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de Las Heras JI, Todorow V, Krečinić-Balić L, Hintze S, Czapiewski R, Webb S, Schoser B, Meinke P, Schirmer EC. Metabolic, fibrotic and splicing pathways are all altered in Emery-Dreifuss muscular dystrophy spectrum patients to differing degrees. Hum Mol Genet 2023; 32:1010-1031. [PMID: 36282542 PMCID: PMC9991002 DOI: 10.1093/hmg/ddac264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/16/2022] [Accepted: 10/20/2022] [Indexed: 11/14/2022] Open
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is a genetically and clinically variable disorder. Previous attempts to use gene expression changes to find its pathomechanism were unavailing, so we engaged a functional pathway analysis. RNA-Seq was performed on cells from 10 patients diagnosed with an EDMD spectrum disease with different mutations in seven genes. Upon comparing to controls, the pathway analysis revealed that multiple genes involved in fibrosis, metabolism, myogenic signaling and splicing were affected in all patients. Splice variant analysis revealed alterations of muscle-specific variants for several important muscle genes. Deeper analysis of metabolic pathways revealed a reduction in glycolytic and oxidative metabolism and reduced numbers of mitochondria across a larger set of 14 EDMD spectrum patients and 7 controls. Intriguingly, the gene expression signatures segregated the patients into three subgroups whose distinctions could potentially relate to differences in clinical presentation. Finally, differential expression analysis of miRNAs changing in the patients similarly highlighted fibrosis, metabolism and myogenic signaling pathways. This pathway approach revealed a transcriptome profile that can both be used as a template for establishing a biomarker panel for EDMD and direct further investigation into its pathomechanism. Furthermore, the segregation of specific gene changes into distinct groups that appear to correlate with clinical presentation may template development of prognostic biomarkers, though this will first require their testing in a wider set of patients with more clinical information.
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Affiliation(s)
| | - Vanessa Todorow
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Lejla Krečinić-Balić
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Stefan Hintze
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benedikt Schoser
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Peter Meinke
- Friedrich-Baur-Institute, Department of Neurology, LMU Clinic, Ludwig-Maximillians-University, Munich, Germany
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
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2
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Czapiewski R, Batrakou DG, de Las Heras JI, Carter RN, Sivakumar A, Sliwinska M, Dixon CR, Webb S, Lattanzi G, Morton NM, Schirmer EC. Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy. Nat Commun 2022; 13:321. [PMID: 35027552 PMCID: PMC8758788 DOI: 10.1038/s41467-021-27869-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/19/2021] [Indexed: 12/13/2022] Open
Abstract
Little is known about how the observed fat-specific pattern of 3D-spatial genome organisation is established. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope transmembrane protein Tmem120a disrupts fat genome organisation, thus causing a lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior. Tmem120a-/- mice, particularly females, exhibit a lipodystrophy syndrome similar to human familial partial lipodystrophy FPLD2, with profound insulin resistance and metabolic defects that manifest upon exposure to an obesogenic diet. Interestingly, similar genome organisation defects occurred in cells from FPLD2 patients that harbour nuclear envelope protein encoding LMNA mutations. Our data indicate TMEM120A genome organisation functions affect many adipose functions and its loss may yield adiposity spectrum disorders, including a miRNA-based mechanism that could explain muscle hypertrophy in human lipodystrophy.
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Affiliation(s)
- Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Dzmitry G Batrakou
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | | | - Roderick N Carter
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | | | | | - Charles R Dixon
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Giovanna Lattanzi
- CNR - National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, 40136, Italy
- IRCCS, Istituto Ortopedico Rizzoli, Bologna, 40136, Italy
| | - Nicholas M Morton
- Molecular Metabolism Group, University/BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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3
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Mudumbi KC, Czapiewski R, Ruba A, Junod SL, Li Y, Luo W, Ngo C, Ospina V, Schirmer EC, Yang W. Nucleoplasmic signals promote directed transmembrane protein import simultaneously via multiple channels of nuclear pores. Nat Commun 2020; 11:2184. [PMID: 32366843 PMCID: PMC7198523 DOI: 10.1038/s41467-020-16033-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Roughly 10% of eukaryotic transmembrane proteins are found on the nuclear membrane, yet how such proteins target and translocate to the nucleus remains in dispute. Most models propose transport through the nuclear pore complexes, but a central outstanding question is whether transit occurs through their central or peripheral channels. Using live-cell high-speed super-resolution single-molecule microscopy we could distinguish protein translocation through the central and peripheral channels, finding that most inner nuclear membrane proteins use only the peripheral channels, but some apparently extend intrinsically disordered domains containing nuclear localization signals into the central channel for directed nuclear transport. These nucleoplasmic signals are critical for central channel transport as their mutation blocks use of the central channels; however, the mutated proteins can still complete their translocation using only the peripheral channels, albeit at a reduced rate. Such proteins can still translocate using only the peripheral channels when central channel is blocked, but blocking the peripheral channels blocks translocation through both channels. This suggests that peripheral channel transport is the default mechanism that was adapted in evolution to include aspects of receptor-mediated central channel transport for directed trafficking of certain membrane proteins.
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Affiliation(s)
- Krishna C Mudumbi
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.
| | - Rafal Czapiewski
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Yichen Li
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Wangxi Luo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Christina Ngo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Valentina Ospina
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Eric C Schirmer
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
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4
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Meinke P, Kerr ARW, Czapiewski R, de Las Heras JI, Dixon CR, Harris E, Kölbel H, Muntoni F, Schara U, Straub V, Schoser B, Wehnert M, Schirmer EC. A multistage sequencing strategy pinpoints novel candidate alleles for Emery-Dreifuss muscular dystrophy and supports gene misregulation as its pathomechanism. EBioMedicine 2019; 51:102587. [PMID: 31862442 PMCID: PMC7000448 DOI: 10.1016/j.ebiom.2019.11.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 12/27/2022] Open
Abstract
Background As genome-wide approaches prove difficult with genetically heterogeneous orphan diseases, we developed a new approach to identify candidate genes. We applied this to Emery-Dreifuss muscular dystrophy (EDMD), characterised by early onset contractures, slowly progressive muscular wasting, and life-threatening heart conduction disturbances with wide intra- and inter-familial clinical variability. Roughly half of EDMD patients are linked to six genes encoding nuclear envelope proteins, but the disease mechanism remains unclear because the affected proteins function in both cell mechanics and genome regulation. Methods A primer library was generated to test for mutations in 301 genes from four categories: (I) all known EDMD-linked genes; (II) genes mutated in related muscular dystrophies; (III) candidates generated by exome sequencing in five families; (IV) functional candidates — other muscle nuclear envelope proteins functioning in mechanical/genome processes affected in EDMD. This was used to sequence 56 unlinked patients with EDMD-like phenotype. Findings Twenty-one patients could be clearly assigned: 18 with mutations in genes of similar muscular dystrophies; 3 with previously missed mutations in EDMD-linked genes. The other categories yielded novel candidate genes, most encoding nuclear envelope proteins with functions in gene regulation. Interpretation Our multi-pronged approach identified new disease alleles and many new candidate EDMD genes. Their known functions strongly argue the EDMD pathomechanism is from altered gene regulation and mechanotransduction due to connectivity of candidates from the nuclear envelope to the plasma membrane. This approach highlights the value of testing for related diseases using primer libraries and may be applied for other genetically heterogeneous orphan diseases. Funding The Wellcome Trust, Muscular Dystrophy UK, Medical Research Council, European Community's Seventh Framework Programme “Integrated European –omics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)”.
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Affiliation(s)
- Peter Meinke
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Friedrich Baur Institute at the Department of Neurology, University Hospital, LMU Munich, Germany
| | - Alastair R W Kerr
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rafal Czapiewski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Charles R Dixon
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Elizabeth Harris
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Heike Kölbel
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London Great Ormond Street Institute of Child Health, London, UK; 1 NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Ulrike Schara
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Benedikt Schoser
- Friedrich Baur Institute at the Department of Neurology, University Hospital, LMU Munich, Germany
| | - Manfred Wehnert
- Institute of Human Genetics, University of Greifswald (retired), Greifswald, Germany
| | - Eric C Schirmer
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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5
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Robson MI, de Las Heras JI, Czapiewski R, Sivakumar A, Kerr ARW, Schirmer EC. Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res 2017; 27:1126-1138. [PMID: 28424353 PMCID: PMC5495065 DOI: 10.1101/gr.212308.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 04/12/2017] [Indexed: 01/15/2023]
Abstract
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome reorganization at the nuclear periphery dominated by release of loci frequently important for T-cell function. To assess how these changes at the nuclear periphery influence wider genome organization, our DamID data sets were contrasted with TADs and compartments. Features of specific repositioning events were then tested by fluorescence in situ hybridization during T-cell activation. First, considerable overlap between TADs and LADs was observed with the TAD repositioning as a unit. Second, A1 and A2 subcompartments are segregated in 3D space through differences in proximity to LADs along chromosomes. Third, genes and a putative enhancer in LADs that were released from the periphery during T-cell activation became preferentially associated with A2 subcompartments and were constrained to the relative proximity of the lamina. Thus, lamina associations influence internal nuclear organization, and changes in LADs during T-cell activation may provide an important additional mode of gene regulation.
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Affiliation(s)
- Michael I Robson
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jose I de Las Heras
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Rafal Czapiewski
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Aishwarya Sivakumar
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Alastair R W Kerr
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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6
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de Las Heras JI, Zuleger N, Batrakou DG, Czapiewski R, Kerr ARW, Schirmer EC. Tissue-specific NETs alter genome organization and regulation even in a heterologous system. Nucleus 2017; 8:81-97. [PMID: 28045568 PMCID: PMC5287206 DOI: 10.1080/19491034.2016.1261230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Different cell types exhibit distinct patterns of 3D genome organization that correlate with changes in gene expression in tissue and differentiation systems. Several tissue-specific nuclear envelope transmembrane proteins (NETs) have been found to influence the spatial positioning of genes and chromosomes that normally occurs during tissue differentiation. Here we study 3 such NETs: NET29, NET39, and NET47, which are expressed preferentially in fat, muscle and liver, respectively. We found that even when exogenously expressed in a heterologous system they can specify particular genome organization patterns and alter gene expression. Each NET affected largely different subsets of genes. Notably, the liver-specific NET47 upregulated many genes in HT1080 fibroblast cells that are normally upregulated in hepatogenesis, showing that tissue-specific NETs can favor expression patterns associated with the tissue where the NET is normally expressed. Similarly, global profiling of peripheral chromatin after exogenous expression of these NETs using lamin B1 DamID revealed that each NET affected the nuclear positioning of distinct sets of genomic regions with a significant tissue-specific component. Thus NET influences on genome organization can contribute to gene expression changes associated with differentiation even in the absence of other factors and overt cellular differentiation changes.
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Affiliation(s)
- Jose I de Las Heras
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Nikolaj Zuleger
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Dzmitry G Batrakou
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Rafal Czapiewski
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Alastair R W Kerr
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Trust Centre for Cell Biology , University of Edinburgh , Edinburgh , UK
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7
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Miwa S, Czapiewski R, Wan T, Bell A, Hill KN, von Zglinicki T, Saretzki G. Decreased mTOR signalling reduces mitochondrial ROS in brain via accumulation of the telomerase protein TERT within mitochondria. Aging (Albany NY) 2016; 8:2551-2567. [PMID: 27777385 PMCID: PMC5115906 DOI: 10.18632/aging.101089] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/02/2016] [Indexed: 01/11/2023]
Abstract
Telomerase in its canonical function maintains telomeres in dividing cells. In addition, the telomerase protein TERT has non-telomeric functions such as shuttling to mitochondria resulting in a decreased oxidative stress, DNA damage and apoptosis. TERT protein persists in adult neurons and can co-localise to mitochondria under various stress conditions. We show here that TERT expression decreased in mouse brain during aging while release of reactive oxygen species (ROS) from the mitochondrial electron transport chain increased. Dietary restriction (DR) caused accumulation of TERT protein in mouse brain mitochondria correlating to decreased ROS release and improved learning and spatial short-term memory. Decreased mTOR signalling is a mediator of DR. Accordingly, feeding mice with rapamycin increased brain mitochondrial TERT and reduced ROS release. Importantly, the beneficial effects of rapamycin on mitochondrial function were absent in brains and fibroblasts from first generation TERT -/- mice, and when TERT shuttling was inhibited by the Src kinase inhibitor bosutinib. Taken together, our data suggests that the mTOR signalling pathway impinges on the mitochondrial localisation of TERT protein, which might in turn contribute to the protection of the brain by DR or rapamycin against age-associated mitochondrial ROS increase and cognitive decline.
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Affiliation(s)
- Satomi Miwa
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Rafal Czapiewski
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Tengfei Wan
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Amy Bell
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Kirsten N. Hill
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Thomas von Zglinicki
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - Gabriele Saretzki
- Institute for Cell and Molecular Biosciences, Newcastle Institute for Ageing, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
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8
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Robson MI, de Las Heras JI, Czapiewski R, Lê Thành P, Booth DG, Kelly DA, Webb S, Kerr ARW, Schirmer EC. Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis. Mol Cell 2016; 62:834-847. [PMID: 27264872 PMCID: PMC4914829 DOI: 10.1016/j.molcel.2016.04.035] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/21/2015] [Accepted: 04/28/2016] [Indexed: 12/28/2022]
Abstract
Whether gene repositioning to the nuclear periphery during differentiation adds another layer of regulation to gene expression remains controversial. Here, we resolve this by manipulating gene positions through targeting the nuclear envelope transmembrane proteins (NETs) that direct their normal repositioning during myogenesis. Combining transcriptomics with high-resolution DamID mapping of nuclear envelope-genome contacts, we show that three muscle-specific NETs, NET39, Tmem38A, and WFS1, direct specific myogenic genes to the nuclear periphery to facilitate their repression. Retargeting a NET39 fragment to nucleoli correspondingly repositioned a target gene, indicating a direct tethering mechanism. Being able to manipulate gene position independently of other changes in differentiation revealed that repositioning contributes ⅓ to ⅔ of a gene’s normal repression in myogenesis. Together, these NETs affect 37% of all genes changing expression during myogenesis, and their combined knockdown almost completely blocks myotube formation. This unequivocally demonstrates that NET-directed gene repositioning is critical for developmental gene regulation. Tissue-specific NETs direct repositioning of critical muscle genes during myogenesis Expression changes for NET-repositioned genes depend on cell differentiation state Isolating position from differentiation reveals its contribution to gene expression Three NETs together affect 37% of all genes normally changing in myogenesis
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Affiliation(s)
- Michael I Robson
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jose I de Las Heras
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Rafal Czapiewski
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Phú Lê Thành
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Daniel G Booth
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David A Kelly
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Shaun Webb
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alastair R W Kerr
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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9
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Abstract
It is well established that the nuclear envelope has many distinct direct connections to chromatin that contribute to genome organization. The functional consequences of genome organization on gene regulation are less clear. Even less understood is how interactions of lamins and nuclear envelope transmembrane proteins (NETs) with chromatin can produce anchoring tethers that can withstand the physical forces of and on the genome. Chromosomes are the largest molecules in the cell, making megadalton protein structures like the nuclear pore complexes and ribosomes seem small by comparison. Thus to withstand strong forces from chromosome dynamics an anchoring tether is likely to be much more complex than a single protein-protein or protein-DNA interaction. Here we will briefly review known NE-genome interactions that likely contribute to spatial genome organization, postulate in the context of experimental data how these anchoring tethers contribute to gene regulation, and posit several hypotheses for the physical nature of these tethers that need to be investigated experimentally. Significantly, disruption of these anchoring tethers and the subsequent consequences for gene regulation could explain how mutations in nuclear envelope proteins cause diseases ranging from muscular dystrophy to lipodystrophy to premature aging progeroid syndromes. The two favored hypotheses for nuclear envelope protein involvement in disease are (1) weakening nuclear and cellular mechanical stability, and (2) disrupting genome organization and gene regulation. Considerable experimental support has been obtained for both. The integration of both mechanical and gene expression defects in the disruption of anchoring tethers could provide a unifying hypothesis consistent with both.
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Affiliation(s)
- Rafal Czapiewski
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh Edinburgh, UK
| | - Michael I Robson
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh Edinburgh, UK
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh Edinburgh, UK
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10
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Correia-Melo C, Marques FDM, Anderson R, Hewitt G, Hewitt R, Cole J, Carroll BM, Miwa S, Birch J, Merz A, Rushton MD, Charles M, Jurk D, Tait SWG, Czapiewski R, Greaves L, Nelson G, Bohlooly-Y M, Rodriguez-Cuenca S, Vidal-Puig A, Mann D, Saretzki G, Quarato G, Green DR, Adams PD, von Zglinicki T, Korolchuk VI, Passos JF. Mitochondria are required for pro-ageing features of the senescent phenotype. EMBO J 2016; 35:724-42. [PMID: 26848154 PMCID: PMC4818766 DOI: 10.15252/embj.201592862] [Citation(s) in RCA: 442] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/12/2016] [Indexed: 01/07/2023] Open
Abstract
Cell senescence is an important tumour suppressor mechanism and driver of ageing. Both functions are dependent on the development of the senescent phenotype, which involves an overproduction of pro‐inflammatory and pro‐oxidant signals. However, the exact mechanisms regulating these phenotypes remain poorly understood. Here, we show the critical role of mitochondria in cellular senescence. In multiple models of senescence, absence of mitochondria reduced a spectrum of senescence effectors and phenotypes while preserving ATP production via enhanced glycolysis. Global transcriptomic analysis by RNA sequencing revealed that a vast number of senescent‐associated changes are dependent on mitochondria, particularly the pro‐inflammatory phenotype. Mechanistically, we show that the ATM, Akt and mTORC1 phosphorylation cascade integrates signals from the DNA damage response (DDR) towards PGC‐1β‐dependent mitochondrial biogenesis, contributing to a ROS‐mediated activation of the DDR and cell cycle arrest. Finally, we demonstrate that the reduction in mitochondrial content in vivo, by either mTORC1 inhibition or PGC‐1β deletion, prevents senescence in the ageing mouse liver. Our results suggest that mitochondria are a candidate target for interventions to reduce the deleterious impact of senescence in ageing tissues.
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Affiliation(s)
- Clara Correia-Melo
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK GABBA Program, Abel Salazar Biomedical Sciences Institute University of Porto, Porto, Portugal
| | - Francisco D M Marques
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Rhys Anderson
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Graeme Hewitt
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Rachael Hewitt
- Institute of Cancer Sciences, CR-UK Beatson Institute, University of Glasgow, Glasgow, UK
| | - John Cole
- Institute of Cancer Sciences, CR-UK Beatson Institute, University of Glasgow, Glasgow, UK
| | - Bernadette M Carroll
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Satomi Miwa
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Jodie Birch
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Alina Merz
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Michael D Rushton
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Michelle Charles
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Diana Jurk
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Stephen W G Tait
- Institute of Cancer Sciences, CR-UK Beatson Institute, University of Glasgow, Glasgow, UK
| | - Rafal Czapiewski
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Greaves
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University Centre for Brain Ageing and Vitality, Newcastle University, Newcastle upon Tyne, UK
| | - Glyn Nelson
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | | | - Sergio Rodriguez-Cuenca
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Derek Mann
- Faculty of Medical Sciences, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Gabriele Saretzki
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Giovanni Quarato
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter D Adams
- Institute of Cancer Sciences, CR-UK Beatson Institute, University of Glasgow, Glasgow, UK
| | - Thomas von Zglinicki
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Viktor I Korolchuk
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - João F Passos
- Institute for Cell and Molecular Biosciences, Campus for Ageing and Vitality, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
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11
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Batrakou DG, de las Heras JI, Czapiewski R, Mouras R, Schirmer EC. TMEM120A and B: Nuclear Envelope Transmembrane Proteins Important for Adipocyte Differentiation. PLoS One 2015; 10:e0127712. [PMID: 26024229 PMCID: PMC4449205 DOI: 10.1371/journal.pone.0127712] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/17/2015] [Indexed: 12/23/2022] Open
Abstract
Recent work indicates that the nuclear envelope is a major signaling node for the cell that can influence tissue differentiation processes. Here we present two nuclear envelope trans-membrane proteins TMEM120A and TMEM120B that are paralogs encoded by the Tmem120A and Tmem120B genes. The TMEM120 proteins are expressed preferentially in fat and both are induced during 3T3-L1 adipocyte differentiation. Knockdown of one or the other protein altered expression of several genes required for adipocyte differentiation, Gata3, Fasn, Glut4, while knockdown of both together additionally affected Pparg and Adipoq. The double knockdown also increased the strength of effects, reducing for example Glut4 levels by 95% compared to control 3T3-L1 cells upon pharmacologically induced differentiation. Accordingly, TMEM120A and B knockdown individually and together impacted on adipocyte differentiation/metabolism as measured by lipid accumulation through binding of Oil Red O and coherent anti-Stokes Raman scattering microscopy (CARS). The nuclear envelope is linked to several lipodystrophies through mutations in lamin A; however, lamin A is widely expressed. Thus it is possible that the TMEM120A and B fat-specific nuclear envelope transmembrane proteins may play a contributory role in the tissue-specific pathology of this disorder or in the wider problem of obesity.
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Affiliation(s)
- Dzmitry G. Batrakou
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Jose I. de las Heras
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rafal Czapiewski
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rabah Mouras
- Institute for Materials and Processes, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Eric C. Schirmer
- Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- * E-mail:
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12
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Yu JSL, Ramasamy TS, Murphy N, Holt MK, Czapiewski R, Wei SK, Cui W. PI3K/mTORC2 regulates TGF-β/Activin signalling by modulating Smad2/3 activity via linker phosphorylation. Nat Commun 2015; 6:7212. [PMID: 25998442 PMCID: PMC4455068 DOI: 10.1038/ncomms8212] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/20/2015] [Indexed: 11/27/2022] Open
Abstract
Crosstalk between the phosphatidylinositol 3-kinase (PI3K) and the transforming growth factor-β signalling pathways play an important role in regulating many cellular functions. However, the molecular mechanisms underpinning this crosstalk remain unclear. Here, we report that PI3K signalling antagonizes the Activin-induced definitive endoderm (DE) differentiation of human embryonic stem cells by attenuating the duration of Smad2/3 activation via the mechanistic target of rapamycin complex 2 (mTORC2). Activation of mTORC2 regulates the phosphorylation of the Smad2/3-T220/T179 linker residue independent of Akt, CDK and Erk activity. This phosphorylation primes receptor-activated Smad2/3 for recruitment of the E3 ubiquitin ligase Nedd4L, which in turn leads to their degradation. Inhibition of PI3K/mTORC2 reduces this phosphorylation and increases the duration of Smad2/3 activity, promoting a more robust mesendoderm and endoderm differentiation. These findings present a new and direct crosstalk mechanism between these two pathways in which mTORC2 functions as a novel and critical mediator. Although crosstalk between the phosphatidylinositol 3-kinase (PI3K) and transforming growth factor-β pathways is important, the mechanism is obscure. Here, Yu et al. show that activation of mTORC2 downstream of PI3K leads to the linker phosphorylation of Smad2/3 and their ubiquitin-dependent degradation.
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Affiliation(s)
- Jason S L Yu
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Thamil Selvee Ramasamy
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Nick Murphy
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Marie K Holt
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Rafal Czapiewski
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Shi-Khai Wei
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Wei Cui
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Imperial College London, Du Cane Road, London W12 0NN, UK
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13
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Singhapol C, Pal D, Czapiewski R, Porika M, Nelson G, Saretzki GC. Mitochondrial telomerase protects cancer cells from nuclear DNA damage and apoptosis. PLoS One 2013; 8:e52989. [PMID: 23326372 PMCID: PMC3541395 DOI: 10.1371/journal.pone.0052989] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/27/2012] [Indexed: 12/31/2022] Open
Abstract
Most cancer cells express high levels of telomerase and proliferate indefinitely. In addition to its telomere maintenance function, telomerase also has a pro-survival function resulting in an increased resistance against DNA damage and decreased apoptosis induction. However, the molecular mechanisms for this protective function remain elusive and it is unclear whether it is connected to telomere maintenance or is rather a non-telomeric function of the telomerase protein, TERT. It was shown recently that the protein subunit of telomerase can shuttle from the nucleus to the mitochondria upon oxidative stress where it protects mitochondrial function and decreases intracellular oxidative stress. Here we show that endogenous telomerase (TERT protein) shuttles from the nucleus into mitochondria upon oxidative stress in cancer cells and analyzed the nuclear exclusion patterns of endogenous telomerase after treatment with hydrogen peroxide in different cell lines. Cell populations excluded TERT from the nucleus upon oxidative stress in a heterogeneous fashion. We found a significant correlation between nuclear localization of telomerase and high DNA damage, while cells which excluded telomerase from the nucleus displayed no or very low DNA damage. We modeled nuclear and mitochondrial telomerase using organelle specific localization vectors and confirmed that mitochondrial localization of telomerase protects the nucleus from inflicted DNA damage and apoptosis while, in contrast, nuclear localization of telomerase correlated with higher amounts of DNA damage and apoptosis. It is known that nuclear DNA damage can be caused by mitochondrially generated reactive oxygen species (ROS). We demonstrate here that mitochondrial localization of telomerase specifically prevents nuclear DNA damage by decreasing levels of mitochondrial ROS. We suggest that this decrease of oxidative stress might be a possible cause for high stress resistance of cancer cells and could be especially important for cancer stem cells.
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Affiliation(s)
- Chatchawan Singhapol
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Deepali Pal
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafal Czapiewski
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mahendar Porika
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Glyn Nelson
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gabriele C. Saretzki
- Institute for Ageing and Health, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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14
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Wang C, Maddick M, Miwa S, Jurk D, Czapiewski R, Saretzki G, Langie SAS, Godschalk RWL, Cameron K, von Zglinicki T. Adult-onset, short-term dietary restriction reduces cell senescence in mice. Aging (Albany NY) 2011; 2:555-66. [PMID: 20844316 PMCID: PMC2984605 DOI: 10.18632/aging.100196] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dietary restriction (DR) extends the lifespan of a wide variety of species and reduces the incidence of major age-related diseases. Cell senescence has been proposed as one causal mechanism for tissue and organism ageing. We show for the first time that adult-onset, short-term DR reduced frequencies of senescent cells in the small intestinal epithelium and liver of mice, which are tissues known to accumulate increased numbers of senescent cells with advancing age. This reduction was associated with improved telomere maintenance without increased telomerase activity. We also found a decrease in cumulative oxidative stress markers in the same compartments despite absence of significant changes in steady-state oxidative stress markers at the whole tissue level. The data suggest the possibility that reduction of cell senescence may be a primary consequence of DR which in turn may explain known effects of DR such as improved mitochondrial function and reduced production of reactive oxygen species.
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Affiliation(s)
- Chunfang Wang
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Newcastle Upon Tyne, UK
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