1
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Souidi A, Nakamori M, Zmojdzian M, Jagla T, Renaud Y, Jagla K. Deregulations of miR-1 and its target Multiplexin promote dilated cardiomyopathy associated with myotonic dystrophy type 1. EMBO Rep 2023; 24:e56616. [PMID: 36852954 PMCID: PMC10074075 DOI: 10.15252/embr.202256616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults. It is caused by the excessive expansion of noncoding CTG repeats, which when transcribed affects the functions of RNA-binding factors with adverse effects on alternative splicing, processing, and stability of a large set of muscular and cardiac transcripts. Among these effects, inefficient processing and down-regulation of muscle- and heart-specific miRNA, miR-1, have been reported in DM1 patients, but the impact of reduced miR-1 on DM1 pathogenesis has been unknown. Here, we use Drosophila DM1 models to explore the role of miR-1 in cardiac dysfunction in DM1. We show that miR-1 down-regulation in the heart leads to dilated cardiomyopathy (DCM), a DM1-associated phenotype. We combined in silico screening for miR-1 targets with transcriptional profiling of DM1 cardiac cells to identify miR-1 target genes with potential roles in DCM. We identify Multiplexin (Mp) as a new cardiac miR-1 target involved in DM1. Mp encodes a collagen protein involved in cardiac tube formation in Drosophila. Mp and its human ortholog Col15A1 are both highly enriched in cardiac cells of DCM-developing DM1 flies and in heart samples from DM1 patients with DCM, respectively. When overexpressed in the heart, Mp induces DCM, whereas its attenuation rescues the DCM phenotype of aged DM1 flies. Reduced levels of miR-1 and consecutive up-regulation of its target Mp/Col15A1 might be critical in DM1-associated DCM.
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Affiliation(s)
- Anissa Souidi
- iGReD Genetics Reproduction and Development Institute, Clermont Auvergne University, Clermont-Ferrand, France
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Monika Zmojdzian
- iGReD Genetics Reproduction and Development Institute, Clermont Auvergne University, Clermont-Ferrand, France
| | - Teresa Jagla
- iGReD Genetics Reproduction and Development Institute, Clermont Auvergne University, Clermont-Ferrand, France
| | - Yoan Renaud
- iGReD Genetics Reproduction and Development Institute, Clermont Auvergne University, Clermont-Ferrand, France
| | - Krzysztof Jagla
- iGReD Genetics Reproduction and Development Institute, Clermont Auvergne University, Clermont-Ferrand, France
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2
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Chang Y, Yang B, Zhang Y, Dong C, Liu L, Zhao X, Wang G. Identification of sex-biased and neurodevelopment genes via brain transcriptome in Ostrinia furnacalis. Front Physiol 2022; 13:953538. [PMID: 36003649 PMCID: PMC9393524 DOI: 10.3389/fphys.2022.953538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Insect brains play important roles in the regulation of sex-biased behaviors such as mating and oviposition. The neural structure and function of brain differences between males and females have been identified, in which the antenna lobes (AL) showed the most discrepancy, however, the whole repertoire of the genes expressed in the brains and the molecular mechanism of neural signaling and structural development are still unclear. In this study, high-throughput transcriptome analysis of male and female brains was carried on in the Asia corn borer, Ostrinia furnacalis, and a total of 39.23 Gb data and 34,092 unigenes were obtained. Among them, 276 genes displayed sex-biased expression by DEG analysis, of which 125 genes were highly expressed in the males and 151 genes were highly expressed in the females. Besides, by homology analysis against genes that have been confirmed to be related to brain neurodevelopment, a total of 24 candidate genes were identified in O. furnacalis. In addition, to further screen the core genes that may be important for sex-biased nerve signaling and neurodevelopment, protein-protein interaction networks were constructed for the sex-biased genes and neurodevelopment genes. We identified 10 (Mhc, Mlc1, Mlc2, Prm, Mf, wupA, TpnC25D, fln, l(2)efl, and Act5C), 11 (PPO2, GNBP3, Spn77Ba, Ppn, yellow-d2, PGRP-LB, PGRP-SD, PGRP-SC2, Hml, Cg25C, and vkg) and 8 (dac, wg, hh, ci, run, Lim1, Rbp9, and Bx) core hub genes that may be related to brain neural development from male-biased, female-biased, and neurodevelopment gene groups. Our results provide a reference for further analysis of the dimorphism of male and female brain structures in agricultural pests.
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Affiliation(s)
- Yajun Chang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bin Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Guirong Wang, ; Bin Yang,
| | - Yu Zhang
- Key Laboratory of Biohazard Monitoring, Green Prevention and Control for Artificial Grassland, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research of Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Chenxi Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xincheng Zhao
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Guirong Wang, ; Bin Yang,
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3
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Monitoring the maturation of the sarcomere network: a super-resolution microscopy-based approach. Cell Mol Life Sci 2022; 79:149. [PMID: 35199227 PMCID: PMC8866374 DOI: 10.1007/s00018-022-04196-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 02/05/2022] [Indexed: 12/17/2022]
Abstract
The in vitro generation of human cardiomyocytes derived from induced pluripotent stem cells (iPSC) is of great importance for cardiac disease modeling, drug-testing applications and for regenerative medicine. Despite the development of various cultivation strategies, a sufficiently high degree of maturation is still a decisive limiting factor for the successful application of these cardiac cells. The maturation process includes, among others, the proper formation of sarcomere structures, mediating the contraction of cardiomyocytes. To precisely monitor the maturation of the contractile machinery, we have established an imaging-based strategy that allows quantitative evaluation of important parameters, defining the quality of the sarcomere network. iPSC-derived cardiomyocytes were subjected to different culture conditions to improve sarcomere formation, including prolonged cultivation time and micro patterned surfaces. Fluorescent images of α-actinin were acquired using super-resolution microscopy. Subsequently, we determined cell morphology, sarcomere density, filament alignment, z-Disc thickness and sarcomere length of iPSC-derived cardiomyocytes. Cells from adult and neonatal heart tissue served as control. Our image analysis revealed a profound effect on sarcomere content and filament orientation when iPSC-derived cardiomyocytes were cultured on structured, line-shaped surfaces. Similarly, prolonged cultivation time had a beneficial effect on the structural maturation, leading to a more adult-like phenotype. Automatic evaluation of the sarcomere filaments by machine learning validated our data. Moreover, we successfully transferred this approach to skeletal muscle cells, showing an improved sarcomere formation cells over different differentiation periods. Overall, our image-based workflow can be used as a straight-forward tool to quantitatively estimate the structural maturation of contractile cells. As such, it can support the establishment of novel differentiation protocols to enhance sarcomere formation and maturity.
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4
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Shi DL, Grifone R. RNA-Binding Proteins in the Post-transcriptional Control of Skeletal Muscle Development, Regeneration and Disease. Front Cell Dev Biol 2021; 9:738978. [PMID: 34616743 PMCID: PMC8488162 DOI: 10.3389/fcell.2021.738978] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
Embryonic myogenesis is a temporally and spatially regulated process that generates skeletal muscle of the trunk and limbs. During this process, mononucleated myoblasts derived from myogenic progenitor cells within the somites undergo proliferation, migration and differentiation to elongate and fuse into multinucleated functional myofibers. Skeletal muscle is the most abundant tissue of the body and has the remarkable ability to self-repair by re-activating the myogenic program in muscle stem cells, known as satellite cells. Post-transcriptional regulation of gene expression mediated by RNA-binding proteins is critically required for muscle development during embryogenesis and for muscle homeostasis in the adult. Differential subcellular localization and activity of RNA-binding proteins orchestrates target gene expression at multiple levels to regulate different steps of myogenesis. Dysfunctions of these post-transcriptional regulators impair muscle development and homeostasis, but also cause defects in motor neurons or the neuromuscular junction, resulting in muscle degeneration and neuromuscular disease. Many RNA-binding proteins, such as members of the muscle blind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) families, display both overlapping and distinct targets in muscle cells. Thus they function either cooperatively or antagonistically to coordinate myoblast proliferation and differentiation. Evidence is accumulating that the dynamic interplay of their regulatory activity may control the progression of myogenic program as well as stem cell quiescence and activation. Moreover, the role of RNA-binding proteins that regulate post-transcriptional modification in the myogenic program is far less understood as compared with transcription factors involved in myogenic specification and differentiation. Here we review past achievements and recent advances in understanding the functions of RNA-binding proteins during skeletal muscle development, regeneration and disease, with the aim to identify the fundamental questions that are still open for further investigations.
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Affiliation(s)
- De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
| | - Raphaëlle Grifone
- Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
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5
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Sabater-Arcis M, Bargiela A, Moreno N, Poyatos-Garcia J, Vilchez JJ, Artero R. Musashi-2 contributes to myotonic dystrophy muscle dysfunction by promoting excessive autophagy through miR-7 biogenesis repression. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:652-667. [PMID: 34589284 PMCID: PMC8463325 DOI: 10.1016/j.omtn.2021.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Skeletal muscle symptoms strongly contribute to mortality of myotonic dystrophy type 1 (DM1) patients. DM1 is a neuromuscular genetic disease caused by CTG repeat expansions that, upon transcription, sequester the Muscleblind-like family of proteins and dysregulate alternative splicing of hundreds of genes. However, mis-splicing does not satisfactorily explain muscle atrophy and wasting, and several other contributing factors have been suggested, including hyperactivated autophagy leading to excessive catabolism. MicroRNA (miR)-7 has been demonstrated to be necessary and sufficient to repress the autophagy pathway in cell models of the disease, but the origin of its low levels in DM1 was unknown. We have found that the RNA-binding protein Musashi-2 (MSI2) is upregulated in patient-derived myoblasts and biopsy samples. Because it has been previously reported that MSI2 controls miR-7 biogenesis, we tested the hypothesis that excessive MSI2 was repressing miR-7 maturation. Using gene-silencing strategies (small interfering RNAs [siRNAs] and gapmers) and the small molecule MSI2-inhibitor Ro 08-2750, we demonstrate that reducing MSI2 levels or activity boosts miR-7 expression, represses excessive autophagy, and downregulates atrophy-related genes of the UPS system. We also detect a significant upregulation of MBNL1 upon MSI2 silencing. Taken together, we propose MSI2 as a new therapeutic target to treat muscle dysfunction in DM1.
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Affiliation(s)
- Maria Sabater-Arcis
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, 46100 Burjasot, Valencia, Spain
- INCLIVA Biomedical Research Institute, 46100 Burjasot, Valencia, Spain
| | - Ariadna Bargiela
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, 46100 Burjasot, Valencia, Spain
- INCLIVA Biomedical Research Institute, 46100 Burjasot, Valencia, Spain
- Corresponding author: Ariadna Bargiela, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr. Moliner, 50, 46100 Burjasot, Valencia, Spain.
| | - Nerea Moreno
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, 46100 Burjasot, Valencia, Spain
- INCLIVA Biomedical Research Institute, 46100 Burjasot, Valencia, Spain
| | - Javier Poyatos-Garcia
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
- Neuromuscular Research Unit, Neurology Department, Instituto de Investigación Sanitaria la Fe, Hospital Universitari i Politécnic La Fe, 46026 Valencia, Spain
| | - Juan J. Vilchez
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
- Neuromuscular Research Unit, Neurology Department, Instituto de Investigación Sanitaria la Fe, Hospital Universitari i Politécnic La Fe, 46026 Valencia, Spain
| | - Ruben Artero
- Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, 46100 Burjasot, Valencia, Spain
- INCLIVA Biomedical Research Institute, 46100 Burjasot, Valencia, Spain
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6
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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle. Sci Rep 2021; 11:11897. [PMID: 34099805 PMCID: PMC8184995 DOI: 10.1038/s41598-021-91373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
Water holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.
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7
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Ozimski LL, Sabater-Arcis M, Bargiela A, Artero R. The hallmarks of myotonic dystrophy type 1 muscle dysfunction. Biol Rev Camb Philos Soc 2020; 96:716-730. [PMID: 33269537 DOI: 10.1111/brv.12674] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is the most prevalent form of muscular dystrophy in adults and yet there are currently no treatment options. Although this disease causes multisystemic symptoms, it is mainly characterised by myopathy or diseased muscles, which includes muscle weakness, atrophy, and myotonia, severely affecting the lives of patients worldwide. On a molecular level, DM1 is caused by an expansion of CTG repeats in the 3' untranslated region (3'UTR) of the DM1 Protein Kinase (DMPK) gene which become pathogenic when transcribed into RNA forming ribonuclear foci comprised of auto complementary CUG hairpin structures that can bind proteins. This leads to the sequestration of the muscleblind-like (MBNL) family of proteins, depleting them, and the abnormal stabilisation of CUGBP Elav-like family member 1 (CELF1), enhancing it. Traditionally, DM1 research has focused on this RNA toxicity and how it alters MBNL and CELF1 functions as key splicing regulators. However, other proteins are affected by the toxic DMPK RNA and there is strong evidence that supports various signalling cascades playing an important role in DM1 pathogenesis. Specifically, the impairment of protein kinase B (AKT) signalling in DM1 increases autophagy, apoptosis, and ubiquitin-proteasome activity, which may also be affected in DM1 by AMP-activated protein kinase (AMPK) downregulation. AKT also regulates CELF1 directly, by affecting its subcellular localisation, and indirectly as it inhibits glycogen synthase kinase 3 beta (GSK3β), which stabilises the repressive form of CELF1 in DM1. Another kinase that contributes to CELF1 mis-regulation, in this case by hyperphosphorylation, is protein kinase C (PKC). Additionally, it has been demonstrated that fibroblast growth factor-inducible 14 (Fn14) is induced in DM1 and is associated with downstream signalling through the nuclear factor κB (NFκB) pathways, associating inflammation with this disease. Furthermore, MBNL1 and CELF1 play a role in cytoplasmic processes involved in DM1 myopathy, altering proteostasis and sarcomere structure. Finally, there are many other elements that could contribute to the muscular phenotype in DM1 such as alterations to satellite cells, non-coding RNA metabolism, calcium dysregulation, and repeat-associated non-ATG (RAN) translation. This review aims to organise the currently dispersed knowledge on the different pathways affected in DM1 and discusses the unexplored connections that could potentially help in providing new therapeutic targets in DM1 research.
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Affiliation(s)
- Lauren L Ozimski
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menéndez Pelayo 4 acc., Valencia, 46010, Spain.,University Institute for Biotechnology and Biomedicine, Dr. Moliner 50, Burjasot, Valencia, 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia, 46012, Spain.,Arthex Biotech, Catedrático Escardino, 9, Paterna, Valencia, 46980, Spain
| | - Maria Sabater-Arcis
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menéndez Pelayo 4 acc., Valencia, 46010, Spain.,University Institute for Biotechnology and Biomedicine, Dr. Moliner 50, Burjasot, Valencia, 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia, 46012, Spain
| | - Ariadna Bargiela
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menéndez Pelayo 4 acc., Valencia, 46010, Spain.,University Institute for Biotechnology and Biomedicine, Dr. Moliner 50, Burjasot, Valencia, 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia, 46012, Spain
| | - Ruben Artero
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menéndez Pelayo 4 acc., Valencia, 46010, Spain.,University Institute for Biotechnology and Biomedicine, Dr. Moliner 50, Burjasot, Valencia, 46100, Spain.,CIPF-INCLIVA Joint Unit, Valencia, 46012, Spain
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8
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Cox DC, Guan X, Xia Z, Cooper TA. Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting. Hum Mol Genet 2020; 29:1729-1744. [PMID: 32412585 PMCID: PMC7322576 DOI: 10.1093/hmg/ddaa095] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer's disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.
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Affiliation(s)
- Diana C Cox
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiangnan Guan
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Thomas A Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston TX, 77030 USA
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9
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Nikonova E, Kao SY, Spletter ML. Contributions of alternative splicing to muscle type development and function. Semin Cell Dev Biol 2020; 104:65-80. [PMID: 32070639 DOI: 10.1016/j.semcdb.2020.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/30/2022]
Abstract
Animals possess a wide variety of muscle types that support different kinds of movements. Different muscles have distinct locations, morphologies and contractile properties, raising the question of how muscle diversity is generated during development. Normal aging processes and muscle disorders differentially affect particular muscle types, thus understanding how muscles normally develop and are maintained provides insight into alterations in disease and senescence. As muscle structure and basic developmental mechanisms are highly conserved, many important insights into disease mechanisms in humans as well as into basic principles of muscle development have come from model organisms such as Drosophila, zebrafish and mouse. While transcriptional regulation has been characterized to play an important role in myogenesis, there is a growing recognition of the contributions of alternative splicing to myogenesis and the refinement of muscle function. Here we review our current understanding of muscle type specific alternative splicing, using examples of isoforms with distinct functions from both vertebrates and Drosophila. Future exploration of the vast potential of alternative splicing to fine-tune muscle development and function will likely uncover novel mechanisms of isoform-specific regulation and a more holistic understanding of muscle development, disease and aging.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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10
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Auxerre-Plantié E, Nakamori M, Renaud Y, Huguet A, Choquet C, Dondi C, Miquerol L, Takahashi MP, Gourdon G, Junion G, Jagla T, Zmojdzian M, Jagla K. Straightjacket/α2δ3 deregulation is associated with cardiac conduction defects in myotonic dystrophy type 1. eLife 2019; 8:51114. [PMID: 31829940 PMCID: PMC6908436 DOI: 10.7554/elife.51114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/30/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiac conduction defects decrease life expectancy in myotonic dystrophy type 1 (DM1), a CTG repeat disorder involving misbalance between two RNA binding factors, MBNL1 and CELF1. However, how DM1 condition translates into conduction disorders remains poorly understood. Here we simulated MBNL1 and CELF1 misbalance in the Drosophila heart and performed TU-tagging-based RNAseq of cardiac cells. We detected deregulations of several genes controlling cellular calcium levels, including increased expression of straightjacket/α2δ3, which encodes a regulatory subunit of a voltage-gated calcium channel. Straightjacket overexpression in the fly heart leads to asynchronous heartbeat, a hallmark of abnormal conduction, whereas cardiac straightjacket knockdown improves these symptoms in DM1 fly models. We also show that ventricular α2δ3 expression is low in healthy mice and humans, but significantly elevated in ventricular muscles from DM1 patients with conduction defects. These findings suggest that reducing ventricular straightjacket/α2δ3 levels could offer a strategy to prevent conduction defects in DM1.
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Affiliation(s)
- Emilie Auxerre-Plantié
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoan Renaud
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Aline Huguet
- Imagine Institute, Inserm UMR1163, Paris, France.,Centre de Recherche en Myologie, Inserm UMRS974, Sorbonne Universités, Institut de Myologie, Paris, France
| | | | - Cristiana Dondi
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | | | - Masanori P Takahashi
- Department of Functional Diagnostic Science, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Geneviève Gourdon
- Imagine Institute, Inserm UMR1163, Paris, France.,Centre de Recherche en Myologie, Inserm UMRS974, Sorbonne Universités, Institut de Myologie, Paris, France
| | - Guillaume Junion
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Teresa Jagla
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Monika Zmojdzian
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Krzysztof Jagla
- GReD, CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
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Bruels CC, Li C, Mendoza T, Khan J, Reddy HM, Estrella EA, Ghosh PS, Darras BT, Lidov HGW, Pacak CA, Kunkel LM, Modave F, Draper I, Kang PB. Identification of a pathogenic mutation in ATP2A1 via in silico analysis of exome data for cryptic aberrant splice sites. Mol Genet Genomic Med 2019; 7:e552. [PMID: 30688039 PMCID: PMC6418371 DOI: 10.1002/mgg3.552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/12/2018] [Accepted: 12/02/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Pathogenic mutations causing aberrant splicing are often difficult to detect. Standard variant analysis of next-generation sequence (NGS) data focuses on canonical splice sites. Noncanonical splice sites are more difficult to ascertain. METHODS We developed a bioinformatics pipeline that screens existing NGS data for potentially aberrant novel essential splice sites (PANESS) and performed a pilot study on a family with a myotonic disorder. Further analyses were performed via qRT-PCR, immunoblotting, and immunohistochemistry. RNAi knockdown studies were performed in Drosophila to model the gene deficiency. RESULTS The PANESS pipeline identified a homozygous ATP2A1 variant (NC_000016.9:g.28905928G>A; NM_004320.4:c.1287G>A:p.(Glu429=)) that was predicted to cause the omission of exon 11. Aberrant splicing of ATP2A1 was confirmed via qRT-PCR, and abnormal expression of the protein product sarcoplasmic/endoplasmic reticulum Ca++ ATPase 1 (SERCA1) was demonstrated in quadriceps femoris tissue from the proband. Ubiquitous knockdown of SERCA led to lethality in Drosophila, as did knockdown targeting differentiating or fusing myoblasts. CONCLUSIONS This study confirms the potential of novel in silico algorithms to detect cryptic mutations in existing NGS data; expands the phenotypic spectrum of ATP2A1 mutations beyond classic Brody myopathy; and suggests that genetic testing of ATP2A1 should be considered in patients with clinical myotonia.
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Affiliation(s)
- Christine C. Bruels
- Division of Pediatric Neurology, Department of PediatricsUniversity of Florida College of MedicineGainesvilleFlorida
| | - Chengcheng Li
- Division of Pediatric Neurology, Department of PediatricsUniversity of Florida College of MedicineGainesvilleFlorida
| | - Tonatiuh Mendoza
- Department of Health Outcomes & Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFlorida
| | - Jamillah Khan
- Department of Health Outcomes & Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFlorida
| | - Hemakumar M. Reddy
- Division of Pediatric Neurology, Department of PediatricsUniversity of Florida College of MedicineGainesvilleFlorida
- Present address:
Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode Island
| | - Elicia A. Estrella
- Division of Genetics & GenomicsBoston Children’s Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Partha S. Ghosh
- Department of NeurologyBoston Children’s Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Basil T. Darras
- Department of NeurologyBoston Children’s Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Hart G. W. Lidov
- Department of PathologyBoston Children’s Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Christina A. Pacak
- Department of PediatricsUniversity of Florida College of MedicineGainesvilleFlorida
| | - Louis M. Kunkel
- Division of Genetics & GenomicsBoston Children’s Hospital and Harvard Medical SchoolBostonMassachusetts
| | - François Modave
- Department of Health Outcomes & Biomedical InformaticsUniversity of Florida College of MedicineGainesvilleFlorida
- Present address:
Health Sciences Division, Department of Medicine, Center for Health Outcomes and Informatics ResearchLoyola University ChicagoChicagoIllinois
| | - Isabelle Draper
- Molecular Cardiology Research InstituteTufts Medical CenterBostonMassachusetts
| | - Peter B. Kang
- Division of Pediatric Neurology, Department of PediatricsUniversity of Florida College of MedicineGainesvilleFlorida
- Department of Molecular Genetics & MicrobiologyUniversity of Florida College of MedicineGainesvilleFlorida
- Department of NeurologyUniversity of Florida College of MedicineGainesvilleFlorida
- Genetics Institute and Myology InstituteUniversity of FloridaGainesvilleFlorida
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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Souidi A, Zmojdzian M, Jagla K. Dissecting Pathogenetic Mechanisms and Therapeutic Strategies in Drosophila Models of Myotonic Dystrophy Type 1. Int J Mol Sci 2018; 19:E4104. [PMID: 30567354 PMCID: PMC6321436 DOI: 10.3390/ijms19124104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/08/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1), the most common cause of adult-onset muscular dystrophy, is autosomal dominant, multisystemic disease with characteristic symptoms including myotonia, heart defects, cataracts and testicular atrophy. DM1 disease is being successfully modelled in Drosophila allowing to identify and validate new pathogenic mechanisms and potential therapeutic strategies. Here we provide an overview of insights gained from fruit fly DM1 models, either: (i) fundamental with particular focus on newly identified gene deregulations and their link with DM1 symptoms; or (ii) applied via genetic modifiers and drug screens to identify promising therapeutic targets.
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Affiliation(s)
- Anissa Souidi
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Monika Zmojdzian
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
| | - Krzysztof Jagla
- GReD, INSERM U1103, CNRS, UMR6293, University of Clermont Auvergne, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
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