li
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43215, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA.
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2
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Afanasyev AY, Kim Y, Tolokh IS, Sharakhov IV, Onufriev AV. The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies. Epigenetics Chromatin 2024; 17:13. [PMID: 38705995 PMCID: PMC11071202 DOI: 10.1186/s13072-024-00528-8] [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: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. RESULTS In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. CONCLUSIONS At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor S Tolokh
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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3
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Hu S, Chapski DJ, Gehred ND, Kimball TH, Gromova T, Flores A, Rowat AC, Chen J, Packard RRS, Olszewski E, Davis J, Rau CD, McKinsey TA, Rosa-Garrido M, Vondriska TM. Histone H1.0 couples cellular mechanical behaviors to chromatin structure. NATURE CARDIOVASCULAR RESEARCH 2024; 3:441-459. [PMID: 38765203 PMCID: PMC11101354 DOI: 10.1038/s44161-024-00460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/06/2024] [Indexed: 05/21/2024]
Abstract
Tuning of genome structure and function is accomplished by chromatin-binding proteins, which determine the transcriptome and phenotype of the cell. Here we investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that histone H1.0, which compacts nucleosomes into higher-order chromatin fibers, controls genome organization and cellular stress response. We show that histone H1.0 has privileged expression in fibroblasts across tissue types and that its expression is necessary and sufficient to induce myofibroblast activation. Depletion of histone H1.0 prevents cytokine-induced fibroblast contraction, proliferation and migration via inhibition of a transcriptome comprising extracellular matrix, cytoskeletal and contractile genes, through a process that involves locus-specific H3K27 acetylation. Transient depletion of histone H1.0 in vivo prevents fibrosis in cardiac muscle. These findings identify an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling force generation, nuclear organization and gene transcription.
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Affiliation(s)
- Shuaishuai Hu
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Douglas J. Chapski
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Natalie D. Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Todd H. Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Angelina Flores
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Amy C. Rowat
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Junjie Chen
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - René R. Sevag Packard
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Emily Olszewski
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Christoph D. Rau
- Department of Genetics and McAllister Heart Institute, University of North Carolina, Chapel Hill, NC USA
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
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4
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Wong KG, Cheng YCF, Wu VH, Kiseleva AA, Li J, Poleshko A, Smith CL, Epstein JA. Growth factor-induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression. SCIENCE ADVANCES 2024; 10:eadm9518. [PMID: 38478612 PMCID: PMC10936876 DOI: 10.1126/sciadv.adm9518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Extracellular signals are transmitted through kinase cascades to modulate gene expression, but it remains unclear how epigenetic changes regulate this response. Here, we provide evidence that growth factor-stimulated changes in the transcript levels of many responsive genes are accompanied by increases in histone phosphorylation levels, specifically at histone H3 serine-10 when the adjacent lysine-9 is dimethylated (H3K9me2S10). Imaging and proteomic approaches show that epidermal growth factor (EGF) stimulation results in H3K9me2S10 phosphorylation, which occurs in genomic regions enriched for regulatory enhancers of EGF-responsive genes. We also demonstrate that the EGF-induced increase in H3K9me2S10ph is dependent on the nuclear kinase MSK2, and this subset of EGF-induced genes is dependent on MSK2 for transcription. Together, our work indicates that growth factor-induced changes in chromatin state can mediate the activation of downstream genes.
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Affiliation(s)
- Karen G. Wong
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yu-Chia F. Cheng
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vincent H. Wu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna A. Kiseleva
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jun Li
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl L. Smith
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Jang J, Bentsen M, Kim YJ, Kim E, Garg V, Cai CL, Looso M, Li D. Endocardial HDAC3 is required for myocardial trabeculation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536668. [PMID: 37886504 PMCID: PMC10602027 DOI: 10.1101/2023.04.12.536668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
BACKGROUND Trabeculation, a key process in early heart development, is the formation of myocardial trabecular meshwork. The failure of trabeculation often leads to embryonic lethality. Support from endocardial cells, including the secretion of extracellular matrix (ECM) and growth factors is critical for trabeculation; however, it is unknown how the secretion of ECM and growth factors is initiated and regulated by endocardial cells. METHODS Various cellular and mouse models in conjunction with biochemical and molecular tools were employed to study the role of histone deacetylase 3 (HDAC3) in the developing endocardium. RESULTS We found that genetic deletion of Hdac3 in endocardial cells in mice resulted in early embryo lethality presenting as a hypotrabeculation cardiac phenotype. Single cell RNA sequencing identified several ECM components including collagens that were significantly downregulated in Hdac3 knockout (KO) endocardial cells. When cultured with supernatant from Hdac3 KO mouse cardiac endothelial cells (MCECs), wild-type mouse embryonic cardiomyocytes showed decreased proliferation, suggesting that growth signaling from Hdac3 KO MCECs is disrupted. Subsequent transcriptomic analysis revealed that transforming growth factor β3 (TGFβ3) was significantly downregulated in Hdac3 KO MCECs and Hdac3 cardiac endothelial KO hearts. Mechanistically, we identified that microRNA (miR)-129-5p was significantly upregulated in Hdac3 KO MCECs and Hdac3 cardiac endothelial KO hearts. Overexpression of miR-129-5p repressed Tgfβ3 expression in wild-type MCECs, whereas knockdown of miR-129-5p restored Tgfβ3 expression in Hdac3 KO MCECs. CONCLUSION Our findings reveal a critical signaling pathway in which endocardial HDAC3 promotes trabecular myocardium growth by stimulating TGFβ signaling through repressing miR-129-5p, providing novel insights into the etiology of congenital heart disease and conceptual strategies to promote myocardial regeneration.
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6
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Sobo JM, Alagna NS, Sun SX, Wilson KL, Reddy KL. Lamins: The backbone of the nucleocytoskeleton interface. Curr Opin Cell Biol 2024; 86:102313. [PMID: 38262116 DOI: 10.1016/j.ceb.2023.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024]
Abstract
The nuclear lamina (NL) is a crucial component of the inner nuclear membrane (INM) and consists of lamin filaments and associated proteins. Lamins are type V intermediate filament proteins essential for maintaining the integrity and mechanical properties of the nucleus. In human cells, 'B-type' lamins (lamin B1 and lamin B2) are ubiquitously expressed, while 'A-type' lamins (lamin A, lamin C, and minor isoforms) are expressed in a tissue- and development-specific manner. Lamins homopolymerize to form filaments that localize primarily near the INM, but A-type lamins also localize to and function in the nucleoplasm. Lamins play central roles in the assembly, structure, positioning, and mechanics of the nucleus, modulating cell signaling and influencing development, differentiation, and other activities. This review highlights recent findings on the structure and regulation of lamin filaments, providing insights into their multifaceted functions, including their role as "mechanosensors", delving into the emerging significance of lamin filaments as vital links between cytoskeletal and nuclear structures, chromatin organization, and the genome.
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Affiliation(s)
- Joan M Sobo
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Nicholas S Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sean X Sun
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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7
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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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8
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Gouhier A, Dumoulin-Gagnon J, Lapointe-Roberge V, Harris J, Balsalobre A, Drouin J. Pioneer factor Pax7 initiates two-step cell-cycle-dependent chromatin opening. Nat Struct Mol Biol 2024; 31:92-101. [PMID: 38177665 DOI: 10.1038/s41594-023-01152-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/16/2023] [Indexed: 01/06/2024]
Abstract
Pioneer transcription factors direct cell differentiation by deploying new enhancer repertoires through their unique ability to target and initiate remodelling of closed chromatin. The initial steps of their action remain undefined, although pioneers have been shown to interact with nucleosomal target DNA and with some chromatin-remodeling complexes. We now define the sequence of events that enables the pioneer Pax7 with its unique abilities. Chromatin condensation exerted by linker histone H1 is the first constraint on Pax7 recruitment, and this establishes the initial speed of chromatin remodeling. The first step of pioneer action involves recruitment of the KDM1A (LSD1) H3K9me2 demethylase for removal of this repressive mark, as well as recruitment of the MLL complex for deposition of the activating H3K4me1 mark. Further progression of pioneer action requires passage through cell division, and this involves dissociation of pioneer targets from perinuclear lamin B. Only then are the SWI-SNF remodeling complex and the coactivator p300 recruited, leading to nucleosome displacement and enhancer activation. Thus, the unique features of pioneer actions are those occurring in the lamin-associated compartment of the nucleus. This model is consistent with previous work that showed a dependence on cell division for establishment of new cell fates.
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Affiliation(s)
- Arthur Gouhier
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Justine Dumoulin-Gagnon
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada
| | - Vincent Lapointe-Roberge
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Juliette Harris
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada
| | - Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM) Montreal, Quebec, Canada.
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada.
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9
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Li Y, Bertozzi A, Mann MRW, Kühn B. Interdependent changes of nuclear lamins, nuclear pore complexes, and ploidy regulate cellular regeneration and stress response in the heart. Nucleus 2023; 14:2246310. [PMID: 37606283 PMCID: PMC10446781 DOI: 10.1080/19491034.2023.2246310] [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: 12/20/2022] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration. In contrast, fetal and neonatal heart muscle cells are diploid, proliferate, and contribute to heart regeneration. We have identified interdependent changes of the nuclear lamina, nuclear pore complexes, and DNA-content (ploidy) in heart muscle cell maturation. These results offer new perspectives on how cells alter their nuclear transport and, with that, their gene regulation in response to extracellular signals. We present how changes of the nuclear lamina alter nuclear pore complexes in heart muscle cells. The consequences of these changes for cellular regeneration and stress response in the heart are discussed.
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Affiliation(s)
- Yao Li
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alberto Bertozzi
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mellissa RW Mann
- Department of Obstetrics, Gynaecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Bernhard Kühn
- Division of Pediatric Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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10
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Kiseleva AA, Cheng YC, Smith CL, Katz RA, Poleshko A. PRR14 organizes H3K9me3-modified heterochromatin at the nuclear lamina. Nucleus 2023; 14:2165602. [PMID: 36633363 PMCID: PMC9839372 DOI: 10.1080/19491034.2023.2165602] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The eukaryotic genome is organized in three dimensions within the nucleus. Transcriptionally active chromatin is spatially separated from silent heterochromatin, a large fraction of which is located at the nuclear periphery. However, the mechanisms by which chromatin is localized at the nuclear periphery remain poorly understood. Here we demonstrate that Proline Rich 14 (PRR14) protein organizes H3K9me3-modified heterochromatin at the nuclear lamina. We show that PRR14 dynamically associates with both the nuclear lamina and heterochromatin, and is able to reorganize heterochromatin in the nucleus of interphase cells independent of mitosis. We characterize two functional HP1-binding sites within PRR14 that contribute to its association with heterochromatin. We also demonstrate that PPR14 forms an anchoring surface for heterochromatin at the nuclear lamina where it interacts dynamically with HP1-associated chromatin. Our study proposes a model of dynamic heterochromatin organization at the nuclear lamina via the PRR14 tethering protein.
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Affiliation(s)
- Anna A. Kiseleva
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yu-Chia Cheng
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cheryl L. Smith
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Richard A. Katz
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Andrey Poleshko Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, SCTR 09-188, 3400 Civic Center Blvd. Philadelphia, PA19104
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11
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Xiao Y, Hale S, Awasthee N, Meng C, Zhang X, Liu Y, Ding H, Huo Z, Lv D, Zhang W, He M, Zheng G, Liao D. HDAC3 and HDAC8 PROTAC dual degrader reveals roles of histone acetylation in gene regulation. Cell Chem Biol 2023; 30:1421-1435.e12. [PMID: 37572669 PMCID: PMC10802846 DOI: 10.1016/j.chembiol.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 05/19/2023] [Accepted: 07/22/2023] [Indexed: 08/14/2023]
Abstract
HDAC3 and HDAC8 have critical biological functions and represent highly sought-after therapeutic targets. Because histone deacetylases (HDACs) have a very conserved catalytic domain, developing isozyme-selective inhibitors remains challenging. HDAC3/8 also have deacetylase-independent activity, which cannot be blocked by conventional enzymatic inhibitors. Proteolysis-targeting chimeras (PROTACs) can selectively degrade a target enzyme, abolishing both enzymatic and scaffolding function. Here, we report a novel HDAC3/8 dual degrader YX968 that induces highly potent, rapid, and selective degradation of both HDAC3/8 without triggering pan-HDAC inhibitory effects. Unbiased quantitative proteomic experiments confirmed its high selectivity. HDAC3/8 degradation by YX968 does not induce histone hyperacetylation and broad transcriptomic perturbation. Thus, histone hyperacetylation may be a major factor for altering transcription. YX968 promotes apoptosis and kills cancer cells with a high potency in vitro. YX968 thus represents a new probe for dissecting the complex biological functions of HDAC3/8.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Seth Hale
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nikee Awasthee
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Chengcheng Meng
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Haocheng Ding
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.
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12
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Alagna NS, Thomas TI, Wilson KL, Reddy KL. Choreography of lamina-associated domains: structure meets dynamics. FEBS Lett 2023; 597:2806-2822. [PMID: 37953467 PMCID: PMC10858991 DOI: 10.1002/1873-3468.14771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 11/14/2023]
Abstract
Lamina-associated domains are large regions of heterochromatin positioned at the nuclear periphery. These domains have been implicated in gene repression, especially in the context of development. In mammals, LAD organization is dependent on nuclear lamins, inner nuclear membrane proteins, and chromatin state. In addition, chromatin readers and modifier proteins have been implicated in this organization, potentially serving as molecular tethers that interact with both nuclear envelope proteins and chromatin. More recent studies have focused on teasing apart the rules that govern dynamic LAD organization and how LAD organization, in turn, relates to gene regulation and overall 3D genome organization. This review highlights recent studies in mammalian cells uncovering factors that instruct the choreography of LAD organization, re-organization, and dynamics at the nuclear lamina, including LAD dynamics in interphase and through mitotic exit, when LAD organization is re-established, as well as intra-LAD subdomain variations.
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Affiliation(s)
- Nicholas S. Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tiera I. Thomas
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L. Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L. Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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13
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Hong T, Li J, Guo L, Cavalier M, Wang T, Dou Y, DeLaFuente A, Fang S, Guzman A, Wohlan K, Kapadia C, Rosas C, Yang Y, Yin CC, Li S, You MJ, Cheng X, Goodell MA, Zhou Y, Huang Y. TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. NATURE AGING 2023; 3:1387-1400. [PMID: 37884767 DOI: 10.1038/s43587-023-00505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
DNA methylation deregulation at partially methylated domains (PMDs) represents an epigenetic signature of aging and cancer, yet the underlying molecular basis and resulting biological consequences remain unresolved. We report herein a mechanistic link between disrupted DNA methylation at PMDs and the spatial relocalization of H3K9me3-marked heterochromatin in aged hematopoietic stem and progenitor cells (HSPCs) or those with impaired DNA methylation. We uncover that TET2 modulates the spatial redistribution of H3K9me3-marked heterochromatin to mediate the upregulation of endogenous retroviruses (ERVs) and interferon-stimulated genes (ISGs), hence contributing to functional decline of aged HSPCs. TET2-deficient HSPCs retain perinuclear distribution of heterochromatin and exhibit age-related clonal expansion. Reverse transcriptase inhibitors suppress ERVs and ISGs expression, thereby restoring age-related defects in aged HSPCs. Collectively, our findings deepen the understanding of the functional interplay between DNA methylation and histone modifications, which is vital for maintaining heterochromatin function and safeguarding genome stability in stem cells.
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Affiliation(s)
- Tingting Hong
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Jia Li
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Maryn Cavalier
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Tianlu Wang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yaling Dou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Aaron DeLaFuente
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Shaohai Fang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Anna Guzman
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Katherina Wohlan
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Chiraag Kapadia
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
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14
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Kiseleva AA, Poleshko A. The secret life of chromatin tethers. FEBS Lett 2023; 597:2782-2790. [PMID: 37339933 PMCID: PMC10730768 DOI: 10.1002/1873-3468.14685] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
The nuclear envelope plays an essential role in organizing the genome inside of the nucleus. The inner nuclear membrane is coated with a meshwork of filamentous lamin proteins that provide a surface to organize a variety of cellular processes. A subset of nuclear lamina- and membrane-associated proteins functions as anchors to hold transcriptionally silent heterochromatin at the nuclear periphery. While most chromatin tethers are integral membrane proteins, a limited number are lamina-bound. One example is the mammalian proline-rich 14 (PRR14) protein. PRR14 is a recently characterized protein with unique function that is different from other known chromatin tethers. Here, we review our current understanding of PRR14 structure and function in organizing heterochromatin at the nuclear periphery.
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Affiliation(s)
- Anna A. Kiseleva
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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15
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Balasooriya GI, Wee TL, Spector DL. A sub-set of guanine- and cytosine-rich genes are actively transcribed at the nuclear Lamin B1 region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564411. [PMID: 37961255 PMCID: PMC10634887 DOI: 10.1101/2023.10.28.564411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Chromatin organization in the mammalian cell nucleus plays a vital role in the regulation of gene expression. The lamina-associated domain at the inner nuclear membrane has been proposed to harbor heterochromatin, while the nuclear interior has been shown to contain most of the euchromatin. Here, we show that a sub-set of actively transcribing genes, marked by RNA Pol II pSer2, are associated with Lamin B1 at the inner nuclear envelop in mESCs and the number of genes proportionally increases upon in vitro differentiation of mESC to olfactory precursor cells. These nuclear periphery-associated actively transcribing genes primarily represent housekeeping genes, and their gene bodies are significantly enriched with guanine and cytosine compared to genes actively transcribed at the nuclear interior. We found the promoters of these genes to also be significantly enriched with guanine and to be predominantly regulated by zinc finger protein transcription factors. We provide evidence supporting the emerging notion that the Lamin B1 region is not solely transcriptionally silent.
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16
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Geng Q, Kong Y, Li W, Zhang J, Ma H, Zhang Y, Da L, Zhao Y, Du H. Dynamic Phosphorylation of G9a Regulates its Repressive Activity on Chromatin Accessibility and Mitotic Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303224. [PMID: 37661576 PMCID: PMC10602519 DOI: 10.1002/advs.202303224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/18/2023] [Indexed: 09/05/2023]
Abstract
Phosphorylation of Ser10 of histone H3 (H3S10p), together with the adjacent methylation of Lys9 (H3K9me), has been proposed to function as a 'phospho-methyl switch' to regulate mitotic chromatin architecture. Despite of immense understanding of the roles of H3S10 phosphorylation, how H3K9me2 are dynamically regulated during mitosis is poorly understood. Here, it is identified that Plk1 kinase phosphorylates the H3K9me1/2 methyltransferase G9a/EHMT2 at Thr1045 (pT1045) during early mitosis, which attenuates its catalytic activity toward H3K9me2. Cells bearing Thr1045 phosphomimic mutant of G9a (T1045E) show decreased H3K9me2 levels, increased chromatin accessibility, and delayed mitotic progression. By contrast, dephosphorylation of pT1045 during late mitosis by the protein phosphatase PPP2CB reactivates G9a activity and upregulates H3K9me2 levels, correlated with decreased levels of H3S10p. Therefore, the results provide a mechanistic explanation of the essential of a 'phospho-methyl switch' and highlight the importance of Plk1 and PPP2CB-mediated dynamic regulation of G9a activity in chromatin organization and mitotic progression.
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Affiliation(s)
- Qizhi Geng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Yue‐Yu Kong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Weizhe Li
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Jianhao Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Haoli Ma
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Yuhang Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Lin‐Tai Da
- Shanghai Center for Systems BiomedicineShanghai JiaoTong UniversityShanghai200240China
| | - Yan Zhao
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Hai‐Ning Du
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
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17
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Arnosti DN. Soft repression and chromatin modification by conserved transcriptional corepressors. Enzymes 2023; 53:69-96. [PMID: 37748837 DOI: 10.1016/bs.enz.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Transcriptional regulation in eukaryotic cells involves the activity of multifarious DNA-binding transcription factors and recruited corepressor complexes. Together, these complexes interact with the core transcriptional machinery, chromatin, and nuclear environment to effect complex patterns of gene regulation. Much focus has been paid to the action of master regulatory switches that are key to developmental and environmental responses, as these genetic elements have important phenotypic effects. The regulation of widely-expressed metabolic control genes has been less well studied, particularly in cases in which physically-interacting repressors and corepressors have subtle influences on steady-state expression. This latter phenomenon, termed "soft repression" is a topic of increasing interest as genomic approaches provide ever more powerful tools to uncover the significance of this level of control. This review provides an oversight of classic and current approaches to the study of transcriptional repression in eukaryotic systems, with a specific focus on opportunities and challenges that lie ahead in the study of soft repression.
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Affiliation(s)
- David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
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18
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Coscarella IL, Landim-Vieira M, Rastegarpouyani H, Chase PB, Irianto J, Pinto JR. Nucleus Mechanosensing in Cardiomyocytes. Int J Mol Sci 2023; 24:13341. [PMID: 37686151 PMCID: PMC10487505 DOI: 10.3390/ijms241713341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Cardiac muscle contraction is distinct from the contraction of other muscle types. The heart continuously undergoes contraction-relaxation cycles throughout an animal's lifespan. It must respond to constantly varying physical and energetic burdens over the short term on a beat-to-beat basis and relies on different mechanisms over the long term. Muscle contractility is based on actin and myosin interactions that are regulated by cytoplasmic calcium ions. Genetic variants of sarcomeric proteins can lead to the pathophysiological development of cardiac dysfunction. The sarcomere is physically connected to other cytoskeletal components. Actin filaments, microtubules and desmin proteins are responsible for these interactions. Therefore, mechanical as well as biochemical signals from sarcomeric contractions are transmitted to and sensed by other parts of the cardiomyocyte, particularly the nucleus which can respond to these stimuli. Proteins anchored to the nuclear envelope display a broad response which remodels the structure of the nucleus. In this review, we examine the central aspects of mechanotransduction in the cardiomyocyte where the transmission of mechanical signals to the nucleus can result in changes in gene expression and nucleus morphology. The correlation of nucleus sensing and dysfunction of sarcomeric proteins may assist the understanding of a wide range of functional responses in the progress of cardiomyopathic diseases.
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Affiliation(s)
| | - Maicon Landim-Vieira
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hosna Rastegarpouyani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
- Institute for Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Prescott Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
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19
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Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 2023; 620:863-872. [PMID: 37587336 PMCID: PMC10447250 DOI: 10.1038/s41586-023-06424-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.
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Affiliation(s)
- Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Westlake Institute for Advanced Study, Hangzhou, China
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Alex de Mendoza
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas Frazer
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landín
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jacob M Paynter
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hun S Chy
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Andrew L Laslett
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - James Breen
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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20
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Tang M, Regadas I, Belikov S, Shilkova O, Xu L, Wernersson E, Liu X, Wu H, Bienko M, Mannervik M. Separation of transcriptional repressor and activator functions in Drosophila HDAC3. Development 2023; 150:dev201548. [PMID: 37455638 PMCID: PMC10445730 DOI: 10.1242/dev.201548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex, and its canonical function is in transcriptional repression, but it can also activate transcription. Here, we show that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhances repressor activity beyond wild type in the early embryo. We conclude that the crucial functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery.
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Affiliation(s)
- Min Tang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Department of Biochemistry and Molecular Biology, University of South China, 421001 Hengyang, China
| | - Isabel Regadas
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Sergey Belikov
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Olga Shilkova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Lei Xu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Erik Wernersson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Xuewen Liu
- Department of Biochemistry and Molecular Biology, University of South China, 421001 Hengyang, China
| | - Hongmei Wu
- Department of Biochemistry and Molecular Biology, University of South China, 421001 Hengyang, China
| | - Magda Bienko
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
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21
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Zhang Y, Ramirez-Martinez A, Chen K, McAnally JR, Cai C, Durbacz MZ, Chemello F, Wang Z, Xu L, Bassel-Duby R, Liu N, Olson EN. Net39 protects muscle nuclei from mechanical stress during the pathogenesis of Emery-Dreifuss muscular dystrophy. J Clin Invest 2023; 133:e163333. [PMID: 37395273 DOI: 10.1172/jci163333] [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: 07/06/2022] [Accepted: 05/16/2023] [Indexed: 07/04/2023] Open
Abstract
Mutations in genes encoding nuclear envelope proteins lead to diseases known as nuclear envelopathies, characterized by skeletal muscle and heart abnormalities, such as Emery-Dreifuss muscular dystrophy (EDMD). The tissue-specific role of the nuclear envelope in the etiology of these diseases has not been extensively explored. We previously showed that global deletion of the muscle-specific nuclear envelope protein NET39 in mice leads to neonatal lethality due to skeletal muscle dysfunction. To study the potential role of the Net39 gene in adulthood, we generated a muscle-specific conditional knockout (cKO) of Net39 in mice. cKO mice recapitulated key skeletal muscle features of EDMD, including muscle wasting, impaired muscle contractility, abnormal myonuclear morphology, and DNA damage. The loss of Net39 rendered myoblasts hypersensitive to mechanical stretch, resulting in stretch-induced DNA damage. Net39 was downregulated in a mouse model of congenital myopathy, and restoration of Net39 expression through AAV gene delivery extended life span and ameliorated muscle abnormalities. These findings establish NET39 as a direct contributor to the pathogenesis of EDMD that acts by protecting against mechanical stress and DNA damage.
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Affiliation(s)
- Yichi Zhang
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Andres Ramirez-Martinez
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, and
| | - John R McAnally
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Chunyu Cai
- Department of Pathology, University of Texas (UT) Southwestern Medical Center, Dallas, Texas, USA
| | - Mateusz Z Durbacz
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Francesco Chemello
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Zhaoning Wang
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, and
| | - Rhonda Bassel-Duby
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Ning Liu
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
| | - Eric N Olson
- Department of Molecular Biology
- Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center
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22
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McCarthy RL, Zhang J, Zaret KS. Diverse heterochromatin states restricting cell identity and reprogramming. Trends Biochem Sci 2023; 48:513-526. [PMID: 36990958 PMCID: PMC10182259 DOI: 10.1016/j.tibs.2023.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.
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Affiliation(s)
- Ryan L McCarthy
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Lovejoy CM, Nagarajan P, Parthun MR. Dynamic Reassociation of the Nuclear Lamina with Newly Replicated DNA. RESEARCH SQUARE 2023:rs.3.rs-2846826. [PMID: 37215015 PMCID: PMC10197746 DOI: 10.21203/rs.3.rs-2846826/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The physical association of specific regions of chromatin with components of the nuclear lamina provides the framework for the 3-dimensionl architecture of the genome. The regulation of these interactions plays a critical role in the maintenance of gene expression patterns and cell identity. The breakdown and reassembly of the nuclear membrane as cells transit mitosis plays a central role in the regulation of the interactions between the genome and the nuclear lamina. However, other nuclear processes, such as transcription, have emerged as regulators of the association of DNA with the nuclear lamina. To determine whether DNA replication also has the potential to regulate DNA-nuclear lamina interactions, we adapted proximity ligation-based chromatin assembly assays to analyze the dynamics of nuclear lamina association with newly replicated DNA. We observe that lamin A/C and lamin B, as well as inner nuclear membrane proteins LBR and emerin, are found in proximity to newly replicated DNA. While core histones rapidly reassociate with DNA following passage of the replication fork, the complete reassociation of nuclear lamina components with newly replicated DNA occurs over a period of approximately 30 minutes. We propose models to describe the disassembly and reassembly of nascent chromatin with the nuclear lamina.
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24
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Shah PP, Santini GT, Shen KM, Jain R. InterLINCing Chromatin Organization and Mechanobiology in Laminopathies. Curr Cardiol Rep 2023; 25:307-314. [PMID: 37052760 PMCID: PMC10185580 DOI: 10.1007/s11886-023-01853-2] [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] [Accepted: 02/22/2023] [Indexed: 04/14/2023]
Abstract
PURPOSE OF REVIEW In this review, we explore the chromatin-related consequences of laminopathy-linked mutations through the lens of mechanotransduction. RECENT FINDINGS Multiple studies have highlighted the role of the nuclear lamina in maintaining the integrity of the nucleus. The lamina also has a critical role in 3D genome organization. Mutations in lamina proteins associated with various laminopathies result in the loss of organization of DNA at the nuclear periphery. However, it remains unclear if or how these two aspects of lamin function are connected. Recent data suggests that unlinking the cytoskeleton from the nuclear lamina may be beneficial to slow progress of deleterious phenotypes observed in laminopathies. In this review, we highlight emerging data that suggest interlinked chromatin- and mechanical biology-related pathways are interconnected in the pathogenesis of laminopathies.
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Affiliation(s)
- Parisha P. Shah
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Smilow Center for Translational Research, 09-184, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Garrett T. Santini
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kaitlyn M. Shen
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Smilow Center for Translational Research, 09-101, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
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25
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Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nat Methods 2023; 20:686-694. [PMID: 37106232 DOI: 10.1038/s41592-023-01845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/13/2023] [Indexed: 04/29/2023]
Abstract
In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties.
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Affiliation(s)
- Sarah M Mangiameli
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Haiqi Chen
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew S Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Julie A Dobkin
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Lesman
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Fei Chen
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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26
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Scott AK, Casas E, Schneider SE, Swearingen AR, Van Den Elzen CL, Seelbinder B, Barthold JE, Kugel JF, Stern JL, Foster KJ, Emery NC, Brumbaugh J, Neu CP. Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophys J 2023; 122:1428-1444. [PMID: 36871159 PMCID: PMC10147835 DOI: 10.1016/j.bpj.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/31/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Understanding how cells remember previous mechanical environments to influence their fate, or mechanical memory, informs the design of biomaterials and therapies in medicine. Current regeneration therapies, such as cartilage regeneration procedures, require 2D cell expansion processes to achieve large cell populations critical for the repair of damaged tissues. However, the limit of mechanical priming for cartilage regeneration procedures before inducing long-term mechanical memory following expansion processes is unknown, and mechanisms defining how physical environments influence the therapeutic potential of cells remain poorly understood. Here, we identify a threshold to mechanical priming separating reversible and irreversible effects of mechanical memory. After 16 population doublings in 2D culture, expression levels of tissue-identifying genes in primary cartilage cells (chondrocytes) are not recovered when transferred to 3D hydrogels, while expression levels of these genes were recovered for cells only expanded for eight population doublings. Additionally, we show that the loss and recovery of the chondrocyte phenotype correlates with a change in chromatin architecture, as shown by structural remodeling of the trimethylation of H3K9. Efforts to disrupt the chromatin architecture by suppressing or increasing levels of H3K9me3 reveal that only with increased levels of H3K9me3 did the chromatin architecture of the native chondrocyte phenotype partially return, along with increased levels of chondrogenic gene expression. These results further support the connection between the chondrocyte phenotype and chromatin architecture, and also reveal the therapeutic potential of inhibitors of epigenetic modifiers as disruptors of mechanical memory when large numbers of phenotypically suitable cells are required for regeneration procedures.
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Affiliation(s)
- Adrienne K Scott
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Eduard Casas
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Stephanie E Schneider
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Alison R Swearingen
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Courtney L Van Den Elzen
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado
| | - Benjamin Seelbinder
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Jeanne E Barthold
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Jennifer F Kugel
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Josh Lewis Stern
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado; Biochemistry and Molecular Genetics, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kyla J Foster
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Nancy C Emery
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado
| | - Justin Brumbaugh
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Corey P Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado; Biomedical Engineering Program, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.
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27
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He R, Liu B, Geng B, Li N, Geng Q. The role of HDAC3 and its inhibitors in regulation of oxidative stress and chronic diseases. Cell Death Discov 2023; 9:131. [PMID: 37072432 PMCID: PMC10113195 DOI: 10.1038/s41420-023-01399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 04/20/2023] Open
Abstract
HDAC3 is a specific and crucial member of the HDAC family. It is required for embryonic growth, development, and physiological function. The regulation of oxidative stress is an important factor in intracellular homeostasis and signal transduction. Currently, HDAC3 has been found to regulate several oxidative stress-related processes and molecules dependent on its deacetylase and non-enzymatic activities. In this review, we comprehensively summarize the knowledge of the relationship of HDAC3 with mitochondria function and metabolism, ROS-produced enzymes, antioxidant enzymes, and oxidative stress-associated transcription factors. We also discuss the role of HDAC3 and its inhibitors in some chronic cardiovascular, kidney, and neurodegenerative diseases. Due to the simultaneous existence of enzyme activity and non-enzyme activity, HDAC3 and the development of its selective inhibitors still need further exploration in the future.
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Affiliation(s)
- Ruyuan He
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bohao Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Boxin Geng
- School of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
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28
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Zocher S, Toda T. Epigenetic aging in adult neurogenesis. Hippocampus 2023; 33:347-359. [PMID: 36624660 DOI: 10.1002/hipo.23494] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 01/11/2023]
Abstract
Neural stem cells (NSCs) in the hippocampus generate new neurons throughout life, which functionally contribute to cognitive flexibility and mood regulation. Yet adult hippocampal neurogenesis substantially declines with age and age-related impairments in NSC activity underlie this reduction. Particularly, increased NSC quiescence and consequently reduced NSC proliferation are considered to be major drivers of the low neurogenesis levels in the aged brain. Epigenetic regulators control the gene expression programs underlying NSC quiescence, proliferation and differentiation and are hence critical to the regulation of adult neurogenesis. Epigenetic alterations have also emerged as central hallmarks of aging, and recent studies suggest the deterioration of the NSC-specific epigenetic landscape as a driver of the age-dependent decline in adult neurogenesis. In this review, we summarize the recently accumulating evidence for a role of epigenetic dysregulation in NSC aging and propose perspectives for future research directions.
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Affiliation(s)
- Sara Zocher
- Nuclear Architecture in Neural Plasticity and Aging Laboratory, German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - Tomohisa Toda
- Nuclear Architecture in Neural Plasticity and Aging Laboratory, German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
- Institute of Medical Physics and Microtissue Engineering, Faculty of Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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29
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Shiraishi K, Shah PP, Morley MP, Loebel C, Santini GT, Katzen J, Basil MC, Lin SM, Planer JD, Cantu E, Jones DL, Nottingham AN, Li S, Cardenas-Diaz FL, Zhou S, Burdick JA, Jain R, Morrisey EE. Biophysical forces mediated by respiration maintain lung alveolar epithelial cell fate. Cell 2023; 186:1478-1492.e15. [PMID: 36870331 PMCID: PMC10065960 DOI: 10.1016/j.cell.2023.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Lungs undergo mechanical strain during breathing, but how these biophysical forces affect cell fate and tissue homeostasis are unclear. We show that biophysical forces through normal respiratory motion actively maintain alveolar type 1 (AT1) cell identity and restrict these cells from reprogramming into AT2 cells in the adult lung. AT1 cell fate is maintained at homeostasis by Cdc42- and Ptk2-mediated actin remodeling and cytoskeletal strain, and inactivation of these pathways causes a rapid reprogramming into the AT2 cell fate. This plasticity induces chromatin reorganization and changes in nuclear lamina-chromatin interactions, which can discriminate AT1 and AT2 cell identity. Unloading the biophysical forces of breathing movements leads to AT1-AT2 cell reprogramming, revealing that normal respiration is essential to maintain alveolar epithelial cell fate. These data demonstrate the integral function of mechanotransduction in maintaining lung cell fate and identifies the AT1 cell as an important mechanosensor in the alveolar niche.
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Affiliation(s)
- Kazushige Shiraishi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Parisha P Shah
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Morley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudia Loebel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Garrett T Santini
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremy Katzen
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria C Basil
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan M Lin
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph D Planer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward Cantu
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dakota L Jones
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ana N Nottingham
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shanru Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Su Zhou
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason A Burdick
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Rajan Jain
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward E Morrisey
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA.
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30
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Toscano-Marquez F, Romero Y, Espina-Ordoñez M, Cisneros J. Absence of HDAC3 by Matrix Stiffness Promotes Chromatin Remodeling and Fibroblast Activation in Idiopathic Pulmonary Fibrosis. Cells 2023; 12:cells12071020. [PMID: 37048093 PMCID: PMC10093275 DOI: 10.3390/cells12071020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/05/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal disease characterized by progressive and irreversible lung scarring associated with persistent activation of fibroblasts. Epigenetics could integrate diverse microenvironmental signals, such as stiffness, to direct persistent fibroblast activation. Histone modifications by deacetylases (HDAC) may play an essential role in the gene expression changes involved in the pathological remodeling of the lung. Particularly, HDAC3 is crucial for maintaining chromatin and regulating gene expression, but little is known about its role in IPF. In the study, control and IPF-derived fibroblasts were used to determine the influence of HDAC3 on chromatin remodeling and gene expression associated with IPF signature. Additionally, the cells were grown on hydrogels to mimic the stiffness of a fibrotic lung. Our results showed a decreased HDAC3 in the nucleus of IPF fibroblasts, which correlates with changes in nucleus size and heterochromatin loss. The inhibition of HDAC3 with a pharmacological inhibitor causes hyperacetylation of H3K9 and provokes an increased expression of Col1A1, ACTA2, and p21. Comparable results were found in hydrogels, where matrix stiffness promotes the loss of nuclear HDAC3 and increases the profibrotic signature. Finally, latrunculin b was used to confirm that changes by stiffness depend on the mechanotransduction signals. Together, these results suggest that HDAC3 could be a link between epigenetic mechanisms and the fibrotic microenvironment.
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Affiliation(s)
- Fernanda Toscano-Marquez
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Departamento de Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City 14080, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Yair Romero
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco Espina-Ordoñez
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Departamento de Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City 14080, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - José Cisneros
- Laboratorio de Biopatología Pulmonar INER-Ciencias-UNAM, Departamento de Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City 14080, Mexico
- Correspondence:
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31
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Yang BA, da Rocha AM, Newton I, Shcherbina A, Wong SW, Fraczek PM, Larouche JA, Hiraki HL, Baker BM, Shin JW, Takayama S, Thouless MD, Aguilar CA. Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532246. [PMID: 36993714 PMCID: PMC10055010 DOI: 10.1101/2023.03.12.532246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the role of the nuclear scaffold as a guardian of cell fate in human fibroblasts by comparing the effects of transient loss (knockdown) and mutation (progeria) of functional Lamin A/C, a core component of the nuclear scaffold. We observed that Lamin A/C deficiency or mutation disrupts nuclear morphology, heterochromatin levels, and increases access to DNA in lamina-associated domains. Changes in Lamin A/C were also found to impact the mechanical properties of the nucleus when measured by a microfluidic cellular squeezing device. We also show that transient loss of Lamin A/C accelerates the kinetics of cellular reprogramming to pluripotency through opening of previously silenced heterochromatin domains while genetic mutation of Lamin A/C into progerin induces a senescent phenotype that inhibits the induction of reprogramming genes. Our results highlight the physical role of the nuclear scaffold in safeguarding cellular fate.
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Affiliation(s)
- Benjamin A. Yang
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Isabel Newton
- Dept. of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Shcherbina
- Dept. of Biomedical Informatics, Stanford University, Palo Alto, CA 94305, USA
| | - Sing-Wan Wong
- Dept. of Pharmacology and Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Paula M. Fraczek
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacqueline A. Larouche
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harrison L. Hiraki
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brendon M. Baker
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jae-Won Shin
- Dept. of Pharmacology and Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Shuichi Takayama
- Wallace Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332
| | - M. D. Thouless
- Dept. of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Dept. of Materials Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A. Aguilar
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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32
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Wang Y, Dobreva G. Epigenetics in LMNA-Related Cardiomyopathy. Cells 2023; 12:cells12050783. [PMID: 36899919 PMCID: PMC10001118 DOI: 10.3390/cells12050783] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/18/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Mutations in the gene for lamin A/C (LMNA) cause a diverse range of diseases known as laminopathies. LMNA-related cardiomyopathy is a common inherited heart disease and is highly penetrant with a poor prognosis. In the past years, numerous investigations using mouse models, stem cell technologies, and patient samples have characterized the phenotypic diversity caused by specific LMNA variants and contributed to understanding the molecular mechanisms underlying the pathogenesis of heart disease. As a component of the nuclear envelope, LMNA regulates nuclear mechanostability and function, chromatin organization, and gene transcription. This review will focus on the different cardiomyopathies caused by LMNA mutations, address the role of LMNA in chromatin organization and gene regulation, and discuss how these processes go awry in heart disease.
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Affiliation(s)
- Yinuo Wang
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), 68167 Mannheim, Germany
- Correspondence: (Y.W.); (G.D.)
| | - Gergana Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), 68167 Mannheim, Germany
- Correspondence: (Y.W.); (G.D.)
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Ren J, Zeng Q, Wu H, Liu X, Guida MC, Huang W, Zhai Y, Li J, Ocorr K, Bodmer R, Tang M. Deacetylase-dependent and -independent role of HDAC3 in cardiomyopathy. J Cell Physiol 2023; 238:647-658. [PMID: 36745702 PMCID: PMC10152801 DOI: 10.1002/jcp.30957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 12/14/2022] [Accepted: 01/11/2023] [Indexed: 02/08/2023]
Abstract
Cardiomyopathy is a common disease of cardiac muscle that negatively affects cardiac function. HDAC3 commonly functions as corepressor by removing acetyl moieties from histone tails. However, a deacetylase-independent role of HDAC3 has also been described. Cardiac deletion of HDAC3 causes reduced cardiac contractility accompanied by lipid accumulation, but the molecular function of HDAC3 in cardiomyopathy remains unknown. We have used powerful genetic tools in Drosophila to investigate the enzymatic and nonenzymatic roles of HDAC3 in cardiomyopathy. Using the Drosophila heart model, we showed that cardiac-specific HDAC3 knockdown (KD) leads to prolonged systoles and reduced cardiac contractility. Immunohistochemistry revealed structural abnormalities characterized by myofiber disruption in HDAC3 KD hearts. Cardiac-specific HDAC3 KD showed increased levels of whole-body triglycerides and increased fibrosis. The introduction of deacetylase-dead HDAC3 mutant in HDAC3 KD background showed comparable results with wild-type HDAC3 in aspects of contractility and Pericardin deposition. However, deacetylase-dead HDAC3 mutants failed to improve triglyceride accumulation. Our data indicate that HDAC3 plays a deacetylase-independent role in maintaining cardiac contractility and preventing Pericardin deposition as well as a deacetylase-dependent role to maintain triglyceride homeostasis.
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Affiliation(s)
- Jieyu Ren
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Qun Zeng
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Hongmei Wu
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Xuewen Liu
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Maria C Guida
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Wen Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yiyuan Zhai
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Junjie Li
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
| | - Karen Ocorr
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Rolf Bodmer
- Development Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Min Tang
- Department of Biochemistry and Molecular Biology, College of Hengyang Medical, University of South China, Hengyang, China
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Sandonà M, Cavioli G, Renzini A, Cedola A, Gigli G, Coletti D, McKinsey TA, Moresi V, Saccone V. Histone Deacetylases: Molecular Mechanisms and Therapeutic Implications for Muscular Dystrophies. Int J Mol Sci 2023; 24:4306. [PMID: 36901738 PMCID: PMC10002075 DOI: 10.3390/ijms24054306] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
Histone deacetylases (HDACs) are enzymes that regulate the deacetylation of numerous histone and non-histone proteins, thereby affecting a wide range of cellular processes. Deregulation of HDAC expression or activity is often associated with several pathologies, suggesting potential for targeting these enzymes for therapeutic purposes. For example, HDAC expression and activity are higher in dystrophic skeletal muscles. General pharmacological blockade of HDACs, by means of pan-HDAC inhibitors (HDACi), ameliorates both muscle histological abnormalities and function in preclinical studies. A phase II clinical trial of the pan-HDACi givinostat revealed partial histological improvement and functional recovery of Duchenne Muscular Dystrophy (DMD) muscles; results of an ongoing phase III clinical trial that is assessing the long-term safety and efficacy of givinostat in DMD patients are pending. Here we review the current knowledge about the HDAC functions in distinct cell types in skeletal muscle, identified by genetic and -omic approaches. We describe the signaling events that are affected by HDACs and contribute to muscular dystrophy pathogenesis by altering muscle regeneration and/or repair processes. Reviewing recent insights into HDAC cellular functions in dystrophic muscles provides new perspectives for the development of more effective therapeutic approaches based on drugs that target these critical enzymes.
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Affiliation(s)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
| | - Alessia Cedola
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy
| | - Giuseppe Gigli
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), 73100 Lecce, Italy
| | - Dario Coletti
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
- CNRS UMR 8256, INSERM ERL U1164, Biological Adaptation and Aging B2A, Sorbonne Université, 75005 Paris, France
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy
| | - Valentina Saccone
- IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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35
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Heo SJ, Thakur S, Chen X, Loebel C, Xia B, McBeath R, Burdick JA, Shenoy VB, Mauck RL, Lakadamyali M. Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. Nat Biomed Eng 2023; 7:177-191. [PMID: 35996026 PMCID: PMC10053755 DOI: 10.1038/s41551-022-00910-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
Changes in the micro-environment of fibrous connective tissue can lead to alterations in the phenotypes of tissue-resident cells, yet the underlying mechanisms are poorly understood. Here, by visualizing the dynamics of histone spatial reorganization in tenocytes and mesenchymal stromal cells from fibrous tissue of human donors via super-resolution microscopy, we show that physiological and pathological chemomechanical cues can directly regulate the spatial nanoscale organization and density of chromatin in these tissue-resident cell populations. Specifically, changes in substrate stiffness, altered oxygen tension and the presence of inflammatory signals drive chromatin relocalization and compaction into the nuclear boundary, mediated by the activity of the histone methyltransferase EZH2 and an intact cytoskeleton. In healthy cells, chemomechanically triggered changes in the spatial organization and density of chromatin are reversible and can be attenuated by dynamically stiffening the substrate. In diseased human cells, however, the link between mechanical or chemical inputs and chromatin remodelling is abrogated. Our findings suggest that aberrant chromatin organization in fibrous connective tissue may be a hallmark of disease progression that could be leveraged for therapeutic intervention.
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Affiliation(s)
- Su-Jin Heo
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xingyu Chen
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudia Loebel
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Boao Xia
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Rowena McBeath
- Department of Orthopaedic Surgery, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jason A Burdick
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Vivek B Shenoy
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Materials Science Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert L Mauck
- McKay Orthopaedic Research Laboratory, Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA.
- Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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36
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Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol 2023; 24:16. [PMID: 36691074 PMCID: PMC9869549 DOI: 10.1186/s13059-023-02849-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamina-associated domains (LADs) are mapped genome-wide in relatively few genetically normal human cell types, which limits our understanding of the role peripheral chromatin plays in development and disease. RESULTS To address this gap, we map LAMIN B1 occupancy across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas with gene expression and repressive histone modification maps reveal that lamina-associated chromatin in all twelve cell types is organized into at least two subtypes defined by differences in LAMIN B1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Imaging of fluorescently labeled DNA in single cells validates these subtypes and shows radial positioning of LADs with higher LAMIN B1 occupancy and heterochromatic histone modifications primarily embedded within the lamina. In contrast, the second subtype of lamina-associated chromatin is relatively gene dense, accessible, dynamic across development, and positioned adjacent to the lamina. Most genes gain or lose LAMIN B1 occupancy consistent with cell types along developmental trajectories; however, we also identify examples where the enhancer, but not the gene body and promoter, changes LAD state. CONCLUSIONS Altogether, this atlas represents the largest resource to date for peripheral chromatin organization studies and reveals an intermediate chromatin subtype.
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Affiliation(s)
- Parisha P. Shah
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Kathleen C. Keough
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Ketrin Gjoni
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Garrett T. Santini
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Richard J. Abdill
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Nadeera M. Wickramasinghe
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Carolyn E. Dundes
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ashley Karnay
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Angela Chen
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Rachel E. A. Salomon
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Patrick J. Walsh
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Son C. Nguyen
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sean Whalen
- grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Eric F. Joyce
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kyle M. Loh
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Nicole Dubois
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Katherine S. Pollard
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
| | - Rajan Jain
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA ,Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
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Vadrot N, Ader F, Moulin M, Merlant M, Chapon F, Gandjbakhch E, Labombarda F, Maragnes P, Réant P, Rooryck C, Probst V, Donal E, Richard P, Ferreiro A, Buendia B. Abnormal Cellular Phenotypes Induced by Three TMPO/LAP2 Variants Identified in Men with Cardiomyopathies. Cells 2023; 12:337. [PMID: 36672271 PMCID: PMC9857342 DOI: 10.3390/cells12020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
A single missense variant of the TMPO/LAP2α gene, encoding LAP2 proteins, has been associated with cardiomyopathy in two brothers. To further evaluate its role in cardiac muscle, we included TMPO in our cardiomyopathy diagnostic gene panel. A screening of ~5000 patients revealed three novel rare TMPO heterozygous variants in six males diagnosed with hypertrophic or dilated cardiomypathy. We identified in different cellular models that (1) the frameshift variant LAP2α p.(Gly395Glufs*11) induced haploinsufficiency, impeding cell proliferation and/or producing a truncated protein mislocalized in the cytoplasm; (2) the C-ter missense variant LAP2α p.(Ala240Thr) led to a reduced proximity events between LAP2α and the nucleosome binding protein HMGN5; and (3) the LEM-domain missense variant p.(Leu124Phe) decreased both associations of LAP2α/β with the chromatin-associated protein BAF and inhibition of the E2F1 transcription factor activity which is known to be dependent on Rb, partner of LAP2α. Additionally, the LAP2α expression was lower in the left ventricles of male mice compared to females. In conclusion, our study reveals distinct altered properties of LAP2 induced by these TMPO/LAP2 variants, leading to altered cell proliferation, chromatin structure or gene expression-regulation pathways, and suggests a potential sex-dependent role of LAP2 in myocardial function and disease.
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Affiliation(s)
- Nathalie Vadrot
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Flavie Ader
- APHP—Sorbonne Université, Unité Fonctionnelle de Cardiogénétique et Myogénétique Moléculaire, Service de Biochimie Métabolique, HU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
- Faculté de Pharmacie Paris Descartes, Département 3, Université Paris Cité, F-75006 Paris, France
| | - Maryline Moulin
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Marie Merlant
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | | | - Estelle Gandjbakhch
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
- Département de cardiologie, APHP—Sorbonne Université, HU Pitié Salpêtrière- Charles Foix, F-75610 Paris, France
| | - Fabien Labombarda
- Service de Cardiologie, CHU de Caen, Université de Caen Normandie, F-14000 Caen, France
| | - Pascale Maragnes
- Cardiologie pédiatrique, Service de pédiatrie, CHU de Caen, F-14000 Caen, France
| | - Patricia Réant
- Service de Cardiologie, Hôpital Haut Lévêque, CHU de Bordeaux, INSERM 1045, Université de Bordeaux, F-33000 Bordeaux, France
| | - Caroline Rooryck
- Service de Génétique Médicale, CHU Bordeaux, F-33000 Bordeaux, France
| | - Vincent Probst
- Centre de référence des maladies rythmiques cardiaques, CHU de Nantes, F-44000 Nantes, France
| | - Erwan Donal
- Centre Cardio-Pneumologique, CHU de Rennes Hôpital de Pontchaillou, F-35000 Rennes, France
| | - Pascale Richard
- APHP—Sorbonne Université, Unité Fonctionnelle de Cardiogénétique et Myogénétique Moléculaire, Service de Biochimie Métabolique, HU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
| | - Ana Ferreiro
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
- APHP, Centre de référence des Maladies Neuromusculaires, Institut de Myologie, Neuromyology Department, CHU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
| | - Brigitte Buendia
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
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38
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Nuclear envelope assembly and dynamics during development. Semin Cell Dev Biol 2023; 133:96-106. [PMID: 35249812 DOI: 10.1016/j.semcdb.2022.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/22/2023]
Abstract
The nuclear envelope (NE) protects but also organizes the eukaryotic genome. In this review we will discuss recent literature on how the NE disassembles and reassembles, how it varies in surface area and protein composition and how this translates into chromatin organization and gene expression in the context of animal development.
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Santini GT, Shah PP, Karnay A, Jain R. Aberrant chromatin organization at the nexus of laminopathy disease pathways. Nucleus 2022; 13:300-312. [PMID: 36503349 PMCID: PMC9746625 DOI: 10.1080/19491034.2022.2153564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Garrett T. Santini
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Parisha P. Shah
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ashley Karnay
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA,CONTACT Rajan Jain Smilow Center for Translational Research, 09-101 3400 Civic Center Blvd, PhiladelphiaPA 19104
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40
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Belcheva KT, Chaudhuri J. Maintenance of Lineage Identity: Lessons from a B Cell. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2073-2081. [PMID: 36426973 DOI: 10.4049/jimmunol.2200497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/17/2022] [Indexed: 01/04/2023]
Abstract
The maintenance of B cell identity requires active transcriptional control that enforces a B cell-specific program and suppresses alternative lineage genes. Accordingly, disrupting the B cell identity regulatory network compromises B cell function and induces cell fate plasticity by allowing derepression of alternative lineage-specific transcriptional programs. Although the B lineage is incredibly resistant to most differentiating factors, loss of just a single B lineage-specific transcription factor or the forced expression of individual non-B cell lineage transcription factors can radically disrupt B cell maintenance and allow dedifferentiation or transdifferentiation into entirely distinct lineages. B lymphocytes thereby offer an insightful and useful case study of how a specific cell lineage can maintain a stable identity throughout life and how perturbations of a single master regulator can induce cellular plasticity. In this article, we review the regulatory mechanisms that safeguard B cell identity, and we discuss how dysregulation of the B cell maintenance program can drive malignant transformation and enable therapeutic resistance.
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Affiliation(s)
- Kalina T Belcheva
- Biochemistry, Cellular and Molecular Biology Allied Program, Weill Cornell Graduate School of Medical Sciences, New York, NY; and
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
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41
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Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function. Nat Commun 2022; 13:6663. [PMID: 36333314 PMCID: PMC9636150 DOI: 10.1038/s41467-022-34366-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We report changes in chromatin compaction and localization of cardiac genes in Lmna-/- ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate. This is accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. We uncover divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which have distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. We conclude that disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.
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42
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Marano N, Holaska JM. Emerin interacts with histone methyltransferases to regulate repressive chromatin at the nuclear periphery. Front Cell Dev Biol 2022; 10:1007120. [PMID: 36274837 PMCID: PMC9583931 DOI: 10.3389/fcell.2022.1007120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
X-Linked Emery-Dreifuss muscular dystrophy is caused by mutations in the gene encoding emerin. Emerin is an inner nuclear membrane protein important for repressive chromatin organization at the nuclear periphery. Myogenic differentiation is a tightly regulated process characterized by genomic reorganization leading to coordinated temporal expression of key transcription factors, including MyoD, Pax7, and Myf5. Emerin was shown to interact with repressive histone modification machinery, including HDAC3 and EZH2. Using emerin-null myogenic progenitor cells we established several EDMD-causing emerin mutant lines in the effort to understand how the functional interaction of emerin with HDAC3 regulates histone methyltransferase localization or function to organize repressive chromatin at the nuclear periphery. We found that, in addition to its interaction with HDAC3, emerin interacts with the histone methyltransferases EZH2 and G9a in myogenic progenitor cells. Further, we show enhanced binding of emerin HDAC3-binding mutants S54F and Q133H to EZH2 and G9a. Treatment with small molecule inhibitors of EZH2 and G9a reduced H3K9me2 or H3K27me3 throughout differentiation. EZH2 and G9a inhibitors impaired cell cycle withdrawal, differentiation commitment, and myotube formation in wildtype progenitors, while they had no effect on emerin-null progenitors. Interestingly, these inhibitors exacerbated the impaired differentiation of emerin S54F and Q133H mutant progenitors. Collectively, these results suggest the functional interaction between emerin and HDAC3, EZH2, and G9a are important for myogenic differentiation.
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43
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Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022; 185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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Affiliation(s)
- Alessa R Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Quentin Szabo
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Konrad Chudzik
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Rothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tobias Zehnder
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Verena Laupert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Sara Hetzel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mai H Q Phan
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Magdalena Schindler
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stefan A Haas
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Michael I Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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44
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Hsia CR, McAllister J, Hasan O, Judd J, Lee S, Agrawal R, Chang CY, Soloway P, Lammerding J. Confined migration induces heterochromatin formation and alters chromatin accessibility. iScience 2022; 25:104978. [PMID: 36117991 PMCID: PMC9474860 DOI: 10.1016/j.isci.2022.104978] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/14/2022] [Accepted: 08/15/2022] [Indexed: 01/17/2023] Open
Abstract
During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that nuclear deformation associated with such confined migration could alter chromatin organization and function. By studying cells migrating through microfluidic devices that mimic interstitial spaces in vivo, we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for days. This "confined migration-induced heterochromatin" (CMiH) was distinct from heterochromatin formation during migration initiation. Confined migration decreased chromatin accessibility at intergenic regions near centromeres and telomeres, suggesting heterochromatin spreading from existing sites. Consistent with the overall decrease in accessibility, global transcription was decreased during confined migration. Intriguingly, we also identified increased accessibility at promoter regions of genes linked to chromatin silencing, tumor invasion, and DNA damage response. Inhibiting CMiH reduced migration speed, suggesting that CMiH promotes confined migration. Together, our findings indicate that confined migration induces chromatin changes that regulate cell migration and other functions.
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Affiliation(s)
- Chieh-Ren Hsia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jawuanna McAllister
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ovais Hasan
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seoyeon Lee
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Richa Agrawal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chao-Yuan Chang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Paul Soloway
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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45
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Jain N, Lord JM, Vogel V. Mechanoimmunology: Are inflammatory epigenetic states of macrophages tuned by biophysical factors? APL Bioeng 2022; 6:031502. [PMID: 36051106 PMCID: PMC9427154 DOI: 10.1063/5.0087699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Many inflammatory diseases that are responsible for a majority of deaths are still uncurable, in part as the underpinning pathomechanisms and how to combat them is still poorly understood. Tissue-resident macrophages play pivotal roles in the maintenance of tissue homeostasis, but if they gradually convert to proinflammatory phenotypes, or if blood-born proinflammatory macrophages persist long-term after activation, they contribute to chronic inflammation and fibrosis. While biochemical factors and how they regulate the inflammatory transcriptional response of macrophages have been at the forefront of research to identify targets for therapeutic interventions, evidence is increasing that physical factors also tune the macrophage phenotype. Recently, several mechanisms have emerged as to how physical factors impact the mechanobiology of macrophages, from the nuclear translocation of transcription factors to epigenetic modifications, perhaps even DNA methylation. Insight into the mechanobiology of macrophages and associated epigenetic modifications will deliver novel therapeutic options going forward, particularly in the context of increased inflammation with advancing age and age-related diseases. We review here how biophysical factors can co-regulate pro-inflammatory gene expression and epigenetic modifications and identify knowledge gaps that require urgent attention if this therapeutic potential is to be realized.
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Affiliation(s)
| | | | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
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46
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Histone Deacetylase 3 Inhibitor Alleviates Cerebellar Defects in Perinatal Hypothyroid Mice by Stimulating Histone Acetylation and Transcription at Thyroid Hormone-Responsive Gene Loci. Int J Mol Sci 2022; 23:ijms23147869. [PMID: 35887216 PMCID: PMC9319938 DOI: 10.3390/ijms23147869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 01/27/2023] Open
Abstract
Perinatal hypothyroidism impairs cerebellar organogenesis and results in motor coordination defects. The thyroid hormone receptor binds to corepressor complexes containing histone deacetylase (HDAC) 3 in the absence of ligands and acts as a transcriptional repressor. Although histone acetylation status is strongly correlated with transcriptional regulation, its role in cerebellar development remains largely unknown. We aimed to study whether the cerebellar developmental defects induced by perinatal hypothyroidism can be rescued by treatment with a specific HDAC3 inhibitor, RGFP966. Motor coordination was analyzed using three behavioral tests. The cerebella were subjected to RT-qPCR and chromatin immunoprecipitation assays for acetylated histone H3. The treatment with RGFP966 partially reversed the cerebellar morphological defects in perinatal hypothyroid mice. These findings were associated with the alleviation of motor coordination defects in these mice. In addition, the RGFP966 administration increased the mRNA levels of cerebellar thyroid hormone-responsive genes. These increases were accompanied by augmented histone acetylation status at these gene loci. These findings indicate that HDAC3 plays an important role in the cerebellar developmental defects induced by perinatal hypothyroidism. The HDAC3 inhibitor might serve as a novel therapeutic agent for hypothyroidism-induced cerebellar defects by acetylating histone tails and stimulating transcription at thyroid hormone-responsive gene loci.
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47
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Jang J, Song G, Pettit SM, Li Q, Song X, Cai CL, Kaushal S, Li D. Epicardial HDAC3 Promotes Myocardial Growth Through a Novel MicroRNA Pathway. Circ Res 2022; 131:151-164. [PMID: 35722872 PMCID: PMC9308743 DOI: 10.1161/circresaha.122.320785] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Establishment of the myocardial wall requires proper growth cues from nonmyocardial tissues. During heart development, the epicardium and epicardium-derived cells instruct myocardial growth by secreting essential factors including FGF (fibroblast growth factor) 9 and IGF (insulin-like growth factor) 2. However, it is poorly understood how the epicardial secreted factors are regulated, in particular by chromatin modifications for myocardial formation. The current study is to investigate whether and how HDAC (histone deacetylase) 3 in the developing epicardium regulates myocardial growth. METHODS Various cellular and mouse models in conjunction with biochemical and molecular tools were employed to study the role of HDAC3 in the developing epicardium. RESULTS We deleted Hdac3 in the developing murine epicardium, and mutant hearts showed ventricular myocardial wall hypoplasia with reduction of epicardium-derived cells. The cultured embryonic cardiomyocytes with supernatants from Hdac3 knockout (KO) mouse epicardial cells also showed decreased proliferation. Genome-wide transcriptomic analysis revealed that Fgf9 and Igf2 were significantly downregulated in Hdac3 KO mouse epicardial cells. We further found that Fgf9 and Igf2 expression is dependent on HDAC3 deacetylase activity. The supplementation of FGF9 or IGF2 can rescue the myocardial proliferation defects treated by Hdac3 KO supernatant. Mechanistically, we identified that microRNA (miR)-322 and miR-503 were upregulated in Hdac3 KO mouse epicardial cells and Hdac3 epicardial KO hearts. Overexpression of miR-322 or miR-503 repressed FGF9 and IGF2 expression, while knockdown of miR-322 or miR-503 restored FGF9 and IGF2 expression in Hdac3 KO mouse epicardial cells. CONCLUSIONS Our findings reveal a critical signaling pathway in which epicardial HDAC3 promotes compact myocardial growth by stimulating FGF9 and IGF2 through repressing miR-322 or miR-503, providing novel insights in elucidating the etiology of congenital heart defects and conceptual strategies to promote myocardial regeneration.
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Affiliation(s)
- Jihyun Jang
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Guang Song
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sarah M. Pettit
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Qinshan Li
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Xiaosu Song
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Chen-leng Cai
- Department of Pediatrics, Herman Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46201
| | - Sunjay Kaushal
- Division of Cardiovascular-Thoracic Surgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Deqiang Li
- Center for Vascular and Inflammation Diseases, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD 21201
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48
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Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters JM, Mirny LA, Garcia BA, Majewski J, Saitou M. Nucleome programming is required for the foundation of totipotency in mammalian germline development. EMBO J 2022; 41:e110600. [PMID: 35703121 DOI: 10.15252/embj.2022110600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres-an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.
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Affiliation(s)
- Masahiro Nagano
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Bo Hu
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Shihori Yokobayashi
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akitoshi Yamamura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiya Umemura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukiko Ishikura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroki Ikeda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Department of Embryology, Nara Medical University, Nara, Japan
| | - Naofumi Kawahira
- Department of Molecular Cell Developmental Biology, School of Life Science, University of California, Los Angeles, CA, USA.,Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sakura Shimizu
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoji Kojima
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ken Mizuta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoko Kasahara
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yusuke Imoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Killian Meehan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Roman Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Yasuaki Hiraoka
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Kyoto, Japan
| | - Kikue Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jan-Michel Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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49
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Yang L, Sun J, Chen Z, Liu L, Sun Y, Lin J, Hu X, Zhao M, Ma Y, Lu D, Li Y, Guo Y, Dong E. The LMNA p.R541C mutation causes dilated cardiomyopathy in human and mice. Int J Cardiol 2022; 363:149-158. [PMID: 35714719 DOI: 10.1016/j.ijcard.2022.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
Dilated cardiomyopathy (DCM) is a major cause of heart failure. LMNA variants contribute to 6-10% DCM cases, but the underlying mechanisms remain incompletely understood. Here, we reported two patients carrying the LMNA c.1621C > T/ p.R541C variant and generated a knock-in mouse model (LmnaRC) to study the role of this variant in DCM pathogenesis. We found LmnaRC/RC mice exhibited ventricular dilation and reduced systolic functions at 6 months after birth. The LmnaRC/RC cardiomyocytes increased in size but no nuclear morphology defects were detected. Transcriptomic and microscopic analyses revealed suppressed gene expression and perturbed ultrastructure in LmnaRC/RC mitochondria. These defects were associated with increased heterochromatin structures and epigenetic markers including H3K9me2/3. Together, these data implied that the LMNA c.1621C > T/ p.R541C variant enhanced heterochromatic gene suppression and disrupted mitochondria functions as a cause of DCM.
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Affiliation(s)
- Luzi Yang
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Jinhuan Sun
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Zhan Chen
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Lei Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education (MOE), Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yueshen Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Junsen Lin
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Xiaomin Hu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Mingming Zhao
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; The Institute of Cardiovascular Sciences, Peking University; National Health Commission of China (NHC) Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Key Laboratory of Molecular Cardiovascular Science of Ministry of Education; Beijing Key Laboratory of Cardiovascular Receptors Research. Beijing 100191, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC) and Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Dan Lu
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC) and Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education (MOE), Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Yuxuan Guo
- Peking University Health Science Center, School of Basic Medical Sciences, The Institute of Cardiovascular Sciences, Key Laboratory of Molecular Cardiovascular Science of Ministry of Education, Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China.
| | - Erdan Dong
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital; The Institute of Cardiovascular Sciences, Peking University; National Health Commission of China (NHC) Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Key Laboratory of Molecular Cardiovascular Science of Ministry of Education; Beijing Key Laboratory of Cardiovascular Receptors Research. Beijing 100191, China
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50
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Feng Y, Cai L, Hong W, Zhang C, Tan N, Wang M, Wang C, Liu F, Wang X, Ma J, Gao C, Kumar M, Mo Y, Geng Q, Luo C, Lin Y, Chen H, Wang SY, Watson MJ, Jegga AG, Pedersen RA, Fu JD, Wang ZV, Fan GC, Sadayappan S, Wang Y, Pauklin S, Huang F, Huang W, Jiang L. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation 2022; 145:1663-1683. [PMID: 35400201 PMCID: PMC9251830 DOI: 10.1161/circulationaha.121.055781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Transcriptional reconfiguration is central to heart failure, the most common cause of which is dilated cardiomyopathy (DCM). The effect of 3-dimensional chromatin topology on transcriptional dysregulation and pathogenesis in human DCM remains elusive. METHODS We generated a compendium of 3-dimensional epigenome and transcriptome maps from 101 biobanked human DCM and nonfailing heart tissues through highly integrative chromatin immunoprecipitation (H3K27ac [acetylation of lysine 27 on histone H3]), in situ high-throughput chromosome conformation capture, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and RNA sequencing. We used human induced pluripotent stem cell-derived cardiomyocytes and mouse models to interrogate the key transcription factor implicated in 3-dimensional chromatin organization and transcriptional regulation in DCM pathogenesis. RESULTS We discovered that the active regulatory elements (H3K27ac peaks) and their connectome (H3K27ac loops) were extensively reprogrammed in DCM hearts and contributed to transcriptional dysregulation implicated in DCM development. For example, we identified that nontranscribing NPPA-AS1 (natriuretic peptide A antisense RNA 1) promoter functions as an enhancer and physically interacts with the NPPA (natriuretic peptide A) and NPPB (natriuretic peptide B) promoters, leading to the cotranscription of NPPA and NPPB in DCM hearts. We revealed that DCM-enriched H3K27ac loops largely resided in conserved high-order chromatin architectures (compartments, topologically associating domains) and their anchors unexpectedly had equivalent chromatin accessibility. We discovered that the DCM-enriched H3K27ac loop anchors exhibited a strong enrichment for HAND1 (heart and neural crest derivatives expressed 1), a key transcription factor involved in early cardiogenesis. In line with this, its protein expression was upregulated in human DCM and mouse failing hearts. To further validate whether HAND1 is a causal driver for the reprogramming of enhancer-promoter connectome in DCM hearts, we performed comprehensive 3-dimensional epigenome mappings in human induced pluripotent stem cell-derived cardiomyocytes. We found that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced a distinct gain of enhancer-promoter connectivity and correspondingly increased the expression of their connected genes implicated in DCM pathogenesis, thus recapitulating the transcriptional signature in human DCM hearts. Electrophysiology analysis demonstrated that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced abnormal calcium handling. Furthermore, cardiomyocyte-specific overexpression of Hand1 in the mouse hearts resulted in dilated cardiac remodeling with impaired contractility/Ca2+ handling in cardiomyocytes, increased ratio of heart weight/body weight, and compromised cardiac function, which were ascribed to recapitulation of transcriptional reprogramming in DCM. CONCLUSIONS This study provided novel chromatin topology insights into DCM pathogenesis and illustrated a model whereby a single transcription factor (HAND1) reprograms the genome-wide enhancer-promoter connectome to drive DCM pathogenesis.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
- These authors contributed equally to this work
| | - Liuyang Cai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR 999077, China
- These authors contributed equally to this work
| | - Wanzi Hong
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- These authors contributed equally to this work
| | - Chunxiang Zhang
- Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
- These authors contributed equally to this work
| | - Ning Tan
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Mingyang Wang
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland D02 VF25
| | - Feng Liu
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Xiaohong Wang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jianyong Ma
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chen Gao
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mohit Kumar
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yuanxi Mo
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Qingshan Geng
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Changjun Luo
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yan Lin
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Haiyang Chen
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shuang-Yin Wang
- Department of Immunology, Weizmann Institute of Science, Rehovot WR35+R8, Israel
| | - Michael J. Watson
- Department of Surgery, Cardiovascular & Thoracic, Duke University, Durham, NC 27710, USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH 45221, USA
| | - Roger A. Pedersen
- Department of OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research, Stanford University, Stanford, California, USA
| | - Ji-dong Fu
- Departments of Physiology and Cell Biology, the Dorothy M. Davis Heart and Lung Research Institute, Frick Center for Heart Failure and Arrhythmia, the Ohio State University, Columbus, OH 43210, USA
| | - Zhao V. Wang
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA, 75390-8573
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Feng Huang
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lei Jiang
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- Lead contact
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