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Dutta S, Kumar V, Barua A, Vasudevan M. Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy. Biochem J 2024; 481:1803-1827. [PMID: 39509247 DOI: 10.1042/bcj20240474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/31/2024] [Accepted: 11/07/2024] [Indexed: 11/15/2024]
Abstract
Lamins form a proteinaceous meshwork as a major structural component of the nucleus. Lamins, along with their interactors, act as determinants for chromatin organization throughout the nucleus. The major dominant missense mutations responsible for autosomal dominant forms of muscular dystrophies reside in the Ig fold domain of lamin A. However, how lamin A contributes to the distribution of heterochromatin and balances euchromatin, and how it relocates epigenetic marks to shape chromatin states, remains poorly defined, making it difficult to draw conclusions about the prognosis of lamin A-mediated muscular dystrophies. In the first part of this report, we identified the in vitro organization of full-length lamin A proteins due to two well-documented Ig LMNA mutations, R453W and W514R. We further demonstrated that both lamin A/C mutant cells predominantly expressed nucleoplasmic aggregates. Labeling specific markers of epigenetics allowed correlation of lamin A mutations with epigenetic mechanisms. In addition to manipulating epigenetic mechanisms, our proteomic studies traced diverse expressions of transcription regulators, RNA synthesis and processing proteins, protein translation components, and posttranslational modifications. These data suggest severe perturbations in targeting other proteins to the nucleus.
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Affiliation(s)
- Subarna Dutta
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India
- Theomics International Private Limited 28, Income Tax Layout, Sadananda Nagar, NGEF Layout, Bengaluru 560038, India
| | - Vikas Kumar
- UMass Chan Medical School, Mass Spectrometry Facility, 222 Maple Avenue, Shrewsbury, MA 01545, U.S.A
| | - Arnab Barua
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Madavan Vasudevan
- Theomics International Private Limited 28, Income Tax Layout, Sadananda Nagar, NGEF Layout, Bengaluru 560038, India
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2
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Kono Y, Pack CG, Ichikawa T, Komatsubara A, Adam SA, Miyazawa K, Rolas L, Nourshargh S, Medalia O, Goldman RD, Fukuma T, Kimura H, Shimi T. Roles of the lamin A-specific tail region in the localization to sites of nuclear envelope rupture. PNAS NEXUS 2024; 3:pgae527. [PMID: 39677369 PMCID: PMC11645434 DOI: 10.1093/pnasnexus/pgae527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 11/13/2024] [Indexed: 12/17/2024]
Abstract
The nuclear lamina (NL) lines the nuclear envelope (NE) to maintain nuclear structure in metazoan cells. The major NL components, the nuclear lamins contribute to the protection against NE rupture induced by mechanical stress. Lamin A (LA) and a short form of the splicing variant lamin C (LC) are diffused from the nucleoplasm to sites of NE rupture in immortalized mouse embryonic fibroblasts (MEFs). LA localization to the rupture sites is significantly slow and weak compared with LC, but the underlying mechanism remains unknown. In this study, wild-type (WT), Hutchinson-Gilford Progeria syndrome (HGPS) knock-in MEFs expressing progerin (PG, an LA mutant lacking the second proteolytic cleavage site), and LA/C-knockout MEFs transiently and heterogeneously expressing LA/C WTs and mutants fused to mEmerald are examined before and after NE rupture induced by single-cell compression and laser microirradiation. The farnesylation at the CaaX motif of unprocessed LA and the inhibition of the second proteolytic cleavage decrease the nucleoplasmic pool and slow the localization to the rupture sites in a long-time window (60-70 min) after the induction of NE rupture. Our data could explain the defective repair of NE rupture in HGPS through the farnesylation at the CaaX motif of unprocessed progerin. In addition, unique segments in LA-specific tail region cooperate with each other to inhibit the rapid accumulation within a short-time window (3 min) that is also observed with LC.
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Affiliation(s)
- Yohei Kono
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Chan-Gi Pack
- Convergence Medicine Research Center, Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Korea
- Department of Biomedical Engineering, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Takehiko Ichikawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Arata Komatsubara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Stephen A Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Keisuke Miyazawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Loïc Rolas
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Sussan Nourshargh
- Centre for Microvascular Research, William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Takeshi Shimi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
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Autosomal dominant Emery-Dreifuss muscular dystrophy caused by a mutation in the lamin A/C gene identified by exome sequencing: a case report. BMC Pediatr 2022; 22:601. [PMID: 36253810 PMCID: PMC9575219 DOI: 10.1186/s12887-022-03662-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Background Emery-Dreifuss Muscular Dystrophy (EDMD) is an uncommon genetic disease among the group of muscular dystrophies. EDMD is clinically heterogeneous and resembles other muscular dystrophies. Mutation of the lamin A/C (LMNA) gene, which causes EDMD, also causes many other diseases. There is inter and intrafamilial variability in clinical presentations. Precise diagnosis can help in patient surveillance, especially before they present with cardiac problems. Hence, this paper shows how a molecular work-out by next-generation sequencing can help this group of disorders. Case presentation A 2-year-10-month-old Javanese boy presented to our clinic with weakness in lower limbs and difficulty climbing stairs. The clinical features of the boy were Gower's sign, waddling gait and high CK level. His father presented with elbow contractures and heels, toe walking and weakness of limbs, pelvic, and peroneus muscles. Exome sequencing on this patient detected a pathogenic variant in the LMNA gene (NM_170707: c.C1357T: NP_733821: p.Arg453Trp) that has been reported to cause Autosomal Dominant Emery-Dreifuss muscular dystrophy. Further examination showed total atrioventricular block and atrial fibrillation in the father. Conclusion EDMD is a rare disabling muscular disease that poses a diagnostic challenge. Family history work-up and thorough neuromuscular physical examinations are needed. Early diagnosis is essential to recognize orthopaedic and cardiac complications, improving the clinical management and prognosis of the disease. Exome sequencing could successfully determine pathogenic variants to provide a conclusive diagnosis.
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4
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Janssen AFJ, Breusegem SY, Larrieu D. Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities. Cells 2022; 11:347. [PMID: 35159153 PMCID: PMC8834579 DOI: 10.3390/cells11030347] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/02/2023] Open
Abstract
Any given cell type has an associated "normal" nuclear morphology, which is important to maintain proper cellular functioning and safeguard genomic integrity. Deviations from this can be indicative of diseases such as cancer or premature aging syndrome. To accurately assess nuclear abnormalities, it is important to use quantitative measures of nuclear morphology. Here, we give an overview of several nuclear abnormalities, including micronuclei, nuclear envelope invaginations, blebs and ruptures, and review the current methods used for image-based quantification of these abnormalities. We discuss several parameters that can be used to quantify nuclear shape and compare their outputs using example images. In addition, we present new pipelines for quantitative analysis of nuclear blebs and invaginations. Quantitative analyses of nuclear aberrations and shape will be important in a wide range of applications, from assessments of cancer cell anomalies to studies of nucleus deformability under mechanical or other types of stress.
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Affiliation(s)
| | | | - Delphine Larrieu
- Department of Clinical Biochemistry, Addenbrookes Biomedical Campus, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; (A.F.J.J.); (S.Y.B.)
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5
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Nekrasov ED, Kiselev SL. Mitochondrial distribution violation and nuclear indentations in neurons differentiated from iPSCs of Huntington's disease patients. J Stem Cells Regen Med 2018. [PMID: 30679892 PMCID: PMC6339978 DOI: 10.46582/jsrm.1402012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIM: Huntington’s disease (HD) is an inherited disease caused by an expansion of cytosine-adenine-guanine (CAG) repeats in the huntingtin gene (HTT) that ultimately leads to neurodegeneration. To study the molecular basis of this disease, induced pluripotent stem cells (iPSCs) generated from patients’ fibroblasts were used to investigate axonal mitochondrial trafficking and the nature of nuclear indentations. METHODS: Pathological and control iPSCs generated from patients with a low number of repeats were differentiated in striatal neurons of the brain. Mitochondrial density was measured along the axon using tubulin beta 3 co-staining in pathological and control neurons. To investigate the connection of nuclear roundness with calcium dysregulation, several calcium inhibitors were used. Proteasome system inhibition was applied to mimic premature neuronal ageing. RESULTS: We found that the mitochondrial density was approximately 7.6 ± 0.2 in neurites in control neurons but was only 5.3 ± 0.2 in mutant neurons with 40-44 CAG repeats (p-value <0.005). Neuronal ageing induced by proteasome inhibitor MG132 significantly decreased the mitochondrial density by 15% and 25% in control and mutant neurons to 6.5 ± 0.1 (p-value < 0.005) and 4.0 ± 0.3 (p-value < 0.005), respectively. Thus, for the first time, an impairment of mitochondrial trafficking in pathological neurons with endogenous mutant huntingtin was demonstrated. We found that inhibiting the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA), the ryanodine-receptor (RyR) or the inositol 1,4,5-trisphosphate receptor (IP3R) by specific inhibitors did not specifically affect the nuclear roundness or survival of pathological neurons differentiated from patient iPSCs. Therefore, nuclear calcium homeostasis is not directly associated with HD pathology. CONCLUSION: Identifying HD iPSCs and differentiating from them neurons provide a unique system for modelling the disease in vitro. Impairments of mitochondrial trafficking and nuclear roundness manifest long before the disease onset, while premature neuronal ageing enhances differences in mitochondrial distribution.
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Affiliation(s)
- Evgeny D Nekrasov
- Vavilov Institute of General Genetics Russian Academy of Science, Moscow, 119991, Russia
| | - Sergey L Kiselev
- Vavilov Institute of General Genetics Russian Academy of Science, Moscow, 119991, Russia
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6
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van Tienen FHJ, Lindsey PJ, Kamps MAF, Krapels IP, Ramaekers FCS, Brunner HG, van den Wijngaard A, Broers JLV. Assessment of fibroblast nuclear morphology aids interpretation of LMNA variants. Eur J Hum Genet 2018; 27:389-399. [PMID: 30420677 DOI: 10.1038/s41431-018-0294-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 01/26/2023] Open
Abstract
The phenotypic heterogeneity of Lamin A/C (LMNA) variants renders it difficult to classify them. As a consequence, many LMNA variants are classified as variant of unknown significance (VUS). A number of studies reported different types of visible nuclear abnormalities in LMNA-variant carriers, such as herniations, honeycomb-like structures and irregular Lamin staining. In this study, we used lamin A/C immunostaining and nuclear DAPI staining to assess the number and type of nuclear abnormalities in primary dermal fibroblast cultures of laminopathy patients and healthy controls. The total number of abnormal nuclei, which includes herniations, honeycomb-structures, and donut-like nuclei, was found to be the most discriminating parameter between laminopathy and control cell cultures. The percentage abnormal nuclei was subsequently scored in fibroblasts of 28 LMNA variant carriers, ranging from (likely) benign to (likely) pathogenic variant. Using this method, 27 out of 28 fibroblast cell cultures could be classified as either normal (n = 14) or laminopathy (n = 13) and no false positive results were obtained. The obtained specificity was 100% (CI 40-100%) and sensitivity 77% (46-95%). We conclude that assessing the percentage of abnormal nuclei is a quick and reliable method, which aids classification or confirms pathogenicity of identified LMNA variants causing formation of aberrant lamin A/C protein.
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Affiliation(s)
- Florence H J van Tienen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands. .,GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | - Patrick J Lindsey
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Miriam A F Kamps
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ingrid P Krapels
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Frans C S Ramaekers
- GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jos L V Broers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.,CARIM-School for Cardiovascular Diseases, Maastricht University Medical Centre, Maastricht, The Netherlands
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7
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Drozdz MM, Jiang H, Pytowski L, Grovenor C, Vaux DJ. Formation of a nucleoplasmic reticulum requires de novo assembly of nascent phospholipids and shows preferential incorporation of nascent lamins. Sci Rep 2017; 7:7454. [PMID: 28785031 PMCID: PMC5547041 DOI: 10.1038/s41598-017-07614-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/29/2017] [Indexed: 01/29/2023] Open
Abstract
Structure of interphase cell nuclei remains dynamic and can undergo various changes of shape and organisation, in health and disease. The double-membraned envelope that separates nuclear genetic material from the rest of the cell frequently includes deep, branching tubular invaginations that form a dynamic nucleoplasmic reticulum (NR). This study addresses mechanisms by which NR can form in interphase nuclei. We present a combination of Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) approach and light microscopy techniques to follow formation of NR by using pulse-chase experiments to examine protein and lipid delivery to nascent NR in cultured cells. Lamina protein incorporation was assessed using precursor accumulation (for lamin A) or a MAPLE3 photoconvertible tag (for lamin B1) and membrane phospholipid incorporation using stable isotope labelling with deuterated precursors followed by high resolution NanoSIMS. In all three cases, nascent molecules were selectively incorporated into newly forming NR tubules; thus strongly suggesting that NR formation is a regulated process involving a focal assembly machine, rather than simple physical perturbation of a pre-existing nuclear envelope.
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Affiliation(s)
- Marek M Drozdz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Haibo Jiang
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Chris Grovenor
- Department of Materials, University of Oxford, Oxford, OX1 3PH, United Kingdom
| | - David J Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.
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8
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Drozdz MM, Vaux DJ. Shared mechanisms in physiological and pathological nucleoplasmic reticulum formation. Nucleus 2017; 8:34-45. [PMID: 27797635 PMCID: PMC5287099 DOI: 10.1080/19491034.2016.1252893] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/13/2016] [Accepted: 10/19/2016] [Indexed: 12/14/2022] Open
Abstract
The mammalian nuclear envelope (NE) can develop complex dynamic membrane-bounded invaginations in response to both physiological and pathological stimuli. Since the formation of these nucleoplasmic reticulum (NR) structures can occur during interphase, without mitotic NE breakdown and reassembly, some other mechanism must drive their development. Here we consider models for deformation of the interphase NE, together with the evidence for their potential roles in NR formation.
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Affiliation(s)
| | - David John Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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9
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Fuchs C, Gawlas S, Heher P, Nikouli S, Paar H, Ivankovic M, Schultheis M, Klammer J, Gottschamel T, Capetanaki Y, Weitzer G. Desmin enters the nucleus of cardiac stem cells and modulates Nkx2.5 expression by participating in transcription factor complexes that interact with the nkx2.5 gene. Biol Open 2016; 5:140-53. [PMID: 26787680 PMCID: PMC4823984 DOI: 10.1242/bio.014993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/13/2015] [Indexed: 12/30/2022] Open
Abstract
The transcription factor Nkx2.5 and the intermediate filament protein desmin are simultaneously expressed in cardiac progenitor cells during commitment of primitive mesoderm to the cardiomyogenic lineage. Up-regulation of Nkx2.5 expression by desmin suggests that desmin may contribute to cardiogenic commitment and myocardial differentiation by directly influencing the transcription of the nkx2.5 gene in cardiac progenitor cells. Here, we demonstrate that desmin activates transcription of nkx2.5 reporter genes, rescues nkx2.5 haploinsufficiency in cardiac progenitor cells, and is responsible for the proper expression of Nkx2.5 in adult cardiac side population stem cells. These effects are consistent with the temporary presence of desmin in the nuclei of differentiating cardiac progenitor cells and its physical interaction with transcription factor complexes bound to the enhancer and promoter elements of the nkx2.5 gene. These findings introduce desmin as a newly discovered and unexpected player in the regulatory network guiding cardiomyogenesis in cardiac stem cells.
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Affiliation(s)
- Christiane Fuchs
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Sonja Gawlas
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Philipp Heher
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Sofia Nikouli
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens 115 27, Greece
| | - Hannah Paar
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Mario Ivankovic
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Martina Schultheis
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Julia Klammer
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Teresa Gottschamel
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
| | - Yassemi Capetanaki
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens 115 27, Greece
| | - Georg Weitzer
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna A1030, Austria
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10
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Vidak S, Kubben N, Dechat T, Foisner R. Proliferation of progeria cells is enhanced by lamina-associated polypeptide 2α (LAP2α) through expression of extracellular matrix proteins. Genes Dev 2016; 29:2022-36. [PMID: 26443848 PMCID: PMC4604344 DOI: 10.1101/gad.263939.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A single heterozygous mutation of LMNA generates the lamin A/C variant progerin and causes Hutchinson-Gilford progeria syndrome (HGPS). Vidak et al. show that this mutation leads to loss of LAP2α and nucleoplasmic lamins A/C, impaired proliferation, and down-regulation of extracellular matrix components. Ectopic expression of LAP2α in cells expressing progerin restores proliferation and extracellular matrix expression but not the levels of nucleoplasmic lamins A/C. Lamina-associated polypeptide 2α (LAP2α) localizes throughout the nucleoplasm and interacts with the fraction of lamins A/C that is not associated with the peripheral nuclear lamina. The LAP2α–lamin A/C complex negatively affects cell proliferation. Lamins A/C are encoded by LMNA, a single heterozygous mutation of which causes Hutchinson-Gilford progeria syndrome (HGPS). This mutation generates the lamin A variant progerin, which we show here leads to loss of LAP2α and nucleoplasmic lamins A/C, impaired proliferation, and down-regulation of extracellular matrix components. Surprisingly, contrary to wild-type cells, ectopic expression of LAP2α in cells expressing progerin restores proliferation and extracellular matrix expression but not the levels of nucleoplasmic lamins A/C. We conclude that, in addition to its cell cycle-inhibiting function with lamins A/C, LAP2α can also regulate extracellular matrix components independently of lamins A/C, which may help explain the proliferation-promoting function of LAP2α in cells expressing progerin.
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Affiliation(s)
- Sandra Vidak
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Nard Kubben
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas Dechat
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories (MFPL), Department of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), A-1030 Vienna, Austria
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11
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Lackner DH, Carré A, Guzzardo PM, Banning C, Mangena R, Henley T, Oberndorfer S, Gapp BV, Nijman SM, Brummelkamp TR, Bürckstümmer T. A generic strategy for CRISPR-Cas9-mediated gene tagging. Nat Commun 2015; 6:10237. [PMID: 26674669 PMCID: PMC4703899 DOI: 10.1038/ncomms10237] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/20/2015] [Indexed: 02/06/2023] Open
Abstract
Genome engineering has been greatly enhanced by the availability of Cas9 endonuclease that can be targeted to almost any genomic locus using so called guide RNAs (gRNAs). However, the introduction of foreign DNA sequences to tag an endogenous gene is still cumbersome as it requires the synthesis or cloning of homology templates. Here we present a strategy that enables the tagging of endogenous loci using one generic donor plasmid. It contains the tag of interest flanked by two gRNA recognition sites that allow excision of the tag from the plasmid. Co-transfection of cells with Cas9, a gRNA specifying the genomic locus of interest, the donor plasmid and a cassette-specific gRNA triggers the insertion of the tag by a homology-independent mechanism. The strategy is efficient and delivers clones that display a predictable integration pattern. As showcases we generated NanoLuc luciferase- and TurboGFP-tagged reporter cell lines.
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Affiliation(s)
| | - Alexia Carré
- Horizon Genomics, Campus Vienna Biocenter 3, 1030 Vienna, Austria
| | | | - Carina Banning
- Horizon Genomics, Campus Vienna Biocenter 3, 1030 Vienna, Austria
| | - Ramu Mangena
- Horizon Discovery, 7100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | - Tom Henley
- Horizon Discovery, 7100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | | | - Bianca V. Gapp
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sebastian M.B. Nijman
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
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12
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Generation of MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes. Proc Natl Acad Sci U S A 2015. [PMID: 26216968 DOI: 10.1073/pnas.1511996112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mutant epitopes encoded by cancer genes are virtually always located in the interior of cells, making them invisible to conventional antibodies. We here describe an approach to identify single-chain variable fragments (scFvs) specific for mutant peptides presented on the cell surface by HLA molecules. We demonstrate that these scFvs can be successfully converted to full-length antibodies, termed MANAbodies, targeting "Mutation-Associated Neo-Antigens" bound to HLA. A phage display library representing a highly diverse array of single-chain variable fragment sequences was first designed and constructed. A competitive selection protocol was then used to identify clones specific for mutant peptides bound to predefined HLA types. In this way, we obtained two scFvs, one specific for a peptide encoded by a common KRAS mutant and the other by a common epidermal growth factor receptor (EGFR) mutant. The scFvs bound to these peptides only when the peptides were complexed with HLA-A2 (KRAS peptide) or HLA-A3 (EGFR peptide). We converted one scFv to a full-length antibody (MANAbody) and demonstrate that the MANAbody specifically reacts with mutant peptide-HLA complex even when the peptide differs by only one amino acid from the normal, WT form.
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13
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Rosner M, Schipany K, Hengstschläger M. Merging high-quality biochemical fractionation with a refined flow cytometry approach to monitor nucleocytoplasmic protein expression throughout the unperturbed mammalian cell cycle. Nat Protoc 2013; 8:602-26. [DOI: 10.1038/nprot.2013.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Pilat U, Dechat T, Bertrand AT, Woisetschläger N, Gotic I, Spilka R, Biadasiewicz K, Bonne G, Foisner R. The muscle dystrophy-causing ΔK32 lamin A/C mutant does not impair the functions of the nucleoplasmic lamin-A/C-LAP2α complex in mice. J Cell Sci 2013; 126:1753-62. [PMID: 23444379 DOI: 10.1242/jcs.115246] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A-type lamins are components of the nuclear lamina, a filamentous network of the nuclear envelope in metazoans that supports nuclear architecture. In addition, lamin A/C can also be found in the interior of the nucleus. This nucleoplasmic lamin pool is soluble in physiological buffer, depends on the presence of the lamin-binding protein, lamina-associated polypeptide 2α (LAP2α) and regulates cell cycle progression in tissue progenitor cells. ΔK32 mutations in A-type lamins cause severe congenital muscle disease in humans and a muscle maturation defect in Lmna(ΔK32/ΔK32) knock-in mice. Mutant ΔK32 lamin A/C protein levels were reduced and all mutant lamin A/C was soluble and mislocalized to the nucleoplasm. To test the role of LAP2α in nucleoplasmic ΔK32 lamin A/C regulation and functions, we deleted LAP2α in Lmna(ΔK32/ΔK32) knock-in mice. In double mutant mice the Lmna(ΔK32/ΔK32)-linked muscle defect was unaffected. LAP2α interacted with mutant lamin A/C, but unlike wild-type lamin A/C, the intranuclear localization of ΔK32 lamin A/C was not affected by loss of LAP2α. In contrast, loss of LAP2α in Lmna(ΔK32/ΔK32) mice impaired the regulation of tissue progenitor cells as in lamin A/C wild-type animals. These data indicate that a LAP2α-independent assembly defect of ΔK32 lamin A/C is the predominant cause of the mouse pathology, whereas the LAP2α-linked functions of nucleoplasmic lamin A/C in the regulation of tissue progenitor cells are not affected in Lmna(ΔK32/ΔK32) mice.
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Affiliation(s)
- Ursula Pilat
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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Goulbourne CN, Malhas AN, Vaux DJ. The induction of a nucleoplasmic reticulum by prelamin A accumulation requires CTP:phosphocholine cytidylyltransferase-α. J Cell Sci 2011; 124:4253-66. [PMID: 22223883 PMCID: PMC3258109 DOI: 10.1242/jcs.091009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2011] [Indexed: 12/24/2022] Open
Abstract
Farnesylated prelamin A accumulates when the final endoproteolytic maturation of the protein fails to occur and causes a dysmorphic nuclear phenotype; however, the morphology and mechanisms of biogenesis of these changes remain unclear. We show here that acute prelamin A accumulation after reduction in the activity of the ZMPSTE24 endoprotease by short interfering RNA knockdown, results in the generation of a complex nucleoplasmic reticulum that depends for its formation on the enzyme CTP:phosphocholine-cytidylyltransferase-α (CCT-α, also known as choline-phosphate cytidylyltransferase A). This structure can form during interphase, confirming that it is independent of mitosis and therefore not a consequence of disordered nuclear envelope assembly. Serial-section dual-axis electron tomography reveals that these invaginations can take two forms: one in which the inner nuclear membrane infolds alone with an inter membrane space interior, and the other in which an invagination of both nuclear membranes occurs, enclosing a cytoplasmic core. Both types of invagination can co-exist in one nucleus and both are frequently studded with nuclear pore complexes (NPC), which reduces NPC abundance on the nuclear surface.
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Affiliation(s)
- Chris N. Goulbourne
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ashraf N. Malhas
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - David J. Vaux
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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Malhas A, Goulbourne C, Vaux DJ. The nucleoplasmic reticulum: form and function. Trends Cell Biol 2011; 21:362-73. [PMID: 21514163 DOI: 10.1016/j.tcb.2011.03.008] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/17/2011] [Accepted: 03/23/2011] [Indexed: 11/29/2022]
Abstract
The nuclear envelope (NE) physically separates nucleoplasm and cytoplasm, contributes to nuclear structural integrity, controls selective bidirectional transport of ions and macromolecular cargo, regulates gene expression, and acts as a mechanotransducer and a platform for signalling. It is noteworthy however that the NE is not simply a smooth-surfaced outer boundary but is interrupted by invaginations that reach deep within the nucleoplasm and could even traverse the nucleus completely. The existence of such a complex branched network of invaginations forming a nucleoplasmic reticulum (NR) provides sites that are capable of carrying out the 'conventional' NE functions deep within the nucleus in regions that would otherwise be remote from the nuclear periphery. In this review, we describe the structural features of NR in normal and pathological states and discuss the current understanding of their functional and possible pathological roles.
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Affiliation(s)
- Ashraf Malhas
- Sir William Dunn School of Pathology, Oxford OX1 3RE, UK
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