51
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Kychygina A, Dall'Osto M, Allen JAM, Cadoret JC, Piras V, Pickett HA, Crabbe L. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools. Sci Rep 2021; 11:13195. [PMID: 34162976 PMCID: PMC8222272 DOI: 10.1038/s41598-021-92631-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
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Affiliation(s)
- Anna Kychygina
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.,INSERM UMR1291, CNRS UMR5051, UT3, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), 31059, Toulouse, France
| | - Marina Dall'Osto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | - Vincent Piras
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
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52
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Murray-Nerger LA, Cristea IM. Lamin post-translational modifications: emerging toggles of nuclear organization and function. Trends Biochem Sci 2021; 46:832-847. [PMID: 34148760 DOI: 10.1016/j.tibs.2021.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
Nuclear lamins are ancient type V intermediate filaments with diverse functions that include maintaining nuclear shape, mechanosignaling, tethering and stabilizing chromatin, regulating gene expression, and contributing to cell cycle progression. Despite these numerous roles, an outstanding question has been how lamins are regulated. Accumulating work indicates that a range of lamin post-translational modifications (PTMs) control their functions both in homeostatic cells and in disease states such as progeria, muscular dystrophy, and viral infection. Here, we review the current knowledge of the diverse types of PTMs that regulate lamins in a site-specific manner. We highlight methods that can be used to characterize lamin PTMs whose functions are currently unknown and provide a perspective on the future of the lamin PTM field.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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53
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Mosquera JV, Bacher MC, Priess JR. Nuclear lipid droplets and nuclear damage in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009602. [PMID: 34133414 PMCID: PMC8208577 DOI: 10.1371/journal.pgen.1009602] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
Fat stored in the form of lipid droplets has long been considered a defining characteristic of cytoplasm. However, recent studies have shown that nuclear lipid droplets occur in multiple cells and tissues, including in human patients with fatty liver disease. The function(s) of stored fat in the nucleus has not been determined, and it is possible that nuclear fat is beneficial in some situations. Conversely, nuclear lipid droplets might instead be deleterious by disrupting nuclear organization or triggering aggregation of hydrophobic proteins. We show here that nuclear lipid droplets occur normally in C. elegans intestinal cells and germ cells, but appear to be associated with damage only in the intestine. Lipid droplets in intestinal nuclei can be associated with novel bundles of microfilaments (nuclear actin) and membrane tubules that might have roles in damage repair. To increase the normal, low frequency of nuclear lipid droplets in wild-type animals, we used a forward genetic screen to isolate mutants with abnormally large or abundant nuclear lipid droplets. Genetic analysis and cloning of three such mutants showed that the genes encode the lipid regulator SEIP-1/seipin, the inner nuclear membrane protein NEMP-1/Nemp1/TMEM194A, and a component of COPI vesicles called COPA-1/α-COP. We present several lines of evidence that the nuclear lipid droplet phenotype of copa-1 mutants results from a defect in retrieving mislocalized membrane proteins that normally reside in the endoplasmic reticulum. The seip-1 mutant causes most germ cells to have nuclear lipid droplets, the largest of which occupy more than a third of the nuclear volume. Nevertheless, the nuclear lipid droplets do not trigger apoptosis, and the germ cells differentiate into gametes that produce viable, healthy progeny. Thus, our results suggest that nuclear lipid droplets are detrimental to intestinal nuclei, but have no obvious deleterious effect on germ nuclei. Several human disorders such as obesity are associated with abnormal fat storage. Cells normally store fat in cytoplasmic organelles called lipid droplets. However, recent studies have shown that fat can also form inside of the cell nucleus, and the effects of nuclear fat are not known. Here we use the cell biology and genetics of the model organism C. elegans to study the causes and consequences of nuclear fat. We show that intestinal cells can contain nuclear fat, particularly during high-low-high changes in cytoplasmic fat that involve de novo fat synthesis. Nuclear fat is associated with multiple changes in intestinal nuclei that appear to represent damage and repair. Germ nuclei that normally differentiate into oocytes can also contain nuclear fat. In germ cells, however, even high levels of nuclear fat appear to cause little or no damage. Our results suggest that intestinal nuclei and germ cell nuclei might have different responses to nuclear fat in part because they differ in chromosomal organization at the nuclear envelope.
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Affiliation(s)
| | - Meghan C. Bacher
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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54
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Liu SY, Ikegami K. Nuclear lamin phosphorylation: an emerging role in gene regulation and pathogenesis of laminopathies. Nucleus 2021; 11:299-314. [PMID: 33030403 PMCID: PMC7588210 DOI: 10.1080/19491034.2020.1832734] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Decades of studies have established that nuclear lamin polymers form the nuclear lamina, a protein meshwork that supports the nuclear envelope structure and tethers heterochromatin to the nuclear periphery. Much less is known about unpolymerized nuclear lamins in the nuclear interior, some of which are now known to undergo specific phosphorylation. A recent finding that phosphorylated lamins bind gene enhancer regions offers a new hypothesis that lamin phosphorylation may influence transcriptional regulation in the nuclear interior. In this review, we discuss the regulation, localization, and functions of phosphorylated lamins. We summarize kinases that phosphorylate lamins in a variety of biological contexts. Our discussion extends to laminopathies, a spectrum of degenerative disorders caused by lamin gene mutations, such as cardiomyopathies and progeria. We compare the prevailing hypothesis for laminopathy pathogenesis based on lamins’ function at the nuclear lamina with an emerging hypothesis based on phosphorylated lamins’ function in the nuclear interior.
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Affiliation(s)
- Sunny Yang Liu
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA
| | - Kohta Ikegami
- Department of Pediatrics, The University of Chicago , Chicago, Illinois, USA.,Division of Molecular and Cardiovascular Biology, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio, USA
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55
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Ricci A, Orazi S, Biancucci F, Magnani M, Menotta M. The nucleoplasmic interactions among Lamin A/C-pRB-LAP2α-E2F1 are modulated by dexamethasone. Sci Rep 2021; 11:10099. [PMID: 33980953 PMCID: PMC8115688 DOI: 10.1038/s41598-021-89608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
Ataxia telangiectasia (AT) is a rare genetic neurodegenerative disease. To date, there is no available cure for the illness, but the use of glucocorticoids has been shown to alleviate the neurological symptoms associated with AT. While studying the effects of dexamethasone (dex) in AT fibroblasts, by chance we observed that the nucleoplasmic Lamin A/C was affected by the drug. In addition to the structural roles of A-type lamins, Lamin A/C has been shown to play a role in the regulation of gene expression and cell cycle progression, and alterations in the LMNA gene is cause of human diseases called laminopathies. Dex was found to improve the nucleoplasmic accumulation of soluble Lamin A/C and was capable of managing the large chromatin Lamin A/C scaffolds contained complex, thus regulating epigenetics in treated cells. In addition, dex modified the interactions of Lamin A/C with its direct partners lamin associated polypeptide (LAP) 2a, Retinoblastoma 1 (pRB) and E2F Transcription Factor 1 (E2F1), regulating local gene expression dependent on E2F1. These effects were differentially observed in both AT and wild type (WT) cells. To our knowledge, this is the first reported evidence of the role of dex in Lamin A/C dynamics in AT cells, and may represent a new area of research regarding the effects of glucocorticoids on AT. Moreover, future investigations could also be extended to healthy subjects or to other pathologies such as laminopathies since glucocorticoids may have other important effects in these contexts as well.
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Affiliation(s)
- Anastasia Ricci
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via A. Saffi 2, 61029, Urbino, Italy
| | - Sara Orazi
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via A. Saffi 2, 61029, Urbino, Italy
| | - Federica Biancucci
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via A. Saffi 2, 61029, Urbino, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via A. Saffi 2, 61029, Urbino, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via A. Saffi 2, 61029, Urbino, Italy.
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56
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Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R. Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. Cell Stem Cell 2021; 28:938-954.e9. [PMID: 33529599 PMCID: PMC8106635 DOI: 10.1016/j.stem.2020.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/13/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023]
Abstract
Pathogenic mutations in LAMIN A/C (LMNA) cause abnormal nuclear structure and laminopathies. These diseases have myriad tissue-specific phenotypes, including dilated cardiomyopathy (DCM), but how LMNA mutations result in tissue-restricted disease phenotypes remains unclear. We introduced LMNA mutations from individuals with DCM into human induced pluripotent stem cells (hiPSCs) and found that hiPSC-derived cardiomyocytes, in contrast to hepatocytes or adipocytes, exhibit aberrant nuclear morphology and specific disruptions in peripheral chromatin. Disrupted regions were enriched for transcriptionally active genes and regions with lower LAMIN B1 contact frequency. The lamina-chromatin interactions disrupted in mutant cardiomyocytes were enriched for genes associated with non-myocyte lineages and correlated with higher expression of those genes. Myocardium from individuals with LMNA variants similarly showed aberrant expression of non-myocyte pathways. We propose that the lamina network safeguards cellular identity and that pathogenic LMNA variants disrupt peripheral chromatin with specific epigenetic and molecular characteristics, causing misexpression of genes normally expressed in other cell types.
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Affiliation(s)
- Parisha P Shah
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Wenjian Lv
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Joshua H Rhoades
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Deepti Abbey
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Matthew A Caporizzo
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Ricardo Linares-Saldana
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Julie G Heffler
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA 94305, USA
| | - Dilip Thomas
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Qiaohong Wang
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Liam J Stanton
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kenneth Bedi
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Michael P Morley
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Lung Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Thomas P Cappola
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Anjali T Owens
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kenneth B Margulies
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - David B Frank
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Department of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel J Rader
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Wenli Yang
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Benjamin L Prosser
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Physiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Pennsylvania Muscle Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA
| | - Kiran Musunuru
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA.
| | - Rajan Jain
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA; Institute for Regenerative Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19014, USA.
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57
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Hoskins VE, Smith K, Reddy KL. The shifting shape of genomes: dynamics of heterochromatin interactions at the nuclear lamina. Curr Opin Genet Dev 2021; 67:163-173. [PMID: 33774266 PMCID: PMC8489734 DOI: 10.1016/j.gde.2021.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022]
Abstract
The nucleus is a highly structured organelle with many chromatin and protein compartments that partition the genome into regulatory domains. One such a compartment within the mammalian nucleus is the microenvironment underlying the nuclear envelope (NE) where intermediate filament proteins, lamins, act as a link between cytoskeletal and inner nuclear membrane (INM) proteins, chromatin binders and modifiers, and heterochromatin. These dynamic interactions regulate many cellular processes and, when they are perturbed, can lead to genome dysregulation and disease.
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Affiliation(s)
- Victoria E Hoskins
- Johns Hopkins University, School of Medicine, Center for Epigenetics, Department of Biological Chemistry, Baltimore, MD 21205, United States
| | - Kristiana Smith
- Johns Hopkins University, School of Medicine, Center for Epigenetics, Department of Biological Chemistry, Baltimore, MD 21205, United States
| | - Karen L Reddy
- Johns Hopkins University, School of Medicine, Center for Epigenetics, Department of Biological Chemistry, Baltimore, MD 21205, United States; Sidney Kimmel Cancer Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, United States; Johns Hopkins University, School of Medicine, Department of Medicine, Baltimore, MD 21205, United States.
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58
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Ito S, Ueda T, Yokoyama A, Fujihara A, Hongo F, Ukimura O. PCA3 controls chromatin organization and p53 signal activation by regulating LAP2α-lamin A complexes. Cancer Gene Ther 2021; 29:358-368. [PMID: 33758375 DOI: 10.1038/s41417-021-00314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 11/09/2022]
Abstract
Prostate cancer antigen 3 (PCA3) is a prostate cancer-specific long noncoding RNA (lncRNA). Here, we report that lncRNA PCA3 plays a role in prostate cancer progression that is mediated by nucleoplasmic lamins. PCA3 interacts with the C-terminal region of lamina-associated polypeptide (LAP) 2α. The C-terminal region of LAP2α includes tumor suppressor protein retinoblastoma (pRb)- and lamin-binding domains, and it is necessary for the regulation and stabilization of the nucleoplasmic pool of lamin A. PCA3 inhibits the interaction of LAP2α with lamin A through binding with the C-terminus of LAP2α. The level of nucleoplasmic lamin A/C is increased by knockdown of PCA3. Together, the level of LAP2α within the nucleus is increased by PCA3 knockdown. In PCA3 knockdown cells, the levels of HP1γ, trimethylation of Lys9 on histone H3 (H3K9me3), and trimethylation of Lys36 on histone H3 (H3K36me3) are upregulated. In contrast, trimethylation of Lys4 on histone H3 (H3K4me3) is downregulated. We further demonstrate that activation of the p53 signaling pathway and cell cycle arrest are promoted in the absence of PCA3. These findings support a unique mechanism in which prostate cancer-specific lncRNA controls chromatin organization via regulation of the nucleoplasmic pool of lamins. This proposed mechanism suggests that cancer progression may be mediated by nuclear lamins.
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Affiliation(s)
- Saya Ito
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto-City, Kyoto, Japan.
| | - Takashi Ueda
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto-City, Kyoto, Japan
| | - Atsushi Yokoyama
- Department of Molecular Endocrinology, Tohoku University Graduate School of Medicine, Sendai-City, Miyagi, Japan
| | - Atsuko Fujihara
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto-City, Kyoto, Japan
| | - Fumiya Hongo
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto-City, Kyoto, Japan
| | - Osamu Ukimura
- Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto-City, Kyoto, Japan
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59
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Murray-Nerger LA, Justice JL, Rekapalli P, Hutton JE, Cristea I. Lamin B1 acetylation slows the G1 to S cell cycle transition through inhibition of DNA repair. Nucleic Acids Res 2021; 49:2044-2064. [PMID: 33533922 PMCID: PMC7913768 DOI: 10.1093/nar/gkab019] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/05/2021] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
The integrity and regulation of the nuclear lamina is essential for nuclear organization and chromatin stability, with its dysregulation being linked to laminopathy diseases and cancer. Although numerous posttranslational modifications have been identified on lamins, few have been ascribed a regulatory function. Here, we establish that lamin B1 (LMNB1) acetylation at K134 is a molecular toggle that controls nuclear periphery stability, cell cycle progression, and DNA repair. LMNB1 acetylation prevents lamina disruption during herpesvirus type 1 (HSV-1) infection, thereby inhibiting virus production. We also demonstrate the broad impact of this site on laminar processes in uninfected cells. LMNB1 acetylation negatively regulates canonical nonhomologous end joining by impairing the recruitment of 53BP1 to damaged DNA. This defect causes a delay in DNA damage resolution and a persistent activation of the G1/S checkpoint. Altogether, we reveal LMNB1 acetylation as a mechanism for controlling DNA repair pathway choice and stabilizing the nuclear periphery.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Pranav Rekapalli
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Josiah E Hutton
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
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60
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Naetar N, Georgiou K, Knapp C, Bronshtein I, Zier E, Fichtinger P, Dechat T, Garini Y, Foisner R. LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior. eLife 2021; 10:e63476. [PMID: 33605210 PMCID: PMC7939549 DOI: 10.7554/elife.63476] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 01/08/2023] Open
Abstract
Lamins form stable filaments at the nuclear periphery in metazoans. Unlike B-type lamins, lamins A and C localize also in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). Using antibody labeling, we previously observed a depletion of nucleoplasmic A-type lamins in mouse cells lacking LAP2α. Here, we show that loss of LAP2α actually causes formation of larger, biochemically stable lamin A/C structures in the nuclear interior that are inaccessible to lamin A/C antibodies. While nucleoplasmic lamin A forms from newly expressed pre-lamin A during processing and from soluble mitotic lamins in a LAP2α-independent manner, binding of LAP2α to lamin A/C during interphase inhibits formation of higher order structures, keeping nucleoplasmic lamin A/C in a mobile state independent of lamin A/C S22 phosphorylation. We propose that LAP2α is essential to maintain a mobile lamin A/C pool in the nuclear interior, which is required for proper nuclear functions.
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Affiliation(s)
- Nana Naetar
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Konstantina Georgiou
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Christian Knapp
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Irena Bronshtein
- Physics Department and Nanotechnology Institute, Bar Ilan UniversityRamat GanIsrael
| | - Elisabeth Zier
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Petra Fichtinger
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Thomas Dechat
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
| | - Yuval Garini
- Physics Department and Nanotechnology Institute, Bar Ilan UniversityRamat GanIsrael
| | - Roland Foisner
- Max Perutz Labs, Center for Medical Biochemistry, Medical University of Vienna, Vienna Biocenter Campus (VBC)ViennaAustria
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61
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Gil L, Niño SA, Capdeville G, Jiménez-Capdeville ME. Aging and Alzheimer's disease connection: Nuclear Tau and lamin A. Neurosci Lett 2021; 749:135741. [PMID: 33610669 DOI: 10.1016/j.neulet.2021.135741] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/12/2021] [Accepted: 02/11/2021] [Indexed: 12/24/2022]
Abstract
Age-related pathologies like Alzheimer`s disease (AD) imply cellular responses directed towards repairing DNA damage. Postmitotic neurons show progressive accumulation of oxidized DNA during decades of brain aging, which is especially remarkable in AD brains. The characteristic cytoskeletal pathology of AD neurons is brought about by the progressive changes that neurons undergo throughout aging, and their irreversible nuclear transformation initiates the disease. This review focusses on critical molecular events leading to the loss of plasticity that underlies cognitive deficits in AD. During healthy neuronal aging, nuclear Tau participates in the regulation of the structure and function of the chromatin. The aberrant cell cycle reentry initiated for DNA repair triggers a cascade of events leading to the dysfunctional AD neuron, whereby Tau protein exits the nucleus leading to chromatin disorganization. Lamin A, which is not typically expressed in neurons, appears at the transformation from senile to AD neurons and contributes to halting the consequences of cell cycle reentry and nuclear Tau exit, allowing the survival of the neuron. Nevertheless, this irreversible nuclear transformation alters the nucleic acid and protein synthesis machinery as well as the nuclear lamina and cytoskeleton structures, leading to neurofibrillary tangles formation and final neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad "Alfonso X el Sabio", Madrid, Spain
| | - Sandra A Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Mexico
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62
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Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
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Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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63
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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64
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Brunet A, Destainville N, Collas P. Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale. Nucleus 2021; 12:6-20. [PMID: 33435761 PMCID: PMC7808377 DOI: 10.1080/19491034.2020.1868105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Interactions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the lamina. Impact of polymer stiffness is greater than stretching on its configurations at the lamina; these are manifested as trains describing extended interactions, and loops describing desorbed regions . Conferring an attraction potential leads to persistent interaction and adsorption-desorption regimes manifested by fluctuations between trains and loops. These are modulated by polymer stiffness and stretching, with a dominant impact of stiffness on resulting structural configurations. We infer that flexible euchromatin is more prone to stochastic interactions with lamins than rigid heterochromatin characterizing constitutive LADs. Our models provide insights on the physical properties of chromatin as a polymer which affect the dynamics and patterns of interactions with the nuclear lamina.
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Affiliation(s)
- Annaël Brunet
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo, Norway
| | - Nicolas Destainville
- Laboratoire De Physique Théorique, IRSAMC, Université De Toulouse (UPS) , CNRS, Toulouse, France
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital , Oslo, Norway
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65
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Zhang X, Shao X, Zhang R, Zhu R, Feng R. Integrated analysis reveals the alterations that LMNA interacts with euchromatin in LMNA mutation-associated dilated cardiomyopathy. Clin Epigenetics 2021; 13:3. [PMID: 33407844 PMCID: PMC7788725 DOI: 10.1186/s13148-020-00996-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a serious cardiac heterogeneous pathological disease, which may be caused by mutations in the LMNA gene. Lamins interact with not only lamina-associated domains (LADs) but also euchromatin by alone or associates with the lamina-associated polypeptide 2 alpha (LAP2α). Numerous studies have documented that LMNA regulates gene expression by interacting with LADs in heterochromatin. However, the role of LMNA in regulating euchromatin in DCM is poorly understood. Here, we determine the differential binding genes on euchromatin in DCM induced by LMNA mutation by performing an integrated analysis of bioinformatics and explore the possible molecular pathogenesis mechanism. RESULTS Six hundred twenty-three and 4484 differential binding genes were identified by ChIP-seq technology. The ChIP-seq analysis results and matched RNA-Seq transcriptome data were integrated to further validate the differential binding genes of ChIP-seq. Five and 60 candidate genes involved in a series of downstream analysis were identified. Finally, 4 key genes (CREBBP, PPP2R2B, BMP4, and BMP7) were harvested, and these genes may regulate LMNA mutation-induced DCM through WNT/β-catenin or TGFβ-BMP pathways. CONCLUSIONS We identified four key genes that may serve as potential biomarkers and novel therapeutic targets. Our study also illuminates the possible molecular pathogenesis mechanism that the abnormal binding between LMNA or LAP2α-lamin A/C complexes and euchromatin DNA in LMNA mutations, which may cause DCM through the changes of CREBBP, PPP2R2B, BMP4, BMP7 expressions, and the dysregulation of WNT/β-catenin or TGFβ-BMP pathways, providing valuable insights to improve the occurrence and development of DCM.
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Affiliation(s)
- Xiaolin Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, China
| | - Xiuli Shao
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, China
| | - Ruijia Zhang
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, China
| | - Rongli Zhu
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, China
| | - Rui Feng
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, China.
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66
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Bizhanova A, Kaufman PD. Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194666. [PMID: 33307247 PMCID: PMC7855492 DOI: 10.1016/j.bbagrm.2020.194666] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, the focus of this review, mainly localizes at the nuclear periphery, forming Lamina-associated domains (LADs), and at the nucleolar periphery, forming Nucleolus-associated domains (NADs). Together, these regions comprise approximately one-half of mammalian genomes, and most but not all loci within these domains are stochastically placed at either of these two locations after exit from mitosis at each cell cycle. Excitement about the role of these heterochromatic domains in early development has recently been heightened by the discovery that LADs appear at some loci in the preimplantation mouse embryo prior to other chromosomal features like compartmental identity and topologically-associated domains (TADs). While LADs have been extensively studied and mapped during cellular differentiation and early embryonic development, NADs have been less thoroughly studied. Here, we summarize pioneering studies of NADs and LADs, more recent advances in our understanding of cis/trans-acting factors that mediate these localizations, and discuss the functional significance of these associations.
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Affiliation(s)
- Aizhan Bizhanova
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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67
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Burla R, La Torre M, Maccaroni K, Verni F, Giunta S, Saggio I. Interplay of the nuclear envelope with chromatin in physiology and pathology. Nucleus 2020; 11:205-218. [PMID: 32835589 PMCID: PMC7529417 DOI: 10.1080/19491034.2020.1806661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer. ABBREVIATIONS na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
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Affiliation(s)
- Romina Burla
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Fiammetta Verni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Giunta
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- Rockefeller University, New York, NY, USA
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
- Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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68
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Mirza AN, Gonzalez F, Ha SK, Oro AE. The Sky's the LEMit: New insights into nuclear structure regulation of transcription factor activity. Curr Opin Cell Biol 2020; 68:173-180. [PMID: 33227657 DOI: 10.1016/j.ceb.2020.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 12/31/2022]
Abstract
The nucleoskeleton has been associated with partitioning the genome into active and inactive compartments that dictate local transcription factor (TF) activity. However, recent data indicate that the nucleoskeleton and TFs reciprocally influence each other in dynamic TF trafficking pathways through the functions of LEM proteins. While the conserved peripheral recruitment of TFs by LEM proteins has been viewed as a mechanism of repressing transcription, a diversity of release mechanisms from the lamina suggest this compartment serves as a refuge for nuclear TF accumulation for rapid mobilization and signal stability. Detailed mechanisms suggest that TFs toggle between nuclear lamina refuge and nuclear matrix lamin-LEM protein complexes at sites of active transcription. In this review we will highlight emerging LEM functions acting at the interface of chromatin and nucleoskeleton to create TF trafficking networks.
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Affiliation(s)
- Amar N Mirza
- Program in Epithelial Biology, Stanford University School of Medicine Stanford, CA, 94305, USA
| | - Fernanda Gonzalez
- Program in Epithelial Biology, Stanford University School of Medicine Stanford, CA, 94305, USA
| | - Sierra K Ha
- Program in Epithelial Biology, Stanford University School of Medicine Stanford, CA, 94305, USA
| | - Anthony E Oro
- Program in Epithelial Biology, Stanford University School of Medicine Stanford, CA, 94305, USA.
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69
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Ikegami K, Secchia S, Almakki O, Lieb JD, Moskowitz IP. Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria. Dev Cell 2020; 52:699-713.e11. [PMID: 32208162 DOI: 10.1016/j.devcel.2020.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/13/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
LMNA encodes nuclear Lamin A/C that tethers lamina-associated domains (LADs) to the nuclear periphery. Mutations in LMNA cause degenerative disorders including the premature aging disorder Hutchinson-Gilford progeria, but the mechanisms are unknown. We report that Ser22-phosphorylated (pS22) Lamin A/C was localized to the nuclear interior in human fibroblasts throughout the cell cycle. pS22-Lamin A/C interacted with a subset of putative active enhancers, not LADs, at locations co-bound by the transcriptional activator c-Jun. In progeria-patient fibroblasts, a subset of pS22-Lamin A/C-binding sites were lost, whereas new pS22-Lamin A/C-binding sites emerged in normally quiescent loci. New pS22-Lamin A/C binding was accompanied by increased histone acetylation, increased c-Jun binding, and upregulation of nearby genes implicated in progeria pathophysiology. These results suggest that Lamin A/C regulates gene expression by enhancer binding. Disruption of the gene regulatory rather than LAD tethering function of Lamin A/C may underlie the pathogenesis of disorders caused by LMNA mutations.
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Affiliation(s)
- Kohta Ikegami
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | - Stefano Secchia
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, Lunds University, Lund 22362, Sweden
| | - Omar Almakki
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Jason D Lieb
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Ivan P Moskowitz
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
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70
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Goswami R, Asnacios A, Hamant O, Chabouté ME. Is the plant nucleus a mechanical rheostat? CURRENT OPINION IN PLANT BIOLOGY 2020; 57:155-163. [PMID: 33128898 DOI: 10.1016/j.pbi.2020.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/29/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Beyond its biochemical nature, the nucleus is also a physical object. There is accumulating evidence that its mechanics plays a key role in gene expression, cytoskeleton organization, and more generally in cell and developmental biology. Building on data mainly obtained from the animal literature, we show how nuclear mechanics may orchestrate development and gene expression. In other words, the nucleus may play the additional role of a mechanical rheostat. Although data from plant systems are still scarce, we pinpoint recent advances and highlight some differences with animal systems. Building on this survey, we propose a list of prospects for future research in plant nuclear mechanotransduction and development.
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Affiliation(s)
- Rituparna Goswami
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France; Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 69364 Lyon, France
| | - Atef Asnacios
- Laboratoire Matières et Systèmes Complexes, Université de Paris, CNRS, Université Paris-Diderot, 75013 Paris, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 69364 Lyon, France.
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67084 Strasbourg, France.
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71
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Penagos-Puig A, Furlan-Magaril M. Heterochromatin as an Important Driver of Genome Organization. Front Cell Dev Biol 2020; 8:579137. [PMID: 33072761 PMCID: PMC7530337 DOI: 10.3389/fcell.2020.579137] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Heterochromatin is a constituent of eukaryotic genomes with functions spanning from gene expression silencing to constraining DNA replication and repair. Inside the nucleus, heterochromatin segregates spatially from euchromatin and is localized preferentially toward the nuclear periphery and surrounding the nucleolus. Despite being an abundant nuclear compartment, little is known about how heterochromatin regulates and participates in the mechanisms driving genome organization. Here, we review pioneer and recent evidence that explores the functional role of heterochromatin in the formation of distinct chromatin compartments and how failure of the molecular mechanisms forming heterochromatin leads to disarray of genome conformation and disease.
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Affiliation(s)
- Andrés Penagos-Puig
- Department of Molecular Genetics, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Department of Molecular Genetics, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
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72
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Varlet AA, Helfer E, Badens C. Molecular and Mechanobiological Pathways Related to the Physiopathology of FPLD2. Cells 2020; 9:cells9091947. [PMID: 32842478 PMCID: PMC7565540 DOI: 10.3390/cells9091947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
Laminopathies are rare and heterogeneous diseases affecting one to almost all tissues, as in Progeria, and sharing certain features such as metabolic disorders and a predisposition to atherosclerotic cardiovascular diseases. These two features are the main characteristics of the adipose tissue-specific laminopathy called familial partial lipodystrophy type 2 (FPLD2). The only gene that is involved in FPLD2 physiopathology is the LMNA gene, with at least 20 mutations that are considered pathogenic. LMNA encodes the type V intermediate filament lamin A/C, which is incorporated into the lamina meshwork lining the inner membrane of the nuclear envelope. Lamin A/C is involved in the regulation of cellular mechanical properties through the control of nuclear rigidity and deformability, gene modulation and chromatin organization. While recent studies have described new potential signaling pathways dependent on lamin A/C and associated with FPLD2 physiopathology, the whole picture of how the syndrome develops remains unknown. In this review, we summarize the signaling pathways involving lamin A/C that are associated with the progression of FPLD2. We also explore the links between alterations of the cellular mechanical properties and FPLD2 physiopathology. Finally, we introduce potential tools based on the exploration of cellular mechanical properties that could be redirected for FPLD2 diagnosis.
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Affiliation(s)
- Alice-Anaïs Varlet
- Marseille Medical Genetics (MMG), INSERM, Aix Marseille University, 13005 Marseille, France;
| | - Emmanuèle Helfer
- Centre Interdisciplinaire de Nanoscience de Marseille (CINAM), CNRS, Aix Marseille University, 13009 Marseille, France
- Correspondence: (E.H.); (C.B.); Tel.: +33-6-60-30-28-91 (E.H.); +33-4-91-78-68-94 (C.B.)
| | - Catherine Badens
- Marseille Medical Genetics (MMG), INSERM, Aix Marseille University, 13005 Marseille, France;
- Correspondence: (E.H.); (C.B.); Tel.: +33-6-60-30-28-91 (E.H.); +33-4-91-78-68-94 (C.B.)
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73
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Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS. Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Mol Cell 2020; 79:677-688.e6. [PMID: 32574554 DOI: 10.1016/j.molcel.2020.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/06/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Abstract
Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin states, while super-resolution microscopy reveals a continuum of chromatin compaction states. Characterizing histone H2B movements by single-molecule tracking (SMT), we resolved chromatin domains ranging from low to high mobility and displaying different subnuclear localizations patterns. Heterochromatin constituents correlated with the lowest mobility chromatin, whereas transcription factors varied widely with regard to their respective mobility with low- or high-mobility chromatin. Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains and enriched in higher mobility domains. Nonspecific DNA and nucleosome binding accounted for most of the low mobility of strong nucleosome interactor FOXA1. Our analysis shows how the parameters of the mobility of chromatin-bound factors, but not their diffusion behaviors or SMT-residence times within chromatin, distinguish functional characteristics of different chromatin-interacting proteins.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Pablo Aurelio Gomez-Garcia
- Center for Genomic Regulation, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; ICFO-Institute of Photonics Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ryan L McCarthy
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Zhe Liu
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Melike Lakadamyali
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA; University of Pennsylvania, Department of Physiology, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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74
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Li M, Gan J, Sun Y, Xu Z, Yang J, Sun Y, Li C. Architectural proteins for the formation and maintenance of the 3D genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:795-810. [PMID: 32249389 DOI: 10.1007/s11427-019-1613-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/26/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic genomes are densely packaged into hierarchical three-dimensional (3D) structures that contain information about gene regulation and many other biological processes. With the development of imaging and sequencing-based technologies, 3D genome studies have revealed that the high-order chromatin structure is composed of hierarchical levels, including chromosome territories, A/B compartments, topologically associated domains, and chromatin loops. However, how this chromatin architecture is formed and maintained is not completely clear. In this review, we introduce experimental methods to investigate the 3D genome, review major architectural proteins that regulate 3D chromatin organization in mammalian cells, such as CTCF (CCCTC-binding factor), cohesin, lamins, and transcription factors, and discuss relevant mechanisms such as phase separation.
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Affiliation(s)
- Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingbo Gan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuao Sun
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Zihan Xu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
| | - Junsheng Yang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies; School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences; Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Cheng Li
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China.
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75
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Lamin A/C Mechanotransduction in Laminopathies. Cells 2020; 9:cells9051306. [PMID: 32456328 PMCID: PMC7291067 DOI: 10.3390/cells9051306] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Mechanotransduction translates forces into biological responses and regulates cell functionalities. It is implicated in several diseases, including laminopathies which are pathologies associated with mutations in lamins and lamin-associated proteins. These pathologies affect muscle, adipose, bone, nerve, and skin cells and range from muscular dystrophies to accelerated aging. Although the exact mechanisms governing laminopathies and gene expression are still not clear, a strong correlation has been found between cell functionality and nuclear behavior. New theories base on the direct effect of external force on the genome, which is indeed sensitive to the force transduced by the nuclear lamina. Nuclear lamina performs two essential functions in mechanotransduction pathway modulating the nuclear stiffness and governing the chromatin remodeling. Indeed, A-type lamin mutation and deregulation has been found to affect the nuclear response, altering several downstream cellular processes such as mitosis, chromatin organization, DNA replication-transcription, and nuclear structural integrity. In this review, we summarize the recent findings on the molecular composition and architecture of the nuclear lamina, its role in healthy cells and disease regulation. We focus on A-type lamins since this protein family is the most involved in mechanotransduction and laminopathies.
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76
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Forsberg F, Brunet A, Ali TML, Collas P. Interplay of lamin A and lamin B LADs on the radial positioning of chromatin. Nucleus 2020; 10:7-20. [PMID: 30663495 PMCID: PMC6363278 DOI: 10.1080/19491034.2019.1570810] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunosuppressive drugs such as cyclosporin A (CsA) can elicit hepatotoxicity by affecting gene expression. Here, we address the link between CsA and large-scale chromatin organization in HepG2 hepatocarcinoma cells. We show the existence of lamina-associated domains (LADs) interacting with lamin A, lamin B, or both. These ‘A-B’, ‘A-only’ and ‘B-only’ LADs display distinct fates after CsA treatment: A-B LADs remain constitutive or lose A, A-only LADs mainly lose A or switch to B, and B-only LADs remain B-only or acquire A. LAD rearrangement is overall uncoupled from changes in gene expression. Three-dimensional (3D) genome modeling predicts changes in radial positioning of LADs as LADs switch identities, which are corroborated by fluorescence in situ hybridization. Our results reveal interplay between A- and B-type lamins on radial locus positioning, suggesting complementary contributions to large-scale genome architecture. The data also unveil a hitherto unsuspected impact of cytotoxic drugs on genome conformation.Abbreviations: ChIP-seq: chromatin immunoprecipitation sequencing; CsA: cyclosporin A; FISH; fluorescence in situ hybridization; ICMT: isoprenylcysteine methyltransferase; LAD: lamina-associated domain; TAD: topologically-associated domain
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Affiliation(s)
- Frida Forsberg
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Annaël Brunet
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Tharvesh M Liyakat Ali
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway
| | - Philippe Collas
- a Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , Oslo , Norway.,b Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine , Oslo University Hospital , Oslo , Norway
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77
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Martins F, Sousa J, Pereira CD, Cruz e Silva OAB, Rebelo S. Nuclear envelope dysfunction and its contribution to the aging process. Aging Cell 2020; 19:e13143. [PMID: 32291910 PMCID: PMC7253059 DOI: 10.1111/acel.13143] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 12/25/2022] Open
Abstract
The nuclear envelope (NE) is the central organizing unit of the eukaryotic cell serving as a genome protective barrier and mechanotransduction interface between the cytoplasm and the nucleus. The NE is mainly composed of a nuclear lamina and a double membrane connected at specific points where the nuclear pore complexes (NPCs) form. Physiological aging might be generically defined as a functional decline across lifespan observed from the cellular to organismal level. Therefore, during aging and premature aging, several cellular alterations occur, including nuclear‐specific changes, particularly, altered nuclear transport, increased genomic instability induced by DNA damage, and telomere attrition. Here, we highlight and discuss proteins associated with nuclear transport dysfunction induced by aging, particularly nucleoporins, nuclear transport factors, and lamins. Moreover, changes in the structure of chromatin and consequent heterochromatin rearrangement upon aging are discussed. These alterations correlate with NE dysfunction, particularly lamins’ alterations. Finally, telomere attrition is addressed and correlated with altered levels of nuclear lamins and nuclear lamina‐associated proteins. Overall, the identification of molecular mechanisms underlying NE dysfunction, including upstream and downstream events, which have yet to be unraveled, will be determinant not only to our understanding of several pathologies, but as here discussed, in the aging process.
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Affiliation(s)
- Filipa Martins
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Jéssica Sousa
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Cátia D. Pereira
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
| | - Odete A. B. Cruz e Silva
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
- The Discoveries CTR Aveiro Portugal
| | - Sandra Rebelo
- Neuroscience and Signaling Laboratory Institute of Biomedicine (iBiMED) Department of Medical Sciences University of Aveiro Aveiro Portugal
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78
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Abstract
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-associated domains (LADs) aid functional organization of the genome. We review the organization of LADs and provide evidence of LAD heterogeneity from cell ensemble and single-cell data. LADs are typically repressive environments in the genome; nonetheless, we discuss findings of lamin interactions with regulatory elements of active genes, and the role lamins may play in genome regulation. We address the relationship between LADs and other genome organizers, and the involvement of LADs in laminopathies. The current data lay the basis for future studies on the significance of lamin-chromatin interactions in health and disease.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway.
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway.
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79
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Wintner O, Hirsch‐Attas N, Schlossberg M, Brofman F, Friedman R, Kupervaser M, Kitsberg D, Buxboim A. A Unified Linear Viscoelastic Model of the Cell Nucleus Defines the Mechanical Contributions of Lamins and Chromatin. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901222. [PMID: 32328409 PMCID: PMC7175345 DOI: 10.1002/advs.201901222] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/22/2020] [Indexed: 05/26/2023]
Abstract
The cell nucleus is constantly subjected to externally applied forces. During metazoan evolution, the nucleus has been optimized to allow physical deformability while protecting the genome under load. Aberrant nucleus mechanics can alter cell migration across narrow spaces in cancer metastasis and immune response and disrupt nucleus mechanosensitivity. Uncovering the mechanical roles of lamins and chromatin is imperative for understanding the implications of physiological forces on cells and nuclei. Lamin-knockout and -rescue fibroblasts and probed nucleus response to physiologically relevant stresses are generated. A minimal viscoelastic model is presented that captures dynamic resistance across different cell types, lamin composition, phosphorylation states, and chromatin condensation. The model is conserved at low and high loading and is validated by micropipette aspiration and nanoindentation rheology. A time scale emerges that separates between dominantly elastic and dominantly viscous regimes. While lamin-A and lamin-B1 contribute to nucleus stiffness, viscosity is specified mostly by lamin-A. Elastic and viscous association of lamin-B1 and lamin-A is supported by transcriptional and proteomic profiling analyses. Chromatin decondensation quantified by electron microscopy softens the nucleus unless lamin-A is expressed. A mechanical framework is provided for assessing nucleus response to applied forces in health and disease.
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Affiliation(s)
- Oren Wintner
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
- Alexander Grass Center for BioengineeringThe Rachel and Selim Benin School of Computer Science and EngineeringJerusalem9190416Israel
| | - Nivi Hirsch‐Attas
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Miriam Schlossberg
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Fani Brofman
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Roy Friedman
- Alexander Grass Center for BioengineeringThe Rachel and Selim Benin School of Computer Science and EngineeringJerusalem9190416Israel
| | - Meital Kupervaser
- The de Botton Institute for Protein ProfilingThe Nancy and Stephen Grand Israel National Center for Personalized MedicineWeizmann Institute of ScienceRehovot7610001Israel
| | - Danny Kitsberg
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
| | - Amnon Buxboim
- Department of Cell and Developmental BiologyThe Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalem9190401Israel
- Alexander Grass Center for BioengineeringThe Rachel and Selim Benin School of Computer Science and EngineeringJerusalem9190416Israel
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80
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Lamin A/C Assembly Defects in LMNA-Congenital Muscular Dystrophy Is Responsible for the Increased Severity of the Disease Compared with Emery-Dreifuss Muscular Dystrophy. Cells 2020; 9:cells9040844. [PMID: 32244403 PMCID: PMC7226786 DOI: 10.3390/cells9040844] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 01/13/2023] Open
Abstract
LMNA encodes for Lamin A/C, type V intermediate filaments that polymerize under the inner nuclear membrane to form the nuclear lamina. A small fraction of Lamin A/C, less polymerized, is also found in the nucleoplasm. Lamin A/C functions include roles in nuclear resistance to mechanical stress and gene regulation. LMNA mutations are responsible for a wide variety of pathologies, including Emery–Dreifuss (EDMD) and LMNA-related congenital muscular dystrophies (L-CMD) without clear genotype–phenotype correlations. Both diseases presented with striated muscle disorders although L-CMD symptoms appear much earlier and are more severe. Seeking for pathomechanical differences to explain the severity of L-CMD mutations, we performed an in silico analysis of the UMD-LMNA database and found that L-CMD mutations mainly affect residues involved in Lamin dimer and tetramer stability. In line with this, we found increased nucleoplasmic Lamin A/C in L-CMD patient fibroblasts and mouse myoblasts compared to the control and EDMD. L-CMD myoblasts show differentiation defects linked to their inability to upregulate muscle specific nuclear envelope (NE) proteins expression. NE proteins were mislocalized, leading to misshapen nuclei. We conclude that these defects are due to both the absence of Lamin A/C from the nuclear lamina and its maintenance in the nucleoplasm of myotubes.
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81
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Saxena S, Kumar S. Pharmacotherapy to gene editing: potential therapeutic approaches for Hutchinson-Gilford progeria syndrome. GeroScience 2020; 42:467-494. [PMID: 32048129 DOI: 10.1007/s11357-020-00167-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS), commonly called progeria, is an extremely rare disorder that affects only one child per four million births. It is characterized by accelerated aging in affected individuals leading to premature death at an average age of 14.5 years due to cardiovascular complications. The main cause of HGPS is a sporadic autosomal dominant point mutation in LMNA gene resulting in differently spliced lamin A protein known as progerin. Accumulation of progerin under nuclear lamina and activation of its downstream effectors cause perturbation in cellular morphology and physiology which leads to a systemic disorder that mainly impairs the cardiovascular system, bones, skin, and overall growth. Till now, no cure has been found for this catastrophic disorder; however, several therapeutic strategies are under development. The current review focuses on the overall progress in the field of therapeutic approaches for the management/cure of HGPS. We have also discussed the new disease models that have been developed for the study of this rare disorder. Moreover, we have highlighted the therapeutic application of extracellular vesicles derived from stem cells against aging and aging-related disorders and, therefore, suggest the same for the treatment of HGPS.
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Affiliation(s)
- Saurabh Saxena
- Department of Medical Laboratory Sciences, Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India.
| | - Sanjeev Kumar
- Faculty of Technology and Sciences, Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
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82
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Cheedipudi SM, Matkovich SJ, Coarfa C, Hu X, Robertson MJ, Sweet M, Taylor M, Mestroni L, Cleveland J, Willerson JT, Gurha P, Marian AJ. Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes Is Associated With Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy. Circ Res 2020; 124:1198-1213. [PMID: 30739589 DOI: 10.1161/circresaha.118.314177] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RATIONALE LMNA (Lamin A/C), a nuclear membrane protein, interacts with genome through lamin-associated domains (LADs) and regulates gene expression. Mutations in the LMNA gene cause a diverse array of diseases, including dilated cardiomyopathy (DCM). DCM is the leading cause of death in laminopathies. OBJECTIVE To identify LADs and characterize their associations with CpG methylation and gene expression in human cardiac myocytes in DCM. METHODS AND RESULTS LMNA chromatin immunoprecipitation-sequencing, reduced representative bisulfite sequencing, and RNA-sequencing were performed in 5 control and 5 LMNA-associated DCM hearts. LADs were identified using enriched domain detector program. Genome-wide 331±77 LADs with an average size of 2.1±1.5 Mbp were identified in control human cardiac myocytes. LADs encompassed ≈20% of the genome and were predominantly located in the heterochromatin and less so in the promoter and actively transcribed regions. LADs were redistributed in DCM as evidenced by a gain of 520 and loss of 149 genomic regions. Approximately, 4500 coding genes and 800 long noncoding RNAs, whose levels correlated with the transcript levels of coding genes in cis, were differentially expressed in DCM. TP53 (tumor protein 53) was the most prominent among the dysregulated pathways. CpG sites were predominantly hypomethylated genome-wide in controls and DCM hearts, but overall CpG methylation was increased in DCM. LADs were associated with increased CpG methylation and suppressed gene expression. Integrated analysis identified genes whose expressions were regulated by LADs or CpG methylation, or by both, the latter pertained to genes involved in cell death, cell cycle, and metabolic regulation. CONCLUSIONS LADs encompass ≈20% of the genome in human cardiac myocytes comprised several hundred coding and noncoding genes. LADs are redistributed in LMNA-associated DCM in association with markedly altered CpG methylation and gene expression. Thus, LADs through genomic alterations contribute to the pathogenesis of DCM in laminopathies.
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Affiliation(s)
- Sirisha M Cheedipudi
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
| | - Scot J Matkovich
- Center for Cardiovascular Research, Washington University, School of Medicine, St Louis, MO (S.J.M.)
| | | | - Xin Hu
- MD Anderson Cancer Center, Houston, TX (X.H.)
| | | | - Mary Sweet
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Matthew Taylor
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Luisa Mestroni
- Division of Cardiology (M.S., M.T., L.M.), University of Colorado, Denver
| | - Joseph Cleveland
- Division of Cardiothoracic Surgery (J.C.), University of Colorado, Denver
| | | | - Priyatansh Gurha
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
| | - Ali J Marian
- From the Center for Cardiovascular Genetics, Department of Medicine, Institute of Molecular Medicine, Texas Heart Institute, University of Texas Health Sciences Center at Houston (S.M.C., P.G., A.J.M.)
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83
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Foo MXR, Ong PF, Dreesen O. Premature aging syndromes: From patients to mechanism. J Dermatol Sci 2019; 96:58-65. [PMID: 31727429 DOI: 10.1016/j.jdermsci.2019.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 12/24/2022]
Abstract
Aging is an inevitable consequence of human life resulting in a gradual deterioration of cell, tissue and organismal function and an increased risk to develop chronic ailments. Premature aging syndromes, also known as progeroid syndromes, recapitulate many clinical features of normal aging and offer a unique opportunity to elucidate fundamental mechanisms that contribute to human aging. Progeroid syndromes can be broadly classified into those caused by perturbations of the nuclear lamina, a meshwork of proteins located underneath the inner nuclear membrane (laminopathies); and a second group that is caused by mutations that directly impair DNA replication and repair. We will focus mainly on laminopathies caused by incorrect processing of lamin A, an intermediate filament protein that resides at the nuclear periphery. Hutchinson-Gilford Progeria (HGPS) is an accelerated aging syndrome caused by a mutation in lamin A and one of the best studied laminopathies. HGPS patients exhibit clinical characteristics of premature aging, including alopecia, aberrant pigmentation, loss of subcutaneous fat and die in their teens as a result of atherosclerosis and cardiovascular complications. Here we summarize how cell- and mouse-based disease models provided mechanistic insights into human aging and discuss experimental strategies under consideration for the treatment of these rare genetic disorders.
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Affiliation(s)
- Mattheus Xing Rong Foo
- Cell Aging Laboratory, Skin Research Institute of Singapore, 8A Biomedical Grove, #06-06 Immunos, 138648 Singapore; Nanyang Technological University, Singapore
| | - Peh Fern Ong
- Cell Aging Laboratory, Skin Research Institute of Singapore, 8A Biomedical Grove, #06-06 Immunos, 138648 Singapore
| | - Oliver Dreesen
- Cell Aging Laboratory, Skin Research Institute of Singapore, 8A Biomedical Grove, #06-06 Immunos, 138648 Singapore; Nanyang Technological University, Singapore.
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84
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Briand N, Collas P. Laminopathy-causing lamin A mutations reconfigure lamina-associated domains and local spatial chromatin conformation. Nucleus 2019. [PMID: 29517398 PMCID: PMC5973257 DOI: 10.1080/19491034.2018.1449498] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The nuclear lamina contributes to the regulation of gene expression and to chromatin organization. Mutations in A-type nuclear lamins cause laminopathies, some of which are associated with a loss of heterochromatin at the nuclear periphery. Until recently however, little if any information has been provided on where and how lamin A interacts with the genome and on how disease-causing lamin A mutations may rearrange genome conformation. Here, we review aspects of nuclear lamin association with the genome. We highlight recent evidence of reorganization of lamin A-chromatin interactions in cellular models of laminopathies, and implications on the 3-dimensional rearrangement of chromatin in these models, including patient cells. We discuss how a hot-spot lipodystrophic lamin A mutation alters chromatin conformation and epigenetic patterns at an anti-adipogenic locus, and conclude with remarks on links between lamin A, Polycomb and the pathophysiology of laminopathies. The recent findings presented here collectively argue towards a deregulation of large-scale and local spatial genome organization by a subset of lamin A mutations causing laminopathies.
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Affiliation(s)
- Nolwenn Briand
- a Department of Molecular Medicine , Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo , Norway
| | - Philippe Collas
- a Department of Molecular Medicine , Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo , Norway.,b Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine , Oslo University Hospital , Oslo , Norway
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85
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Graziano S, Kreienkamp R, Coll-Bonfill N, Gonzalo S. Causes and consequences of genomic instability in laminopathies: Replication stress and interferon response. Nucleus 2019; 9:258-275. [PMID: 29637811 PMCID: PMC5973265 DOI: 10.1080/19491034.2018.1454168] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mammalian nuclei are equipped with a framework of intermediate filaments that function as a karyoskeleton. This nuclear scaffold, formed primarily by lamins (A-type and B-type), maintains the spatial and functional organization of the genome and of sub-nuclear compartments. Over the past decade, a body of evidence has highlighted the significance of these structural nuclear proteins in the maintenance of nuclear architecture and mechanical stability, as well as genome function and integrity. The importance of these structures is now unquestioned given the wide range of degenerative diseases that stem from LMNA gene mutations, including muscular dystrophy disorders, peripheral neuropathies, lipodystrophies, and premature aging syndromes. Here, we review our knowledge about how alterations in nuclear lamins, either by mutation or reduced expression, impact cellular mechanisms that maintain genome integrity. Despite the fact that DNA replication is the major source of DNA damage and genomic instability in dividing cells, how alterations in lamins function impact replication remains minimally explored. We summarize recent studies showing that lamins play a role in DNA replication, and that the DNA damage that accumulates upon lamins dysfunction is elicited in part by deprotection of replication forks. We also discuss the emerging model that DNA damage and replication stress are “sensed” at the cytoplasm by proteins that normally survey this space in search of foreign nucleic acids. In turn, these cytosolic sensors activate innate immune responses, which are materializing as important players in aging and cancer, as well as in the response to cancer immunotherapy.
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Affiliation(s)
- Simona Graziano
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Ray Kreienkamp
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Nuria Coll-Bonfill
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
| | - Susana Gonzalo
- a Edward A. Doisy Department of Biochemistry and Molecular Biology , Saint Louis University School of Medicine , St. Louis , MO , USA
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86
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Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H, Zhang JZ, Chen X, Gil IP, Ameen M, Sallam K, Rhee JW, Churko JM, Chaudhary R, Chour T, Wang PJ, Snyder MP, Chang HY, Karakikes I, Wu JC. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy. Nature 2019; 572:335-340. [PMID: 31316208 PMCID: PMC6779479 DOI: 10.1038/s41586-019-1406-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Lamin A/C (LMNA) is one of the most frequently mutated genes associated with dilated cardiomyopathy (DCM). DCM related to mutations in LMNA is a common inherited cardiomyopathy that is associated with systolic dysfunction and cardiac arrhythmias. Here we modelled the LMNA-related DCM in vitro using patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Electrophysiological studies showed that the mutant iPSC-CMs displayed aberrant calcium homeostasis that led to arrhythmias at the single-cell level. Mechanistically, we show that the platelet-derived growth factor (PDGF) signalling pathway is activated in mutant iPSC-CMs compared to isogenic control iPSC-CMs. Conversely, pharmacological and molecular inhibition of the PDGF signalling pathway ameliorated the arrhythmic phenotypes of mutant iPSC-CMs in vitro. Taken together, our findings suggest that the activation of the PDGF pathway contributes to the pathogenesis of LMNA-related DCM and point to PDGF receptor-β (PDGFRB) as a potential therapeutic target.
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MESH Headings
- Arrhythmias, Cardiac/metabolism
- Arrhythmias, Cardiac/pathology
- Calcium/metabolism
- Cardiomyopathy, Dilated/genetics
- Cells, Cultured
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly/genetics
- Haploinsufficiency/genetics
- Homeostasis
- Humans
- In Vitro Techniques
- Induced Pluripotent Stem Cells/pathology
- Lamin Type A/genetics
- Models, Biological
- Mutation
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Nonsense Mediated mRNA Decay
- Platelet-Derived Growth Factor/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Receptor, Platelet-Derived Growth Factor beta/metabolism
- Signal Transduction
- Single-Cell Analysis
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Affiliation(s)
- Jaecheol Lee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea.
| | - Vittavat Termglinchan
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastian Diecke
- Berlin Institute of Health, Berlin, Germany
- Max Delbrueck Center, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Ilanit Itzhaki
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Chi Keung Lam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Priyanka Garg
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Edward Lau
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew Greenhaw
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Timon Seeger
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Haodi Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Joe Z Zhang
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Isaac Perea Gil
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohamed Ameen
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Karim Sallam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - June-Wha Rhee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Jared M Churko
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Rinkal Chaudhary
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Chour
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Wang
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA.
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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87
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Buchwalter A, Kaneshiro JM, Hetzer MW. Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 2019; 20:39-50. [PMID: 30356165 DOI: 10.1038/s41576-018-0063-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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88
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Osmanagic-Myers S, Foisner R. The structural and gene expression hypotheses in laminopathic diseases-not so different after all. Mol Biol Cell 2019; 30:1786-1790. [PMID: 31306095 PMCID: PMC6727745 DOI: 10.1091/mbc.e18-10-0672] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/09/2019] [Accepted: 05/16/2019] [Indexed: 01/06/2023] Open
Abstract
Laminopathies are a diverse group of rare diseases with various pathologies in different tissues, which are linked to mutations in the LMNA gene. Historically, the structural disease model proposed mechanical defects of the lamina and nuclear fragility, the gene expression model impairment of spatial chromatin organization and signaling pathways as underlying mechanisms leading to the pathologies. Exciting findings in the past few years showing that mechanical forces are directly transmitted into the nucleus, where they affect chromatin organization and mechanoresponsive signaling molecules, have led to a revised concept of an integrative unified disease model, in which lamin-mediated pathways in mechanotransduction and chromatin regulation are highly interconnected and mutually dependent. In this Perspective we highlight breakthrough findings providing new insight into lamin-linked mechanisms of mechanotransduction and chromatin regulation and discuss how a combined and interrelated impairment of these functions by LMNA mutations may impair the complex mechanosignaling network and cause tissue-specific pathologies in laminopathies.
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Affiliation(s)
- Selma Osmanagic-Myers
- Max F. Perutz Laboratories, Center of Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories, Center of Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
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89
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Romero-Bueno R, de la Cruz Ruiz P, Artal-Sanz M, Askjaer P, Dobrzynska A. Nuclear Organization in Stress and Aging. Cells 2019; 8:cells8070664. [PMID: 31266244 PMCID: PMC6678840 DOI: 10.3390/cells8070664] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.
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Affiliation(s)
- Raquel Romero-Bueno
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Patricia de la Cruz Ruiz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain.
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90
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Collas P, Liyakat Ali TM, Brunet A, Germier T. Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic Domains. Front Genet 2019; 10:602. [PMID: 31275364 PMCID: PMC6593077 DOI: 10.3389/fgene.2019.00602] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
Abstract
The mammalian genome is intricately folded in a three-dimensional topology believed to be important for the orchestration of gene expression regulating development, differentiation and tissue homeostasis. Important features of spatial genome conformation in the nucleus are promoter-enhancer contacts regulating gene expression within topologically-associated domains (TADs), short- and long-range interactions between TADs and associations of chromatin with nucleoli and nuclear speckles. In addition, anchoring of chromosomes to the nuclear lamina via lamina-associated domains (LADs) at the nuclear periphery is a key regulator of the radial distribution of chromatin. To what extent TADs and LADs act in concert as genomic organizers to shape the three-dimensional topology of chromatin has long remained unknown. A new study addressing this key question provides evidence of (i) preferred long-range associations between TADs forming TAD “cliques” which organize large heterochromatin domains, and (ii) stabilization of TAD cliques by LADs at the nuclear periphery after induction of terminal differentiation. Here, we review these findings, address the issue of whether TAD cliques exist in single cells and discuss the extent of cell-to-cell heterogeneity in higher-order chromatin conformation. The recent observations provide a first appreciation of changes in 4-dimensional higher-order genome topologies during differentiation.
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Affiliation(s)
- Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Annaël Brunet
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Thomas Germier
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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91
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Jia Y, Vong JSL, Asafova A, Garvalov BK, Caputo L, Cordero J, Singh A, Boettger T, Günther S, Fink L, Acker T, Barreto G, Seeger W, Braun T, Savai R, Dobreva G. Lamin B1 loss promotes lung cancer development and metastasis by epigenetic derepression of RET. J Exp Med 2019; 216:1377-1395. [PMID: 31015297 PMCID: PMC6547854 DOI: 10.1084/jem.20181394] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 02/13/2019] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Although abnormal nuclear structure is an important criterion for cancer diagnostics, remarkably little is known about its relationship to tumor development. Here we report that loss of lamin B1, a determinant of nuclear architecture, plays a key role in lung cancer. We found that lamin B1 levels were reduced in lung cancer patients. Lamin B1 silencing in lung epithelial cells promoted epithelial-mesenchymal transition, cell migration, tumor growth, and metastasis. Mechanistically, we show that lamin B1 recruits the polycomb repressive complex 2 (PRC2) to alter the H3K27me3 landscape and repress genes involved in cell migration and signaling. In particular, epigenetic derepression of the RET proto-oncogene by loss of PRC2 recruitment, and activation of the RET/p38 signaling axis, play a crucial role in mediating the malignant phenotype upon lamin B1 disruption. Importantly, loss of a single lamin B1 allele induced spontaneous lung tumor formation and RET activation. Thus, lamin B1 acts as a tumor suppressor in lung cancer, linking aberrant nuclear structure and epigenetic patterning with malignancy.
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Affiliation(s)
- Yanhan Jia
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Joaquim Si-Long Vong
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Alina Asafova
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Boyan K Garvalov
- Microvascular Biology and Pathobiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany
| | - Luca Caputo
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Julio Cordero
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anshu Singh
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Boettger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Ludger Fink
- Institute of Pathology and Cytology, Überregionale Gemeinschaftspraxis für Pathologie (ÜGP), Wetzlar, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany
| | - Guillermo Barreto
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Gergana Dobreva
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Medical Faculty, J.W. Goethe University Frankfurt, Frankfurt, Germany
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92
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Ranade D, Pradhan R, Jayakrishnan M, Hegde S, Sengupta K. Lamin A/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus. BMC Mol Cell Biol 2019; 20:11. [PMID: 31117946 PMCID: PMC6532135 DOI: 10.1186/s12860-019-0192-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear lamins are type V intermediate filament proteins that maintain nuclear structure and function. Furthermore, Emerin - an interactor of Lamin A/C, facilitates crosstalk between the cytoskeleton and the nucleus as it also interacts with actin and Nuclear Myosin 1 (NM1). Results Here we show that the depletion of Lamin A/C or Emerin, alters the localization of the nuclear motor protein - Nuclear Myosin 1 (NM1) that manifests as an increase in NM1 foci in the nucleus and are rescued to basal levels upon the combined knockdown of Lamin A/C and Emerin. Furthermore, Lamin A/C-Emerin co-depletion destabilizes cytoskeletal organization as it increases actin stress fibers. This further impinges on nuclear organization, as it enhances chromatin mobility more toward the nuclear interior in Lamin A/C-Emerin co-depleted cells. This enhanced chromatin mobility was restored to basal levels either upon inhibition of Nuclear Myosin 1 (NM1) activity or actin depolymerization. In addition, the combined loss of Lamin A/C and Emerin alters the otherwise highly conserved spatial positions of chromosome territories. Furthermore, knockdown of Lamin A/C or Lamin A/C-Emerin combined, deregulates expression levels of a candidate subset of genes. Amongst these genes, both KLK10 (Chr.19, Lamina Associated Domain (LAD+)) and MADH2 (Chr.18, LAD-) were significantly repressed, while BCL2L12 (Chr.19, LAD-) is de-repressed. These genes differentially reposition with respect to the nuclear envelope. Conclusions Taken together, these studies underscore a remarkable interplay between Lamin A/C and Emerin in modulating cytoskeletal organization of actin and NM1 that impinges on chromatin dynamics and function in the interphase nucleus. Electronic supplementary material The online version of this article (10.1186/s12860-019-0192-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devika Ranade
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Roopali Pradhan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Muhunden Jayakrishnan
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Sushmitha Hegde
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India
| | - Kundan Sengupta
- Indian Institute of Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Biology, Room#B-216, 1st Floor, Main Building, Pashan, Pune, Maharashtra, 411008, India.
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93
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Lamina Associated Domains and Gene Regulation in Development and Cancer. Cells 2019; 8:cells8030271. [PMID: 30901978 PMCID: PMC6468596 DOI: 10.3390/cells8030271] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 12/02/2022] Open
Abstract
The nuclear lamina (NL) is a thin meshwork of filaments that lines the inner nuclear membrane, thereby providing a platform for chromatin binding and supporting genome organization. Genomic regions contacting the NL are lamina associated domains (LADs), which contain thousands of genes that are lowly transcribed, and enriched for repressive histone modifications. LADs are dynamic structures that shift spatial positioning in accordance with cell-type specific gene expression changes during differentiation and development. Furthermore, recent studies have linked the disruption of LADs and alterations in the epigenome with the onset of diseases such as cancer. Here we focus on the role of LADs and the NL in gene regulation during development and cancer.
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94
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Briand N, Guénantin AC, Jeziorowska D, Shah A, Mantecon M, Capel E, Garcia M, Oldenburg A, Paulsen J, Hulot JS, Vigouroux C, Collas P. The lipodystrophic hotspot lamin A p.R482W mutation deregulates the mesodermal inducer T/Brachyury and early vascular differentiation gene networks. Hum Mol Genet 2019; 27:1447-1459. [PMID: 29438482 DOI: 10.1093/hmg/ddy055] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022] Open
Abstract
The p.R482W hotspot mutation in A-type nuclear lamins causes familial partial lipodystrophy of Dunnigan-type (FPLD2), a lipodystrophic syndrome complicated by early onset atherosclerosis. Molecular mechanisms underlying endothelial cell dysfunction conferred by the lamin A mutation remain elusive. However, lamin A regulates epigenetic developmental pathways and mutations could perturb these functions. Here, we demonstrate that lamin A R482W elicits endothelial differentiation defects in a developmental model of FPLD2. Genome modeling in fibroblasts from patients with FPLD2 caused by the lamin A R482W mutation reveals repositioning of the mesodermal regulator T/Brachyury locus towards the nuclear center relative to normal fibroblasts, suggesting enhanced activation propensity of the locus in a developmental model of FPLD2. Addressing this issue, we report phenotypic and transcriptional alterations in mesodermal and endothelial differentiation of induced pluripotent stem cells we generated from a patient with R482W-associated FPLD2. Correction of the LMNA mutation ameliorates R482W-associated phenotypes and gene expression. Transcriptomics links endothelial differentiation defects to decreased Polycomb-mediated repression of the T/Brachyury locus and over-activation of T target genes. Binding of the Polycomb repressor complex 2 to T/Brachyury is impaired by the mutated lamin A network, which is unable to properly associate with the locus. This leads to a deregulation of vascular gene expression over time. By connecting a lipodystrophic hotspot lamin A mutation to a disruption of early mesodermal gene expression and defective endothelial differentiation, we propose that the mutation rewires the fate of several lineages, resulting in multi-tissue pathogenic phenotypes.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.,Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Anne-Claire Guénantin
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Dorota Jeziorowska
- Sorbonne Université, UPMC Université Paris 6, UMR-S1166 ICAN, 75013 Paris, France
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Matthieu Mantecon
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Emilie Capel
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Marie Garcia
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France
| | - Anja Oldenburg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jean-Sebastien Hulot
- Sorbonne Université, UPMC Université Paris 6, UMR-S1166 ICAN, 75013 Paris, France
| | - Corinne Vigouroux
- Sorbonne Université, Inserm UMR S938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, 75012 Paris, France.,AP-HP Saint-Antoine Hospital, Molecular Biology and Genetics Laboratory, Endocrinology Department, National Reference Center for Insulin Secretion and Insulin Sensitivity Rare Diseases, 75012 Paris, France
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway.,Department of Immunology and Transfusion Medicine, Norwegian Center for Stem Cell Research, Oslo University Hospital, 0424 Oslo, Norway
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95
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Shevelyov YY, Ulianov SV. The Nuclear Lamina as an Organizer of Chromosome Architecture. Cells 2019; 8:E136. [PMID: 30744037 PMCID: PMC6406483 DOI: 10.3390/cells8020136] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/20/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork of lamins and lamin-associated proteins adjoining the inner side of the nuclear envelope. In early embryonic cells, the NL mainly suppresses background transcription, whereas, in differentiated cell types, its disruption affects gene expression more severely. Normally, the NL serves as a backbone for multiple chromatin anchoring sites, thus shaping the spatial organization of chromosomes in the interphase nucleus. However, upon cell senescence, aging, or in some types of terminally differentiated cells and lamin-associated diseases, the loss of NL-chromatin tethering causes drastic alterations in chromosome architecture. Here, we provide an overview of the recent advances in the field of NL-chromatin interactions, focusing on their impact on chromatin positioning, compaction, repression, and spatial organization.
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Affiliation(s)
- Yuri Y. Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia;
| | - Sergey V. Ulianov
- Division of the Regulation of Transcription and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia;
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96
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Lee JH, Kim DH, Lee HH, Kim HW. Role of nuclear mechanosensitivity in determining cellular responses to forces and biomaterials. Biomaterials 2019; 197:60-71. [PMID: 30641265 DOI: 10.1016/j.biomaterials.2019.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/25/2018] [Accepted: 01/05/2019] [Indexed: 01/17/2023]
Abstract
Tissue engineers use biomaterials or apply forces to alter cell behaviors and cure damaged/diseased tissues. The external physical cues perceived by cells are transduced intracellularly along the mechanosensitive machineries, including subcellular adhesion molecules and cytoskeletons. The signals are further channeled to a nucleus through the physical links of nucleoskeleton and cytoskeleton or the biochemical translocation of transcription factors. Thus, the external cues are thought to affect directly or indirectly the nucleus and the genetic transcriptional process, ultimately determining cell fate. Here we communicate the importance of such mechanotransductory processes in cell and tissue engineering where external forces- or biomaterials-related physical cues essentially regulate cellular behaviors, with an emphasis on the mechanosensing and signaling along the road to a nucleus.
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Affiliation(s)
- Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Dong-Hwee Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 20841, South Korea
| | - Hae-Hyoung Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Republic of Korea; Department of Biomaterials Science, College of Dentistry, Dankook University, Cheonan 31116, Republic of Korea; Department of Nanobiomedical Science & BK21 PLUS Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea; UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan 31116, Republic of Korea.
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97
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Crasto S, Di Pasquale E. Induced Pluripotent Stem Cells to Study Mechanisms of Laminopathies: Focus on Epigenetics. Front Cell Dev Biol 2018; 6:172. [PMID: 30619852 PMCID: PMC6306496 DOI: 10.3389/fcell.2018.00172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
Laminopathies are a group of rare degenerative disorders that manifest with a wide spectrum of clinical phenotypes, including both systemic multi-organ disorders, such as the Hutchinson-Gilford Progeria Syndrome (HGPS), and tissue-restricted diseases, such as Emery-Dreifuss muscular dystrophy, dilated cardiomyopathy and lipodystrophies, often overlapping. Despite their clinical heterogeneity, which remains an open question, laminopathies are commonly caused by mutations in the LMNA gene, encoding the nuclear proteins Lamin A and C. These two proteins are main components of the nuclear lamina and are involved in several biological processes. Besides the well-known structural function in the nucleus, their role in regulating chromatin organization and transcription has emerged in the last decade, supporting the hypothesis that the disruption of this layer of regulation may be mechanism underlying the disease. Indeed, recent studies that show various epigenetic defects in cells carrying LMNA mutations, such as loss of heterochromatin, changes in gene expression and chromatin remodeling, strongly support this view. However, those findings are restricted to few cell types in humans, mainly because of the limited accessibility of primary cells and the difficulties to culture them ex-vivo. On the other hand, animal models might fail to recapitulate phenotypic hallmarks of the disease as of humans. To fill this gap, models based on induced pluripotent stem cell (iPSCs) technology have been recently generated that allowed investigations on diverse cells types, such as mesenchymal stem cells (MSCs), vascular and smooth muscle cells and cardiomyocytes, and provided a platform for investigating mechanisms underlying the pathogenesis of laminopathies in a cell-type specific human context. Nevertheless, studies on iPSC-based models of laminopathy have expanded only in the last few years and, with the advancement of reprogramming and differentiation protocols, their number is expecting to further increase over time. This review will give an overview of models developed thus far, with a focus on the novel insights on epigenetic mechanisms underlying the disease in different human cellular contexts. Perspectives and future directions of the field will be also given, highlighting the potential of those models for preclinical studies for identifying molecular targets and their translational impact on patients' cure.
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Affiliation(s)
- Silvia Crasto
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Milan, Milan, Italy.,Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Elisa Di Pasquale
- Institute of Genetic and Biomedical Research, National Research Council of Italy, UOS of Milan, Milan, Italy.,Humanitas Research Hospital, Rozzano, Milan, Italy
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98
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Osmanagic-Myers S, Kiss A, Manakanatas C, Hamza O, Sedlmayer F, Szabo PL, Fischer I, Fichtinger P, Podesser BK, Eriksson M, Foisner R. Endothelial progerin expression causes cardiovascular pathology through an impaired mechanoresponse. J Clin Invest 2018; 129:531-545. [PMID: 30422822 PMCID: PMC6355303 DOI: 10.1172/jci121297] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/06/2018] [Indexed: 01/09/2023] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disorder characterized by accelerated cardiovascular disease with extensive fibrosis. It is caused by a mutation in LMNA leading to expression of truncated prelamin A (progerin) in the nucleus. To investigate the contribution of the endothelium to cardiovascular HGPS pathology, we generated an endothelium-specific HGPS mouse model with selective endothelial progerin expression. Transgenic mice develop interstitial myocardial and perivascular fibrosis and left ventricular hypertrophy associated with diastolic dysfunction and premature death. Endothelial cells show impaired shear stress response and reduced levels of endothelial nitric oxide synthase (eNOS) and NO. On the molecular level, progerin impairs nucleocytoskeletal coupling in endothelial cells through changes in mechanoresponsive components at the nuclear envelope, increased F-actin/G-actin ratios, and deregulation of mechanoresponsive myocardin-related transcription factor-A (MRTFA). MRTFA binds to the Nos3 promoter and reduces eNOS expression, thereby mediating a profibrotic paracrine response in fibroblasts. MRTFA inhibition rescues eNOS levels and ameliorates the profibrotic effect of endothelial cells in vitro. Although this murine model lacks the key anatomical feature of vascular smooth muscle cell loss seen in HGPS patients, our data show that progerin-induced impairment of mechanosignaling in endothelial cells contributes to excessive fibrosis and cardiovascular disease in HGPS patients.
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Affiliation(s)
- Selma Osmanagic-Myers
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Attila Kiss
- Ludwig Boltzmann Cluster for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Christina Manakanatas
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Ouafa Hamza
- Ludwig Boltzmann Cluster for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Franziska Sedlmayer
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Petra L Szabo
- Ludwig Boltzmann Cluster for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Irmgard Fischer
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Petra Fichtinger
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Bruno K Podesser
- Ludwig Boltzmann Cluster for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Vienna, Austria
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Roland Foisner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna and University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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99
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Manley HR, Keightley MC, Lieschke GJ. The Neutrophil Nucleus: An Important Influence on Neutrophil Migration and Function. Front Immunol 2018; 9:2867. [PMID: 30564248 PMCID: PMC6288403 DOI: 10.3389/fimmu.2018.02867] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/21/2018] [Indexed: 11/13/2022] Open
Abstract
Neutrophil nuclear morphology has historically been used in haematology for neutrophil identification and characterisation, but its exact role in neutrophil function has remained enigmatic. During maturation, segmentation of the neutrophil nucleus into its mature, multi-lobulated shape is accompanied by distinct changes in nuclear envelope composition, resulting in a unique nucleus that is believed to be imbued with extraordinary nuclear flexibility. As a rate-limiting factor for cell migration, nuclear morphology and biomechanics are particularly important in the context of neutrophil migration during immune responses. Being an extremely plastic and fast migrating cell type, it is to be expected that neutrophils have an especially deformable nucleus. However, many questions still surround the dynamic capacities of the neutrophil nucleus, and which nuclear and cytoskeletal elements determine these dynamics. The biomechanics of the neutrophil nucleus should also be considered for their influences on the production of neutrophil extracellular traps (NETs), given this process sees the release of chromatin "nets" from nucleoplasm to extracellular space. Although past studies have investigated neutrophil nuclear composition and shape, in a new era of more sophisticated biomechanical and genetic techniques, 3D migration studies, and higher resolution microscopy we now have the ability to further investigate and understand neutrophil nuclear plasticity at an unprecedented level. This review addresses what is currently understood about neutrophil nuclear structure and its role in migration and the release of NETs, whilst highlighting open questions surrounding neutrophil nuclear dynamics.
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Affiliation(s)
- Harriet R Manley
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | | | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
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100
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Jiang Y, Ji JY. Understanding lamin proteins and their roles in aging and cardiovascular diseases. Life Sci 2018; 212:20-29. [DOI: 10.1016/j.lfs.2018.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 02/04/2023]
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