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Lee GE, Byun J, Lee CJ, Cho YY. Molecular Mechanisms for the Regulation of Nuclear Membrane Integrity. Int J Mol Sci 2023; 24:15497. [PMID: 37895175 PMCID: PMC10607757 DOI: 10.3390/ijms242015497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
The nuclear membrane serves a critical role in protecting the contents of the nucleus and facilitating material and signal exchange between the nucleus and cytoplasm. While extensive research has been dedicated to topics such as nuclear membrane assembly and disassembly during cell division, as well as interactions between nuclear transmembrane proteins and both nucleoskeletal and cytoskeletal components, there has been comparatively less emphasis on exploring the regulation of nuclear morphology through nuclear membrane integrity. In particular, the role of type II integral proteins, which also function as transcription factors, within the nuclear membrane remains an area of research that is yet to be fully explored. The integrity of the nuclear membrane is pivotal not only during cell division but also in the regulation of gene expression and the communication between the nucleus and cytoplasm. Importantly, it plays a significant role in the development of various diseases. This review paper seeks to illuminate the biomolecules responsible for maintaining the integrity of the nuclear membrane. It will delve into the mechanisms that influence nuclear membrane integrity and provide insights into the role of type II membrane protein transcription factors in this context. Understanding these aspects is of utmost importance, as it can offer valuable insights into the intricate processes governing nuclear membrane integrity. Such insights have broad-reaching implications for cellular function and our understanding of disease pathogenesis.
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Affiliation(s)
- Ga-Eun Lee
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Jiin Byun
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Cheol-Jung Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Chungcheongnam-do, Republic of Korea
| | - Yong-Yeon Cho
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
- RCD Control and Material Research Institute, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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2
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Lecoutre S, Lambert M, Drygalski K, Dugail I, Maqdasy S, Hautefeuille M, Clément K. Importance of the Microenvironment and Mechanosensing in Adipose Tissue Biology. Cells 2022; 11:cells11152310. [PMID: 35954152 PMCID: PMC9367348 DOI: 10.3390/cells11152310] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 11/16/2022] Open
Abstract
The expansion of adipose tissue is an adaptive mechanism that increases nutrient buffering capacity in response to an overall positive energy balance. Over the course of expansion, the adipose microenvironment undergoes continual remodeling to maintain its structural and functional integrity. However, in the long run, adipose tissue remodeling, typically characterized by adipocyte hypertrophy, immune cells infiltration, fibrosis and changes in vascular architecture, generates mechanical stress on adipose cells. This mechanical stimulus is then transduced into a biochemical signal that alters adipose function through mechanotransduction. In this review, we describe the physical changes occurring during adipose tissue remodeling, and how they regulate adipose cell physiology and promote obesity-associated dysfunction in adipose tissue.
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Affiliation(s)
- Simon Lecoutre
- Nutrition and Obesities: Systemic Approaches Research Group (Nutri-Omics), Sorbonne Université, INSERM, F-75013 Paris, France; (S.L.); (K.D.); (I.D.)
| | - Mélanie Lambert
- Labex Inflamex, Université Sorbonne Paris Nord, INSERM, F-93000 Bobigny, France;
| | - Krzysztof Drygalski
- Nutrition and Obesities: Systemic Approaches Research Group (Nutri-Omics), Sorbonne Université, INSERM, F-75013 Paris, France; (S.L.); (K.D.); (I.D.)
| | - Isabelle Dugail
- Nutrition and Obesities: Systemic Approaches Research Group (Nutri-Omics), Sorbonne Université, INSERM, F-75013 Paris, France; (S.L.); (K.D.); (I.D.)
| | - Salwan Maqdasy
- Department of Medicine (H7), Karolinska Institutet Hospital, C2-94, 14186 Stockholm, Sweden;
| | - Mathieu Hautefeuille
- Laboratoire de Biologie du Développement (UMR 7622), IBPS, Sorbonne Université, F-75005 Paris, France;
| | - Karine Clément
- Nutrition and Obesities: Systemic Approaches Research Group (Nutri-Omics), Sorbonne Université, INSERM, F-75013 Paris, France; (S.L.); (K.D.); (I.D.)
- Assistance Publique Hôpitaux de Paris, Nutrition Department, CRNH Ile-de-France, Pitié-Salpêtrière Hospital, F-75013 Paris, France
- Correspondence: or
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3
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Selezneva A, Gibb AJ, Willis D. The Nuclear Envelope as a Regulator of Immune Cell Function. Front Immunol 2022; 13:840069. [PMID: 35757775 PMCID: PMC9226455 DOI: 10.3389/fimmu.2022.840069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/10/2022] [Indexed: 01/07/2023] Open
Abstract
The traditional view of the nuclear envelope (NE) was that it represented a relatively inert physical barrier within the cell, whose main purpose was to separate the nucleoplasm from the cytoplasm. However, recent research suggests that this is far from the case, with new and important cellular functions being attributed to this organelle. In this review we describe research suggesting an important contribution of the NE and its constituents in regulating the functions of cells of the innate and adaptive immune system. One of the standout properties of immune cells is their ability to migrate around the body, allowing them to carry out their physiological/pathophysiology cellular role at the appropriate location. This together with the physiological role of the tissue, changes in tissue matrix composition due to disease and aging, and the activation status of the immune cell, all result in immune cells being subjected to different mechanical forces. We report research which suggests that the NE may be an important sensor/transducer of these mechanical signals and propose that the NE is an integrator of both mechanical and chemical signals, allowing the cells of the innate immune system to precisely regulate gene transcription and functionality. By presenting this overview we hope to stimulate the interests of researchers into this often-overlooked organelle and propose it should join the ranks of mitochondria and phagosome, which are important organelles contributing to immune cell function.
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Affiliation(s)
- Anna Selezneva
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
| | - Alasdair J Gibb
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
| | - Dean Willis
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, United Kingdom
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4
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Zheng M, Jin G, Zhou Z. Post-Translational Modification of Lamins: Mechanisms and Functions. Front Cell Dev Biol 2022; 10:864191. [PMID: 35656549 PMCID: PMC9152177 DOI: 10.3389/fcell.2022.864191] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/17/2022] [Indexed: 12/22/2022] Open
Abstract
Lamins are the ancient type V intermediate filament proteins contributing to diverse biological functions, such as the maintenance of nuclear morphology, stabilization of chromatin architecture, regulation of cell cycle progression, regulation of spatial-temporal gene expressions, and transduction of mechano-signaling. Deregulation of lamins is associated with abnormal nuclear morphology and chromatin disorganization, leading to a variety of diseases such as laminopathy and premature aging, and might also play a role in cancer. Accumulating evidence indicates that lamins are functionally regulated by post-translational modifications (PTMs) including farnesylation, phosphorylation, acetylation, SUMOylation, methylation, ubiquitination, and O-GlcNAcylation that affect protein stabilization and the association with chromatin or associated proteins. The mechanisms by which these PTMs are modified and the relevant functionality become increasingly appreciated as understanding of these changes provides new insights into the molecular mechanisms underlying the laminopathies concerned and novel strategies for the management. In this review, we discussed a range of lamin PTMs and their roles in both physiological and pathological processes, as well as potential therapeutic strategies by targeting lamin PTMs.
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Affiliation(s)
- Mingyue Zheng
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guoxiang Jin
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
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5
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Skupien-Jaroszek A, Walczak A, Czaban I, Pels KK, Szczepankiewicz AA, Krawczyk K, Ruszczycki B, Wilczynski GM, Dzwonek J, Magalska A. The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy. PLoS One 2021; 16:e0239111. [PMID: 34086671 PMCID: PMC8177504 DOI: 10.1371/journal.pone.0239111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/17/2021] [Indexed: 01/19/2023] Open
Abstract
The Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity. In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting-an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning occurring after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.
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Affiliation(s)
- Anna Skupien-Jaroszek
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Walczak
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Karolina Pels
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Błażej Ruszczycki
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Dzwonek
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (AM); (JD)
| | - Adriana Magalska
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (AM); (JD)
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6
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Patil S, Sengupta K. Role of A- and B-type lamins in nuclear structure-function relationships. Biol Cell 2021; 113:295-310. [PMID: 33638183 DOI: 10.1111/boc.202000160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022]
Abstract
Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A- and B-type lamins localizes in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling. Lamins form a scaffold that partially tethers chromatin at the nuclear envelope. The nuclear lamina also stabilises protein-protein interactions involved in gene regulation and DNA repair. The lamin-based protein sub-complexes are implicated in both nuclear and cytoskeletal organisation, the mechanical stability of the nucleus, genome organisation, transcriptional regulation, genome stability and cellular differentiation. Here, we review recent research on nuclear lamins and unique roles of A- and B-type lamins in modulating various nuclear processes and their impact on cell function.
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Affiliation(s)
- Shalaka Patil
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Kundan Sengupta
- Biology, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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7
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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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8
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Saez A, Herrero-Fernandez B, Gomez-Bris R, Somovilla-Crespo B, Rius C, Gonzalez-Granado JM. Lamin A/C and the Immune System: One Intermediate Filament, Many Faces. Int J Mol Sci 2020; 21:E6109. [PMID: 32854281 PMCID: PMC7504305 DOI: 10.3390/ijms21176109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
Nuclear envelope lamin A/C proteins are a major component of the mammalian nuclear lamina, a dense fibrous protein meshwork located in the nuclear interior. Lamin A/C proteins regulate nuclear mechanics and structure and control cellular signaling, gene transcription, epigenetic regulation, cell cycle progression, cell differentiation, and cell migration. The immune system is composed of the innate and adaptive branches. Innate immunity is mediated by myeloid cells such as neutrophils, macrophages, and dendritic cells. These cells produce a rapid and nonspecific response through phagocytosis, cytokine production, and complement activation, as well as activating adaptive immunity. Specific adaptive immunity is activated by antigen presentation by antigen presenting cells (APCs) and the cytokine microenvironment, and is mainly mediated by the cellular functions of T cells and the production of antibodies by B cells. Unlike most cell types, immune cells regulate their lamin A/C protein expression relatively rapidly to exert their functions, with expression increasing in macrophages, reducing in neutrophils, and increasing transiently in T cells. In this review, we discuss and summarize studies that have addressed the role played by lamin A/C in the functions of innate and adaptive immune cells in the context of human inflammatory and autoimmune diseases, pathogen infections, and cancer.
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Affiliation(s)
- Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Pozuelo de Alarcón, 28223 Madrid, Spain;
| | - Beatriz Herrero-Fernandez
- LamImSys Lab, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain; (B.H.-F.); (R.G.-B.); (B.S.-C.)
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Raquel Gomez-Bris
- LamImSys Lab, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain; (B.H.-F.); (R.G.-B.); (B.S.-C.)
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Beatriz Somovilla-Crespo
- LamImSys Lab, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain; (B.H.-F.); (R.G.-B.); (B.S.-C.)
| | - Cristina Rius
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid (UEM), Villaviciosa de Odón, 28670 Madrid, Spain;
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, 28029 Madrid, Spain
| | - Jose M. Gonzalez-Granado
- LamImSys Lab, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain; (B.H.-F.); (R.G.-B.); (B.S.-C.)
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares, 28029 Madrid, Spain
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9
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Toribio‐Fernández R, Herrero‐Fernandez B, Zorita V, López JA, Vázquez J, Criado G, Pablos JL, Collas P, Sánchez‐Madrid F, Andrés V, Gonzalez‐Granado JM. Lamin A/C deficiency in CD4
+
T‐cells enhances regulatory T‐cells and prevents inflammatory bowel disease. J Pathol 2019; 249:509-522. [DOI: 10.1002/path.5332] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 07/15/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - Virginia Zorita
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
| | - Juan A López
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
- CIBER de Enfermedades Cardiovasculares Madrid Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
- CIBER de Enfermedades Cardiovasculares Madrid Spain
| | - Gabriel Criado
- Instituto de Investigación Hospital 12 de Octubre (imas12) Madrid Spain
| | - Jose L Pablos
- Instituto de Investigación Hospital 12 de Octubre (imas12) Madrid Spain
| | - Philippe Collas
- Institute of Basic Medical SciencesUniversity of Oslo Oslo Norway
| | - Francisco Sánchez‐Madrid
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
- CIBER de Enfermedades Cardiovasculares Madrid Spain
- Servicio de Inmunología, Hospital de la PrincesaInstituto de Investigación Sanitaria La Princesa (IIS Princesa) Madrid Spain
| | - Vicente Andrés
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
- CIBER de Enfermedades Cardiovasculares Madrid Spain
| | - Jose M Gonzalez‐Granado
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Madrid Spain
- Instituto de Investigación Hospital 12 de Octubre (imas12) Madrid Spain
- CIBER de Enfermedades Cardiovasculares Madrid Spain
- Departamento de Fisiología, Facultad de MedicinaUniversidad Autónoma de Madrid (UAM) Madrid Spain
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10
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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: 40] [Impact Index Per Article: 8.0] [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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11
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Stachecka J, Nowacka-Woszuk J, Kolodziejski PA, Szczerbal I. The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis. Chromosome Res 2019; 27:271-284. [PMID: 30656515 PMCID: PMC6733831 DOI: 10.1007/s10577-019-09604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 01/27/2023]
Abstract
Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene’s nuclear positioning for its activity during in vitro adipogenesis in the pig. We used an established system of differentiation of mesenchymal stem cells derived from bone marrow and adipose tissue into adipocytes. The differentiation process was carried out for 7 days, and the cells were examined using the 3D DNA/immuno-FISH and RNA/DNA-FISH approaches. PPARG transcript level was measured using real-time PCR, and PPARγ activity was detected with colorimetric assay. Changes in the nuclear location of the PPARG gene were observed when we compared undifferentiated mesenchymal stem cells with mature adipocytes. The gene moved from the nuclear periphery to the nuclear center as its transcriptional activity increased. The RNA/DNA-FISH approach shows that differences in primary transcript production correlated with the allele’s nuclear positioning. Transcriptionally active alleles preferentially occupy the central part of the nucleus, while inactive alleles are found on the nuclear periphery. We also show that transcription of PPARG begins with one allele, but that both alleles are active in later stages of differentiation. Our results provide evidence that functionally distinct alleles of the PPARG gene are positioned in different parts of the cell nucleus. This confirms the importance of nuclear architecture to the regulation of PPARG gene transcription, and thus to the fate of the adipose cell.
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Affiliation(s)
- Joanna Stachecka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Pawel A Kolodziejski
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637, Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
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12
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Mattioli E, Andrenacci D, Garofalo C, Prencipe S, Scotlandi K, Remondini D, Gentilini D, Di Blasio AM, Valente S, Scarano E, Cicchilitti L, Piaggio G, Mai A, Lattanzi G. Altered modulation of lamin A/C-HDAC2 interaction and p21 expression during oxidative stress response in HGPS. Aging Cell 2018; 17:e12824. [PMID: 30109767 PMCID: PMC6156291 DOI: 10.1111/acel.12824] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/22/2018] [Accepted: 06/26/2018] [Indexed: 02/01/2023] Open
Abstract
Defects in stress response are main determinants of cellular senescence and organism aging. In fibroblasts from patients affected by Hutchinson-Gilford progeria, a severe LMNA-linked syndrome associated with bone resorption, cardiovascular disorders, and premature aging, we found altered modulation of CDKN1A, encoding p21, upon oxidative stress induction, and accumulation of senescence markers during stress recovery. In this context, we unraveled a dynamic interaction of lamin A/C with HDAC2, an histone deacetylase that regulates CDKN1A expression. In control skin fibroblasts, lamin A/C is part of a protein complex including HDAC2 and its histone substrates; protein interaction is reduced at the onset of DNA damage response and recovered after completion of DNA repair. This interplay parallels modulation of p21 expression and global histone acetylation, and it is disrupted by LMNAmutations leading to progeroid phenotypes. In fact, HGPS cells show impaired lamin A/C-HDAC2 interplay and accumulation of p21 upon stress recovery. Collectively, these results link altered physical interaction between lamin A/C and HDAC2 to cellular and organism aging. The lamin A/C-HDAC2 complex may be a novel therapeutic target to slow down progression of progeria symptoms.
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Affiliation(s)
- Elisabetta Mattioli
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Davide Andrenacci
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Cecilia Garofalo
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab; Rizzoli Institute; Bologna Italy
| | - Sabino Prencipe
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
| | - Katia Scotlandi
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
- CRS Development of Biomolecular Therapies, Experimental Oncology Lab; Rizzoli Institute; Bologna Italy
| | - Daniel Remondini
- Department of Physics and Astronomy; University of Bologna; Bologna Italy
| | - Davide Gentilini
- Centre for Biomedical Research and Technologies; Italian Auxologic Institute, IRCCS; Milan Italy
| | - Anna Maria Di Blasio
- Centre for Biomedical Research and Technologies; Italian Auxologic Institute, IRCCS; Milan Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies; Pasteur Institute Italy; Cenci-Bolognetti Foundation; Sapienza University of Rome; Rome Italy
| | - Emanuela Scarano
- Pediatric Endocrinology and Rare Diseases Unit; University of Bologna; Bologna Italy
| | - Lucia Cicchilitti
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies; IRCCS - Regina Elena National Cancer Institute; Rome Italy
| | - Giulia Piaggio
- UOSD SAFU, Department of Research, Diagnosis and Innovative Technologies; IRCCS - Regina Elena National Cancer Institute; Rome Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies; Pasteur Institute Italy; Cenci-Bolognetti Foundation; Sapienza University of Rome; Rome Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics, Unit of Bologna; Bologna Italy
- Rizzoli Orthopedic Institute; IRCCS; Bologna Italy
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13
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Maraldi NM. The lamin code. Biosystems 2018; 164:68-75. [DOI: 10.1016/j.biosystems.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 12/24/2022]
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14
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Lamin A/C augments Th1 differentiation and response against vaccinia virus and Leishmania major. Cell Death Dis 2018; 9:9. [PMID: 29311549 PMCID: PMC5849043 DOI: 10.1038/s41419-017-0007-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Differentiation of naive CD4+ T-cells into functionally distinct T helper (Th) subsets is critical to immunity against pathogen infection. Little is known about the role of signals emanating from the nuclear envelope for T-cell differentiation. The nuclear envelope protein lamin A/C is induced in naive CD4+ T-cells upon antigen recognition and acts as a link between the nucleus and the plasma membrane during T-cell activation. Here we demonstrate that the absence of lamin A/C in naive T-cell reduces Th1 differentiation without affecting Th2 differentiation in vitro and in vivo. Moreover, Rag1−/− mice reconstituted with Lmna−/−CD4+CD25− T-cells and infected with vaccinia virus show weaker Th1 responses and viral removal than mice reconstituted with wild-type T-cells. Th1 responses and pathogen clearance upon Leishmania major infection were similarly diminished in mice lacking lamin A/C in the complete immune system or selectively in T-cells. Lamin A/C mediates Th1 polarization by a mechanism involving T-bet and IFNγ production. Our results reveal a novel role for lamin A/C as key regulator of Th1 differentiation in response to viral and intracellular parasite infections.
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15
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Branch MR, Hepler JR. Endogenous RGS14 is a cytoplasmic-nuclear shuttling protein that localizes to juxtanuclear membranes and chromatin-rich regions of the nucleus. PLoS One 2017; 12:e0184497. [PMID: 28934222 PMCID: PMC5608220 DOI: 10.1371/journal.pone.0184497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023] Open
Abstract
Regulator of G protein signaling 14 (RGS14) is a multifunctional scaffolding protein that integrates G protein and H-Ras/MAPkinase signaling pathways to regulate synaptic plasticity important for hippocampal learning and memory. However, to date, little is known about the subcellular distribution and roles of endogenous RGS14 in a neuronal cell line. Most of what is known about RGS14 cellular behavior is based on studies of tagged, recombinant RGS14 ectopically overexpressed in unnatural host cells. Here, we report for the first time a comprehensive assessment of the subcellular distribution and dynamic localization of endogenous RGS14 in rat B35 neuroblastoma cells. Using confocal imaging and 3D-structured illumination microscopy, we find that endogenous RGS14 localizes to subcellular compartments not previously recognized in studies of recombinant RGS14. RGS14 localization was observed most notably at juxtanuclear membranes encircling the nucleus, at nuclear pore complexes (NPC) on both sides of the nuclear envelope and within intranuclear membrane channels, and within both chromatin-poor and chromatin-rich regions of the nucleus in a cell cycle-dependent manner. In addition, a subset of nuclear RGS14 localized adjacent to active RNA polymerase II. Endogenous RGS14 was absent from the plasma membrane in resting cells; however, the protein could be trafficked to the plasma membrane from juxtanuclear membranes in endosomes derived from ER/Golgi, following constitutive activation of endogenous RGS14 G protein binding partners using AlF4¯. Finally, our findings show that endogenous RGS14 behaves as a cytoplasmic-nuclear shuttling protein confirming what has been shown previously for recombinant RGS14. Taken together, the findings highlight possible cellular roles for RGS14 not previously recognized that are distinct from the regulation of conventional GPCR-G protein signaling, in particular undefined roles for RGS14 in the nucleus.
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Affiliation(s)
- Mary Rose Branch
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - John R. Hepler
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia, United States of America
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16
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Design of a nanocomposite substrate inducing adult stem cell assembly and progression toward an Epiblast-like or Primitive Endoderm-like phenotype via mechanotransduction. Biomaterials 2017; 144:211-229. [PMID: 28841465 DOI: 10.1016/j.biomaterials.2017.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/01/2017] [Accepted: 08/13/2017] [Indexed: 01/10/2023]
Abstract
This work shows that the active interaction between human umbilical cord matrix stem cells and Poly (l-lactide)acid (PLLA) and PLLA/Multi Walled Carbon Nanotubes (MWCNTs) nanocomposite films results in the stem cell assembly as a spheroid conformation and affects the stem cell fate transition. We demonstrated that spheroids directly respond to a tunable surface and the bulk properties (electric, dielectric and thermal) of plain and nanocomposite PLLA films by triggering a mechanotransduction axis. This stepwise process starts from tethering of the cells' focal adhesion proteins to the surface, together with the adherens junctions between cells. Both complexes transmit traction forces to F-Actin stress fibres that link Filamin-A and Myosin-IIA proteins, generating a biological scaffold, with increased stiffening conformation from PLLA to PLLA/MWCNTs, and enable the nucleoskeleton proteins to boost chromatin reprogramming processes. Herein, the opposite expression of NANOG and GATA6 transcription factors, together with other lineage specification related proteins, steer spheroids toward an Epiblast-like or Primitive Endoderm-like lineage commitment, depending on the absence or presence of 1 wt% MWCNTs, respectively. This work represents a pioneering effort to create a stem cell/material interface that can model the stem cell fate transition under growth culture conditions.
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17
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Golubtsova NN, Filippov FN, Gunin AG. Lamin A and lamin-associated polypeptide 2 (LAP-2) in human skin fibroblasts in the process of aging. ADVANCES IN GERONTOLOGY 2017. [DOI: 10.1134/s2079057017010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Association of lamin A/C with muscle gene-specific promoters in myoblasts. Biochem Biophys Rep 2015; 4:76-82. [PMID: 29124189 PMCID: PMC5668900 DOI: 10.1016/j.bbrep.2015.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/10/2015] [Accepted: 08/26/2015] [Indexed: 11/20/2022] Open
Abstract
The A-type and B-type lamins form a filamentous meshwork underneath the inner nuclear membrane called the nuclear lamina, which is an important component of nuclear architecture in metazoan cells. The lamina interacts with large, mostly repressive chromatin domains at the nuclear periphery. In addition, genome–lamina interactions also involve dynamic association of lamin A/C with gene promoters in adipocytes. Mutations in the human lamin A gene cause a spectrum of hereditary diseases called the laminopathies which affect muscle, cardiac and adipose tissues. Since most mutations in lamin A/C affect skeletal muscle, we investigated lamin–chromatin interactions at promoters of muscle specific genes in both muscle and non-muscle cell lines by ChIP-qPCR. We observed that lamin A/C was specifically associated with promoter regions of muscle genes in myoblasts but not in fibroblasts. Lamin A/C dissociated from the promoter regions of the differentiation specific MyoD, myogenin and muscle creatine kinase genes when myoblasts were induced to differentiate. In the promoter regions of the myogenin and MyoD genes, the binding of lamin A/C in myoblasts inversely correlated with the active histone mark, H3K4me3. Lamin A/C binding on muscle genes was reduced and differentiation potential was enhanced on treatment of myoblasts with a histone deacetylase inhibitor. These findings suggest a role for lamina–chromatin interactions in muscle differentiation and have important implications for the pathological mechanisms of striated muscle associated laminopathies. Lamina–chromatin interactions are important for nuclear processes. We show lamin A/C binding to promoters of muscle genes in myoblasts. Lamin A/C binding is reduced upon myoblast differentiation. Lamin A/C binding inversely correlates with active histone marks on muscle genes. Our findings suggest that lamin A/C binding to promoters is cell-type specific.
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Chen YC, Huang LT, Tain YL, Chen CC, Sheen JM, Tiao MM, Tsai CM, Kuo HC, Huang CC, Chang KA, Yu HR. Prenatal glucocorticoid contributed to rat lung dysplasia is related to asymmetric dimethylarginine/nitric oxide pathway. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0859-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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Vadrot N, Duband-Goulet I, Cabet E, Attanda W, Barateau A, Vicart P, Gerbal F, Briand N, Vigouroux C, Oldenburg AR, Lund EG, Collas P, Buendia B. The p.R482W substitution in A-type lamins deregulates SREBP1 activity in Dunnigan-type familial partial lipodystrophy. Hum Mol Genet 2014; 24:2096-109. [PMID: 25524705 DOI: 10.1093/hmg/ddu728] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Nuclear lamins are involved in many cellular functions due to their ability to bind numerous partners including chromatin and transcription factors, and affect their properties. Dunnigan type familial partial lipodystrophy (FPLD2; OMIM#151660) is caused in most cases by the A-type lamin R482W mutation. We report here that the R482W mutation affects the regulatory activity of sterol response element binding protein 1 (SREBP1), a transcription factor that regulates hundreds of genes involved in lipid metabolism and adipocyte differentiation. Using in situ proximity ligation assays (PLA), reporter assays and biochemical and transcriptomic approaches, we show that interactions of SREBP1 with lamin A and lamin C occur at the nuclear periphery and in the nucleoplasm. These interactions involve the Ig-fold of A-type lamins and are favored upon SREBP1 binding to its DNA target sequences. We show that SREBP1, LMNA and sterol response DNA elements form ternary complexes in vitro. In addition, overexpression of A-type lamins reduces transcriptional activity of SREBP1. In contrast, both overexpression of LMNA R482W in primary human preadipocytes and endogenous expression of A-type lamins R482W in FPLD2 patient fibroblasts, reduce A-type lamins-SREBP1 in situ interactions and upregulate a large number of SREBP1 target genes. As this LMNA mutant was previously shown to inhibit adipogenic differentiation, we propose that deregulation of SREBP1 by mutated A-type lamins constitutes one underlying mechanism of the physiopathology of FPLD2. Our data suggest that SREBP1 targeting molecules could be considered in a therapeutic context.
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Affiliation(s)
- Nathalie Vadrot
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Isabelle Duband-Goulet
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Eva Cabet
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Wikayatou Attanda
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Alice Barateau
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Patrick Vicart
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France
| | - Fabien Gerbal
- Université Paris Diderot, Matière et Systèmes Complexes, CNRS UMR 7057, 10 rue Alice Domon et Leonie Duquet, Paris Cedex 13 75205, France, Physics Department, Université Pierre et Marie Curie, Paris UFR925, France
| | - Nolwenn Briand
- Faculté de Médecine Pierre et Marie Curie, Inserm, UMR S938, Centre de Recherche Saint-Antoine, 27 rue Chaligny, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 6, UMR S938, Paris F-75005, France, ICAN, Institute of Cardiometabolism and Nutrition, Paris F-75013, France
| | - Corinne Vigouroux
- Faculté de Médecine Pierre et Marie Curie, Inserm, UMR S938, Centre de Recherche Saint-Antoine, 27 rue Chaligny, Paris F-75012, France, Sorbonne Universités, UPMC Univ Paris 6, UMR S938, Paris F-75005, France, ICAN, Institute of Cardiometabolism and Nutrition, Paris F-75013, France, Laboratoire Commun de Biologie et Génétique Moléculaires, AP-HP, Hôpital Saint-Antoine, Paris F-75012, France and
| | - Anja R Oldenburg
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, Oslo 0317, Norway
| | - Eivind G Lund
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, Oslo 0317, Norway
| | - Philippe Collas
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, Oslo 0317, Norway
| | - Brigitte Buendia
- Unit of Functional and Adaptive Biology (BFA), Université Paris Diderot-Paris 7 Affiliated with CNRS, 4 rue Marie-Andrée Lagroua Weill-Halle, Paris Cedex 13 75205, France,
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21
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Lund E, Oldenburg AR, Collas P. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92. [PMID: 24782521 PMCID: PMC4066758 DOI: 10.1093/nar/gku324] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
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