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Czapiewski R, Schirmer EC. Enhancers on the edge - how the nuclear envelope controls gene regulatory elements. Curr Opin Genet Dev 2024; 87:102234. [PMID: 39047586 DOI: 10.1016/j.gde.2024.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/20/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Precise temporal and sequential control of gene expression during development and in response to environmental stimuli requires tight regulation of the physical contact between gene regulatory elements and promoters. Current models describing how the genome folds in 3D space to establish these interactions often ignore the role of the most stable structural nuclear feature - the nuclear envelope. While contributions of 3D folding within/between topologically associated domains (TADs) have been extensively described, mechanical contributions from the nuclear envelope can impact enhancer-promoter interactions both directly and indirectly through influencing intra/inter-TAD interactions. Importantly, these nuclear envelope contributions clearly link this mechanism to development and, when defective, to human disease. Here, we discuss evidence for nuclear envelope regulation of tissue-specific enhancer-promoter pairings, potential mechanisms for this regulation, exciting recent findings that other regulatory elements such as microRNAs and long noncoding RNAs are under nuclear envelope regulation, the possible involvement of condensates, and how disruption of this regulation can lead to disease.
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Affiliation(s)
- Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.
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2
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Schätzl T, Todorow V, Kaiser L, Weinschrott H, Schoser B, Deigner HP, Meinke P, Kohl M. Meta-analysis towards FSHD reveals misregulation of neuromuscular junction, nuclear envelope, and spliceosome. Commun Biol 2024; 7:640. [PMID: 38796645 PMCID: PMC11127974 DOI: 10.1038/s42003-024-06325-z] [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: 10/04/2023] [Accepted: 05/13/2024] [Indexed: 05/28/2024] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common autosomal dominant muscle disorders, yet no cure or amelioration exists. The clinical presentation is diverse, making it difficult to identify the actual driving pathomechanism among many downstream events. To unravel this complexity, we performed a meta-analysis of 13 original omics datasets (in total 171 FSHD and 129 control samples). Our approach confirmed previous findings about the disease pathology and specified them further. We confirmed increased expression of former proposed DUX4 biomarkers, and furthermore impairment of the respiratory chain. Notably, the meta-analysis provides insights about so far not reported pathways, including misregulation of neuromuscular junction protein encoding genes, downregulation of the spliceosome, and extensive alterations of nuclear envelope protein expression. Finally, we developed a publicly available shiny app to provide a platform for researchers who want to search our analysis for genes of interest in the future.
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Affiliation(s)
- Teresa Schätzl
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Vanessa Todorow
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Helga Weinschrott
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
| | - Benedikt Schoser
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany
- Faculty of Science, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Rostock, Germany
| | - Peter Meinke
- Friedrich-Baur-Institute at the Department of Neurology, LMU University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Matthias Kohl
- Institute of Precision Medicine, Furtwangen University, Furtwangen, Germany.
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3
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Stoyek MR, Doane SE, Dallaire SE, Long ZD, Ramia JM, Cassidy-Nolan DL, Poon KL, Brand T, Quinn TA. POPDC1 Variants Cause Atrioventricular Node Dysfunction and Arrhythmogenic Changes in Cardiac Electrophysiology and Intracellular Calcium Handling in Zebrafish. Genes (Basel) 2024; 15:280. [PMID: 38540339 PMCID: PMC10969970 DOI: 10.3390/genes15030280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 06/15/2024] Open
Abstract
Popeye domain-containing (POPDC) proteins selectively bind cAMP and mediate cellular responses to sympathetic nervous system (SNS) stimulation. The first discovered human genetic variant (POPDC1S201F) is associated with atrioventricular (AV) block, which is exacerbated by increased SNS activity. Zebrafish carrying the homologous mutation (popdc1S191F) display a similar phenotype to humans. To investigate the impact of POPDC1 dysfunction on cardiac electrophysiology and intracellular calcium handling, homozygous popdc1S191F and popdc1 knock-out (popdc1KO) zebrafish larvae and adult isolated popdc1S191F hearts were studied by functional fluorescent analysis. It was found that in popdc1S191F and popdc1KO larvae, heart rate (HR), AV delay, action potential (AP) and calcium transient (CaT) upstroke speed, and AP duration were less than in wild-type larvae, whereas CaT duration was greater. SNS stress by β-adrenergic receptor stimulation with isoproterenol increased HR, lengthened AV delay, slowed AP and CaT upstroke speed, and shortened AP and CaT duration, yet did not result in arrhythmias. In adult popdc1S191F zebrafish hearts, there was a higher incidence of AV block, slower AP upstroke speed, and longer AP duration compared to wild-type hearts, with no differences in CaT. SNS stress increased AV delay and led to further AV block in popdc1S191F hearts while decreasing AP and CaT duration. Overall, we have revealed that arrhythmogenic effects of POPDC1 dysfunction on cardiac electrophysiology and intracellular calcium handling in zebrafish are varied, but already present in early development, and that AV node dysfunction may underlie SNS-induced arrhythmogenesis associated with popdc1 mutation in adults.
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Affiliation(s)
- Matthew R. Stoyek
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Sarah E. Doane
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Shannon E. Dallaire
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Zachary D. Long
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Jessica M. Ramia
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Donovan L. Cassidy-Nolan
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
| | - Kar-Lai Poon
- National Heart & Lung Institute, Imperial College London, London W12 0NN, UK; (K.-L.P.); (T.B.)
| | - Thomas Brand
- National Heart & Lung Institute, Imperial College London, London W12 0NN, UK; (K.-L.P.); (T.B.)
| | - T. Alexander Quinn
- Department of Physiology & Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.S.); (S.E.D.); (S.E.D.); (Z.D.L.); (J.M.R.); (D.L.C.-N.)
- School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Elzamzami FD, Samal A, Arun AS, Dharmaraj T, Prasad NR, Rendon-Jonguitud A, DeVine L, Walston JD, Cole RN, Wilson KL. Native lamin A/C proteomes and novel partners from heart and skeletal muscle in a mouse chronic inflammation model of human frailty. Front Cell Dev Biol 2023; 11:1240285. [PMID: 37936983 PMCID: PMC10626543 DOI: 10.3389/fcell.2023.1240285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Clinical frailty affects ∼10% of people over age 65 and is studied in a chronically inflamed (Interleukin-10 knockout; "IL10-KO") mouse model. Frailty phenotypes overlap the spectrum of diseases ("laminopathies") caused by mutations in LMNA. LMNA encodes nuclear intermediate filament proteins lamin A and lamin C ("lamin A/C"), important for tissue-specific signaling, metabolism and chromatin regulation. We hypothesized that wildtype lamin A/C associations with tissue-specific partners are perturbed by chronic inflammation, potentially contributing to dysfunction in frailty. To test this idea we immunoprecipitated native lamin A/C and associated proteins from skeletal muscle, hearts and brains of old (21-22 months) IL10-KO versus control C57Bl/6 female mice, and labeled with Tandem Mass Tags for identification and quantitation by mass spectrometry. We identified 502 candidate lamin-binding proteins from skeletal muscle, and 340 from heart, including 62 proteins identified in both tissues. Candidates included frailty phenotype-relevant proteins Perm1 and Fam210a, and nuclear membrane protein Tmem38a, required for muscle-specific genome organization. These and most other candidates were unaffected by IL10-KO, but still important as potential lamin A/C-binding proteins in native heart or muscle. A subset of candidates (21 in skeletal muscle, 30 in heart) showed significantly different lamin A/C-association in an IL10-KO tissue (p < 0.05), including AldoA and Gins3 affected in heart, and Lmcd1 and Fabp4 affected in skeletal muscle. To screen for binding, eleven candidates plus prelamin A and emerin controls were arrayed as synthetic 20-mer peptides (7-residue stagger) and incubated with recombinant purified lamin A "tail" residues 385-646 under relatively stringent conditions. We detected strong lamin A binding to peptides solvent exposed in Lmcd1, AldoA, Perm1, and Tmem38a, and plausible binding to Csrp3 (muscle LIM protein). These results validated both proteomes as sources for native lamin A/C-binding proteins in heart and muscle, identified four candidate genes for Emery-Dreifuss muscular dystrophy (CSRP3, LMCD1, ALDOA, and PERM1), support a lamin A-interactive molecular role for Tmem38A, and supported the hypothesis that lamin A/C interactions with at least two partners (AldoA in heart, transcription factor Lmcd1 in muscle) are altered in the IL10-KO model of frailty.
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Affiliation(s)
- Fatima D. Elzamzami
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arushi Samal
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adith S. Arun
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Neeti R. Prasad
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex Rendon-Jonguitud
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lauren DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeremy D. Walston
- Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert N. Cole
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Katherine L. Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Rawls A, Diviak BK, Smith CI, Severson GW, Acosta SA, Wilson-Rawls J. Pharmacotherapeutic Approaches to Treatment of Muscular Dystrophies. Biomolecules 2023; 13:1536. [PMID: 37892218 PMCID: PMC10605463 DOI: 10.3390/biom13101536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Muscular dystrophies are a heterogeneous group of genetic muscle-wasting disorders that are subdivided based on the region of the body impacted by muscle weakness as well as the functional activity of the underlying genetic mutations. A common feature of the pathophysiology of muscular dystrophies is chronic inflammation associated with the replacement of muscle mass with fibrotic scarring. With the progression of these disorders, many patients suffer cardiomyopathies with fibrosis of the cardiac tissue. Anti-inflammatory glucocorticoids represent the standard of care for Duchenne muscular dystrophy, the most common muscular dystrophy worldwide; however, long-term exposure to glucocorticoids results in highly adverse side effects, limiting their use. Thus, it is important to develop new pharmacotherapeutic approaches to limit inflammation and fibrosis to reduce muscle damage and promote repair. Here, we examine the pathophysiology, genetic background, and emerging therapeutic strategies for muscular dystrophies.
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Affiliation(s)
- Alan Rawls
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
| | - Bridget K. Diviak
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Tempe, AZ 85287 4501, USA
| | - Cameron I. Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Tempe, AZ 85287 4501, USA
| | - Grant W. Severson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Tempe, AZ 85287 4501, USA
| | - Sofia A. Acosta
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Tempe, AZ 85287 4501, USA
| | - Jeanne Wilson-Rawls
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA; (B.K.D.); (C.I.S.); (G.W.S.); (S.A.A.)
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6
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Maggi L, Quijano-Roy S, Bönnemann C, Bonne G. 253rd ENMC international workshop: Striated muscle laminopathies - natural history and clinical trial readiness. 24-26 June 2022, Hoofddorp, the Netherlands. Neuromuscul Disord 2023; 33:498-510. [PMID: 37235886 DOI: 10.1016/j.nmd.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Lorenzo Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Instituto Neurologico Carlo Besta, Milano, Italy.
| | - Susana Quijano-Roy
- APHP-Université Paris-Saclay, Neuromuscular Disorders Reference Center of Nord-Est-Île de France, FILNEMUS, ERN-Euro-NMD, Creteil, France; Pediatric Neurology and ICU Department, DMU Santé Enfant Adolescent (SEA), Raymond Poincaré University Hospital, Garches, France
| | - Carsten Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Gisèle Bonne
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, Paris, France.
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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] [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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Todorow V, Hintze S, Schoser B, Meinke P. Nuclear envelope transmembrane proteins involved in genome organization are misregulated in myotonic dystrophy type 1 muscle. Front Cell Dev Biol 2023; 10:1007331. [PMID: 36699009 PMCID: PMC9868253 DOI: 10.3389/fcell.2022.1007331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Myotonic dystrophy type 1 is a multisystemic disorder with predominant muscle and neurological involvement. Despite a well described pathomechanism, which is primarily a global missplicing due to sequestration of RNA-binding proteins, there are still many unsolved questions. One such question is the disease etiology in the different affected tissues. We observed alterations at the nuclear envelope in primary muscle cell cultures before. This led us to reanalyze a published RNA-sequencing dataset of DM1 and control muscle biopsies regarding the misregulation of NE proteins. We could identify several muscle NE protein encoding genes to be misregulated depending on the severity of the muscle phenotype. Among these misregulated genes were NE transmembrane proteins (NETs) involved in nuclear-cytoskeletal coupling as well as genome organization. For selected genes, we could confirm that observed gene-misregulation led to protein expression changes. Furthermore, we investigated if genes known to be under expression-regulation by genome organization NETs were also misregulated in DM1 biopsies, which revealed that misregulation of two NETs alone is likely responsible for differential expression of about 10% of all genes being differentially expressed in DM1. Notably, the majority of NETs identified here to be misregulated in DM1 muscle are mutated in Emery-Dreifuss muscular dystrophy or clinical similar muscular dystrophies, suggesting a broader similarity on the molecular level for muscular dystrophies than anticipated. This shows not only the importance of muscle NETs in muscle health and disease, but also highlights the importance of the NE in DM1 disease progression.
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Lee B, Kim SK, Shin YJ, Son YH, Yang JW, Lee SM, Yang YR, Lee KP, Kwon KS. Genome-wide analysis of a cellular exercise model based on electrical pulse stimulation. Sci Rep 2022; 12:21251. [PMID: 36481702 PMCID: PMC9731977 DOI: 10.1038/s41598-022-25758-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle communicates with other organs via myokines, which are secreted by muscle during exercise and exert various effects. Despite much investigation of the exercise, the underlying molecular mechanisms are still not fully understood. Here, we applied an in vitro exercise model in which cultured C2C12 myotubes were subjected to electrical pulse stimulation (EPS), which mimics contracting muscle. Based on the significantly up- and down-regulated genes in EPS, we constructed an in silico model to predict exercise responses at the transcriptional level. The in silico model revealed similarities in the transcriptomes of the EPS and exercised animals. Comparative analysis of the EPS data and exercised mouse muscle identified putative biomarkers in exercise signaling pathways and enabled to discover novel exercise-induced myokines. Biochemical analysis of selected exercise signature genes in muscle from exercised mice showed that EPS mimics in vivo exercise, at least in part, at the transcriptional level. Consequently, we provide a novel myokine, Amphiregulin (AREG), up-regulated both in vitro and in vivo, that would be a potential target for exercise mimetics.
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Affiliation(s)
- Bora Lee
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Seon Kyu Kim
- grid.249967.70000 0004 0636 3099Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Yeo Jin Shin
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Young Hoon Son
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Jae Won Yang
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Seung-Min Lee
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Yong Ryul Yang
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Kwang-Pyo Lee
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113 Republic of Korea ,Aventi Inc., Daejeon, 34141 Republic of Korea
| | - Ki-Sun Kwon
- grid.249967.70000 0004 0636 3099Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea ,grid.412786.e0000 0004 1791 8264Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113 Republic of Korea ,Aventi Inc., Daejeon, 34141 Republic of Korea
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10
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Schirmer EC. Nuclear organization and dynamics: The final Frontier for understanding genome regulation. Front Cell Dev Biol 2022; 10:951875. [PMID: 35923850 PMCID: PMC9340541 DOI: 10.3389/fcell.2022.951875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
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Pfeffer G, Lee G, Pontifex CS, Fanganiello RD, Peck A, Weihl CC, Kimonis V. Multisystem Proteinopathy Due to VCP Mutations: A Review of Clinical Heterogeneity and Genetic Diagnosis. Genes (Basel) 2022; 13:963. [PMID: 35741724 PMCID: PMC9222868 DOI: 10.3390/genes13060963] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
In this work, we review clinical features and genetic diagnosis of diseases caused by mutations in the gene encoding valosin-containing protein (VCP/p97), the functionally diverse AAA-ATPase. VCP is crucial to a multitude of cellular functions including protein quality control, stress granule formation and clearance, and genomic integrity functions, among others. Pathogenic mutations in VCP cause multisystem proteinopathy (VCP-MSP), an autosomal dominant, adult-onset disorder causing dysfunction in several tissue types. It can result in complex neurodegenerative conditions including inclusion body myopathy, frontotemporal dementia, amyotrophic lateral sclerosis, or combinations of these. There is also an association with other neurodegenerative phenotypes such as Alzheimer-type dementia and Parkinsonism. Non-neurological presentations include Paget disease of bone and may also include cardiac dysfunction. We provide a detailed discussion of genotype-phenotype correlations, recommendations for genetic diagnosis, and genetic counselling implications of VCP-MSP.
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Affiliation(s)
- Gerald Pfeffer
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Grace Lee
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California Irvine Medical Center, Orange, CA 92868, USA; (G.L.); (V.K.)
| | - Carly S. Pontifex
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Roberto D. Fanganiello
- Oral Ecology Research Group, Faculty of Dental Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Allison Peck
- Cure VCP Disease, Inc., Americus, GA 31709, USA;
| | - Conrad C. Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Virginia Kimonis
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California Irvine Medical Center, Orange, CA 92868, USA; (G.L.); (V.K.)
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12
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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] [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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13
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Padilla-Mejia NE, Makarov AA, Barlow LD, Butterfield ER, Field MC. Evolution and diversification of the nuclear envelope. Nucleus 2021; 12:21-41. [PMID: 33435791 PMCID: PMC7889174 DOI: 10.1080/19491034.2021.1874135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.
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Affiliation(s)
- Norma E. Padilla-Mejia
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexandr A. Makarov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lael D. Barlow
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Erin R. Butterfield
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České, Czech Republic
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14
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Gruscheski L, Brand T. The Role of POPDC Proteins in Cardiac Pacemaking and Conduction. J Cardiovasc Dev Dis 2021; 8:160. [PMID: 34940515 PMCID: PMC8706714 DOI: 10.3390/jcdd8120160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
The Popeye domain-containing (POPDC) gene family, consisting of Popdc1 (also known as Bves), Popdc2, and Popdc3, encodes transmembrane proteins abundantly expressed in striated muscle. POPDC proteins have recently been identified as cAMP effector proteins and have been proposed to be part of the protein network involved in cAMP signaling. However, their exact biochemical activity is presently poorly understood. Loss-of-function mutations in animal models causes abnormalities in skeletal muscle regeneration, conduction, and heart rate adaptation after stress. Likewise, patients carrying missense or nonsense mutations in POPDC genes have been associated with cardiac arrhythmias and limb-girdle muscular dystrophy. In this review, we introduce the POPDC protein family, and describe their structure function, and role in cAMP signaling. Furthermore, the pathological phenotypes observed in zebrafish and mouse models and the clinical and molecular pathologies in patients carrying POPDC mutations are described.
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Affiliation(s)
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK;
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15
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Vogel P, Read RW, Hansen GM, Powell DR. Histopathology is required to identify and characterize myopathies in high-throughput phenotype screening of genetically engineered mice. Vet Pathol 2021; 58:1158-1171. [PMID: 34269122 DOI: 10.1177/03009858211030541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of mouse models that replicate the genetic and pathological features of human disease is important in preclinical research because these types of models enable the completion of meaningful pharmacokinetic, safety, and efficacy studies. Numerous relevant mouse models of human disease have been discovered in high-throughput screening programs, but there are important specific phenotypes revealed by histopathology that are not reliably detected by any other physiological or behavioral screening tests. As part of comprehensive phenotypic analyses of over 4000 knockout (KO) mice, histopathology identified 12 lines of KO mice with lesions indicative of an autosomal recessive myopathy. This report includes a brief summary of histological and other findings in these 12 lines. Notably, the inverted screen test detected muscle weakness in only 4 of these 12 lines (Scyl1, Plpp7, Chkb, and Asnsd1), all 4 of which have been previously recognized and published. In contrast, 6 of 8 KO lines showing negative or inconclusive findings on the inverted screen test (Plppr2, Pnpla7, Tenm1, Srpk3, Sidt2, Yif1b, Mrs2, and Pnpla2) had not been previously identified as having myopathies. These findings support the need to include histopathology in phenotype screening protocols in order to identify novel genetic myopathies that are not clinically evident or not detected by the inverted screen test.
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Affiliation(s)
- Peter Vogel
- 5417St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert W Read
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
| | | | - David R Powell
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
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16
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Pawar S, Kutay U. The Diverse Cellular Functions of Inner Nuclear Membrane Proteins. Cold Spring Harb Perspect Biol 2021; 13:a040477. [PMID: 33753404 PMCID: PMC8411953 DOI: 10.1101/cshperspect.a040477] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear compartment is delimited by a specialized expanded sheet of the endoplasmic reticulum (ER) known as the nuclear envelope (NE). Compared to the outer nuclear membrane and the contiguous peripheral ER, the inner nuclear membrane (INM) houses a unique set of transmembrane proteins that serve a staggering range of functions. Many of these functions reflect the exceptional position of INM proteins at the membrane-chromatin interface. Recent research revealed that numerous INM proteins perform crucial roles in chromatin organization, regulation of gene expression, genome stability, and mediation of signaling pathways into the nucleus. Other INM proteins establish mechanical links between chromatin and the cytoskeleton, help NE remodeling, or contribute to the surveillance of NE integrity and homeostasis. As INM proteins continue to gain prominence, we review these advancements and give an overview on the functional versatility of the INM proteome.
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Affiliation(s)
- Sumit Pawar
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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17
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Skeletal and Cardiac Muscle Disorders Caused by Mutations in Genes Encoding Intermediate Filament Proteins. Int J Mol Sci 2021; 22:ijms22084256. [PMID: 33923914 PMCID: PMC8073371 DOI: 10.3390/ijms22084256] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 02/08/2023] Open
Abstract
Intermediate filaments are major components of the cytoskeleton. Desmin and synemin, cytoplasmic intermediate filament proteins and A-type lamins, nuclear intermediate filament proteins, play key roles in skeletal and cardiac muscle. Desmin, encoded by the DES gene (OMIM *125660) and A-type lamins by the LMNA gene (OMIM *150330), have been involved in striated muscle disorders. Diseases include desmin-related myopathy and cardiomyopathy (desminopathy), which can be manifested with dilated, restrictive, hypertrophic, arrhythmogenic, or even left ventricular non-compaction cardiomyopathy, Emery–Dreifuss Muscular Dystrophy (EDMD2 and EDMD3, due to LMNA mutations), LMNA-related congenital Muscular Dystrophy (L-CMD) and LMNA-linked dilated cardiomyopathy with conduction system defects (CMD1A). Recently, mutations in synemin (SYNM gene, OMIM *606087) have been linked to cardiomyopathy. This review will summarize clinical and molecular aspects of desmin-, lamin- and synemin-related striated muscle disorders with focus on LMNA and DES-associated clinical entities and will suggest pathogenetic hypotheses based on the interplay of desmin and lamin A/C. In healthy muscle, such interplay is responsible for the involvement of this network in mechanosignaling, nuclear positioning and mitochondrial homeostasis, while in disease it is disturbed, leading to myocyte death and activation of inflammation and the associated secretome alterations.
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18
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Colombe AS, Pidoux G. Cardiac cAMP-PKA Signaling Compartmentalization in Myocardial Infarction. Cells 2021; 10:cells10040922. [PMID: 33923648 PMCID: PMC8073060 DOI: 10.3390/cells10040922] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/02/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
Under physiological conditions, cAMP signaling plays a key role in the regulation of cardiac function. Activation of this intracellular signaling pathway mirrors cardiomyocyte adaptation to various extracellular stimuli. Extracellular ligand binding to seven-transmembrane receptors (also known as GPCRs) with G proteins and adenylyl cyclases (ACs) modulate the intracellular cAMP content. Subsequently, this second messenger triggers activation of specific intracellular downstream effectors that ensure a proper cellular response. Therefore, it is essential for the cell to keep the cAMP signaling highly regulated in space and time. The temporal regulation depends on the activity of ACs and phosphodiesterases. By scaffolding key components of the cAMP signaling machinery, A-kinase anchoring proteins (AKAPs) coordinate both the spatial and temporal regulation. Myocardial infarction is one of the major causes of death in industrialized countries and is characterized by a prolonged cardiac ischemia. This leads to irreversible cardiomyocyte death and impairs cardiac function. Regardless of its causes, a chronic activation of cardiac cAMP signaling is established to compensate this loss. While this adaptation is primarily beneficial for contractile function, it turns out, in the long run, to be deleterious. This review compiles current knowledge about cardiac cAMP compartmentalization under physiological conditions and post-myocardial infarction when it appears to be profoundly impaired.
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19
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Zhou X, Li A, Lin PH, Zhou J, Ma J. TRIC-A regulates intracellular Ca 2+ homeostasis in cardiomyocytes. Pflugers Arch 2021; 473:547-556. [PMID: 33474637 PMCID: PMC7940156 DOI: 10.1007/s00424-021-02513-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 01/26/2023]
Abstract
Trimeric intracellular cation (TRIC) channels have been identified as monovalent cation channels that are located in the ER/SR membrane. Two isoforms discovered in mammals are TRIC-A (TMEM38a) and TRIC-B (TMEM38b). TRIC-B ubiquitously expresses in all tissues, and TRIC-B-/- mice is lethal at the neonatal stage. TRIC-A mainly expresses in excitable cells. TRIC-A-/- mice survive normally but show abnormal SR Ca2+ handling in both skeletal and cardiac muscle cells. Importantly, TRIC-A mutations have been identified in human patients with stress-induced arrhythmia. In the past decade, important discoveries have been made to understand the structure and function of TRIC channels, especially its role in regulating intracellular Ca2+ homeostasis. In this review article, we focus on the potential roles of TRIC-A in regulating cardiac function, particularly its effects on intracellular Ca2+ signaling of cardiomyocytes and discuss the current knowledge gaps.
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Affiliation(s)
- Xinyu Zhou
- Department of Surgery, The Ohio State University Columbus, Columbus, OH, 43210, USA
| | - Ang Li
- Department of Kinesiology, College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, 76019, USA
| | - Pei-Hui Lin
- Department of Surgery, The Ohio State University Columbus, Columbus, OH, 43210, USA
| | - Jingsong Zhou
- Department of Kinesiology, College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, 76019, USA
| | - Jianjie Ma
- Department of Surgery, The Ohio State University Columbus, Columbus, OH, 43210, USA.
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20
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The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization. Nat Commun 2021; 12:690. [PMID: 33514739 PMCID: PMC7846557 DOI: 10.1038/s41467-021-20987-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 12/24/2020] [Indexed: 01/14/2023] Open
Abstract
Lamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear envelope transmembrane protein 39 (Net39) is a muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression, and metabolism. These abnormalities resemble those of Emery-Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.
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21
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Gatticchi L, de Las Heras JI, Sivakumar A, Zuleger N, Roberti R, Schirmer EC. Tm7sf2 Disruption Alters Radial Gene Positioning in Mouse Liver Leading to Metabolic Defects and Diabetes Characteristics. Front Cell Dev Biol 2020; 8:592573. [PMID: 33330474 PMCID: PMC7719783 DOI: 10.3389/fcell.2020.592573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/26/2020] [Indexed: 01/23/2023] Open
Abstract
Tissue-specific patterns of radial genome organization contribute to genome regulation and can be established by nuclear envelope proteins. Studies in this area often use cancer cell lines, and it is unclear how well such systems recapitulate genome organization of primary cells or animal tissues; so, we sought to investigate radial genome organization in primary liver tissue hepatocytes. Here, we have used a NET47/Tm7sf2–/– liver model to show that manipulating one of these nuclear membrane proteins is sufficient to alter tissue-specific gene positioning and expression. Dam-LaminB1 global profiling in primary liver cells shows that nearly all the genes under such positional regulation are related to/important for liver function. Interestingly, Tm7sf2 is a paralog of the HP1-binding nuclear membrane protein LBR that, like Tm7sf2, also has an enzymatic function in sterol reduction. Fmo3 gene/locus radial mislocalization could be rescued with human wild-type, but not TM7SF2 mutants lacking the sterol reductase function. One central pathway affected is the cholesterol synthesis pathway. Within this pathway, both Cyp51 and Msmo1 are under Tm7sf2 positional and expression regulation. Other consequences of the loss of Tm7sf2 included weight gain, insulin sensitivity, and reduced levels of active Akt kinase indicating additional pathways under its regulation, several of which are highlighted by mispositioning genes. This study emphasizes the importance for tissue-specific radial genome organization in tissue function and the value of studying genome organization in animal tissues and primary cells over cell lines.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Jose I de Las Heras
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Aishwarya Sivakumar
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Nikolaj Zuleger
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Rita Roberti
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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22
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Holt I, Fuller HR, Schindler RFR, Shirran SL, Brand T, Morris GE. An interaction of heart disease-associated proteins POPDC1/2 with XIRP1 in transverse tubules and intercalated discs. BMC Mol Cell Biol 2020; 21:88. [PMID: 33261556 PMCID: PMC7709239 DOI: 10.1186/s12860-020-00329-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/18/2020] [Indexed: 11/25/2022] Open
Abstract
Background Popeye domain-containing proteins 1 and 2 (POPDC1 and POPDC2) are transmembrane proteins involved in cyclic AMP-mediated signalling processes and are required for normal cardiac pacemaking and conduction. In order to identify novel protein interaction partners, POPDC1 and 2 proteins were attached to beads and compared by proteomic analysis with control beads in the pull-down of proteins from cultured human skeletal myotubes. Results There were highly-significant interactions of both POPDC1 and POPDC2 with XIRP1 (Xin actin binding repeat-containing protein 1), actin and, to a lesser degree, annexin A5. In adult human skeletal muscle, both XIRP1 and POPDC1/2 were present at the sarcolemma and in T-tubules. The interaction of POPDC1 with XIRP1 was confirmed in adult rat heart extracts. Using new monoclonal antibodies specific for POPDC1 and POPDC2, both proteins, together with XIRP1, were found mainly at intercalated discs but also at T-tubules in adult rat and human heart. Conclusions Mutations in human POPDC1, POPDC2 and in human XIRP1, all cause pathological cardiac arrhythmias, suggesting a possible role for POPDC1/2 and XIRP1 interaction in normal cardiac conduction. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-020-00329-3.
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Affiliation(s)
- Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK. .,School of Pharmacy and Bioengineering, Keele University, Keele, ST5 5BG, UK.
| | - Heidi R Fuller
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,School of Pharmacy and Bioengineering, Keele University, Keele, ST5 5BG, UK
| | - Roland F R Schindler
- Imperial Centre of Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College, 4th Floor, Du Cane Road, London, W12 0NN, UK
| | - Sally L Shirran
- BSRC Mass Spectrometry and Proteomics Facility, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Thomas Brand
- Imperial Centre of Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College, 4th Floor, Du Cane Road, London, W12 0NN, UK
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, UK.,School of Pharmacy and Bioengineering, Keele University, Keele, ST5 5BG, UK
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23
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The Molecular Basis and Biologic Significance of the β-Dystroglycan-Emerin Interaction. Int J Mol Sci 2020; 21:ijms21175944. [PMID: 32824881 PMCID: PMC7504044 DOI: 10.3390/ijms21175944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
β-dystroglycan (β-DG) assembles with lamins A/C and B1 and emerin at the nuclear envelope (NE) to maintain proper nuclear architecture and function. To provide insight into the nuclear function of β-DG, we characterized the interaction between β-DG and emerin at the molecular level. Emerin is a major NE protein that regulates multiple nuclear processes and whose deficiency results in Emery–Dreifuss muscular dystrophy (EDMD). Using truncated variants of β-DG and emerin, via a series of in vitro and in vivo binding experiments and a tailored computational analysis, we determined that the β-DG–emerin interaction is mediated at least in part by their respective transmembrane domains (TM). Using surface plasmon resonance assays we showed that emerin binds to β-DG with high affinity (KD in the nanomolar range). Remarkably, the analysis of cells in which DG was knocked out demonstrated that loss of β-DG resulted in a decreased emerin stability and impairment of emerin-mediated processes. β-DG and emerin are reciprocally required for their optimal targeting within the NE, as shown by immunofluorescence, western blotting and immunoprecipitation assays using emerin variants with mutations in the TM domain and B-lymphocytes of a patient with EDMD. In summary, we demonstrated that β-DG plays a role as an emerin interacting partner modulating its stability and function.
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24
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PCAF Involvement in Lamin A/C-HDAC2 Interplay during the Early Phase of Muscle Differentiation. Cells 2020; 9:cells9071735. [PMID: 32698523 PMCID: PMC7409167 DOI: 10.3390/cells9071735] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/09/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023] Open
Abstract
Lamin A/C has been implicated in the epigenetic regulation of muscle gene expression through dynamic interaction with chromatin domains and epigenetic enzymes. We previously showed that lamin A/C interacts with histone deacetylase 2 (HDAC2). In this study, we deepened the relevance and regulation of lamin A/C-HDAC2 interaction in human muscle cells. We present evidence that HDAC2 binding to lamina A/C is related to HDAC2 acetylation on lysine 75 and expression of p300-CBP associated factor (PCAF), an acetyltransferase known to acetylate HDAC2. Our findings show that lamin A and farnesylated prelamin A promote PCAF recruitment to the nuclear lamina and lamin A/C binding in human myoblasts committed to myogenic differentiation, while protein interaction is decreased in differentiating myotubes. Interestingly, PCAF translocation to the nuclear envelope, as well as lamin A/C-PCAF interaction, are reduced by transient expression of lamin A mutated forms causing Emery Dreifuss muscular dystrophy. Consistent with this observation, lamin A/C interaction with both PCAF and HDAC2 is significantly reduced in Emery-Dreifuss muscular dystrophy myoblasts. Overall, these results support the view that, by recruiting PCAF and HDAC2 in a molecular platform, lamin A/C might contribute to regulate their epigenetic activity required in the early phase of muscle differentiation.
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25
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Carmelo VAO, Kadarmideen HN. Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs. Front Genet 2020; 11:650. [PMID: 32655625 PMCID: PMC7324801 DOI: 10.3389/fgene.2020.00650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/28/2020] [Indexed: 01/03/2023] Open
Abstract
Improvement of feed efficiency (FE) is key for Sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc; n = 13) and Danbred Landrace (Landrace; n = 28), in relation to FE for identifying potential biomarkers. RNA-seq data on the 41 pigs was analyzed employing differential gene expression methods, gene-gene interaction and network analysis, including pathway and functional analysis. We also compared the results with genome regulation in human exercise data, hypothesizing that increased FE mimics processes triggered in exercised muscle. In the differential expression analysis, 13 genes were differentially expressed, including: MRPS11, MTRF1, TRIM63, MGAT4A, KLH30. Based on a novel gene selection method, the divergent count, we performed pathway enrichment analysis. We found five significantly enriched pathways related to feed conversion ratio (FCR). These pathways were mainly related to mitochondria, and summarized in the mitochondrial translation elongation (MTR) pathway. In the gene interaction analysis, the most interesting genes included the mitochondrial genes: PPIF, MRPL35, NDUFS4 and the fat metabolism and obesity genes: AACS, SMPDL3B, CTNNBL1, NDUFS4, and LIMD2. In the network analysis, we identified two modules significantly correlated with FCR. Pathway enrichment of module genes identified MTR, electron transport chain and DNA repair as enriched pathways. The network analysis revealed the mitochondrial gene group NDUF as key network hub genes, showing their potential as biomarkers. Results show that genes related to human exercise were enriched in identified FCR related genes. We conclude that mitochondrial activity is a key driver for FCR in muscle tissue, and mitochondrial genes could be potential biomarkers for FCR in pigs.
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Affiliation(s)
- Victor A O Carmelo
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
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An Omics View of Emery-Dreifuss Muscular Dystrophy. J Pers Med 2020; 10:jpm10020050. [PMID: 32549253 PMCID: PMC7354601 DOI: 10.3390/jpm10020050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Recent progress in Omics technologies has started to empower personalized healthcare development at a thorough biomolecular level. Omics have subsidized medical breakthroughs that have started to enter clinical proceedings. The use of this scientific know-how has surfaced as a way to provide a more far-reaching view of the biological mechanisms behind diseases. This review will focus on the discoveries made using Omics and the utility of these approaches for Emery–Dreifuss muscular dystrophy.
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Xiong H. Novel candidate alleles associated with gene regulation for Emery-Dreifuss muscular dystrophy. EBioMedicine 2020; 52:102620. [PMID: 31981977 PMCID: PMC6992946 DOI: 10.1016/j.ebiom.2019.102620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Hui Xiong
- Department of Pediatrics, Peking University First Hospital, 1, Xi anmen St., West District, Beijing, China.
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