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Mei H, Boom J, El Abdellaoui S, Abdelmohsen K, Munk R, Martindale JL, Kloet S, Kielbasa SM, Sharp TH, Gorospe M, Raz V. Alternative polyadenylation utilization results in ribosome assembly and mRNA translation deficiencies in a model for muscle aging. J Gerontol A Biol Sci Med Sci 2022; 77:1130-1140. [PMID: 35245938 PMCID: PMC9159670 DOI: 10.1093/gerona/glac058] [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: 11/09/2021] [Indexed: 11/15/2022] Open
Abstract
Aging-associated muscle wasting is regulated by multiple molecular processes, whereby aberrant mRNA processing regulation induces muscle wasting. The poly(A)-binding protein nuclear 1 (PABPN1) regulates polyadenylation site (PAS) utilization, in the absence of PABPN1 the alternative PAS (APA) is utilized. Reduced PABPN1 levels induce muscle wasting where the expression of cellular processes regulating protein homeostasis, the ubiquitin-proteasome system, and translation, are robustly dysregulated. Translation is impacted by mRNA levels, but PABPN1 impact on translation is not fully understood. Here we show that a persistent reduction in PABPN1 levels led to a significant loss of translation efficiency. RNA sequencing of rRNA-depleted libraries from polysome traces revealed reduced mRNA abundance across ribosomal fractions, as well as reduced levels of small RNAs. We show that the abundance of translated mRNAs in the polysomes correlated with PAS switches at the 3'-UTR. Those mRNAs are enriched in cellular processes that are essential for proper muscle function. This study suggests that the effect of PABPN1 on translation efficiency impacts protein homeostasis in aging-associated muscle atrophy.
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Affiliation(s)
- Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Salma El Abdellaoui
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Szymone M Kielbasa
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden The Netherlands
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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2
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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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3
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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4
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Regulation of Kv11.1 Isoform Expression by Polyadenylate Binding Protein Nuclear 1. Int J Mol Sci 2021; 22:ijms22020863. [PMID: 33467093 PMCID: PMC7829756 DOI: 10.3390/ijms22020863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/03/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
The Kv11.1 voltage-gated potassium channel, encoded by the KCNH2 gene, conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation to generate two C-terminal Kv11.1 isoforms in the heart. Utilization of a poly(A) signal in exon 15 produces the full-length, functional Kv11.1a isoform, while intron 9 polyadenylation generates the C-terminally truncated, nonfunctional Kv11.1a-USO isoform. The relative expression of Kv11.1a and Kv11.1a-USO isoforms plays an important role in the regulation of Kv11.1 channel function. In this study, we tested the hypothesis that the RNA polyadenylate binding protein nuclear 1 (PABPN1) interacts with a unique 22 nt adenosine stretch adjacent to the intron 9 poly(A) signal and regulates KCNH2 pre-mRNA alternative polyadenylation and the relative expression of Kv11.1a C-terminal isoforms. We showed that PABPN1 inhibited intron 9 poly(A) activity using luciferase reporter assays, tandem poly(A) reporter assays, and RNA pulldown assays. We also showed that PABPN1 increased the relative expression level of the functional Kv11.1a isoform using RNase protection assays, immunoblot analyses, and patch clamp recordings. Our present findings suggest a novel role for the RNA-binding protein PABPN1 in the regulation of functional and nonfunctional Kv11.1 isoform expression.
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5
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Olie CS, van der Wal E, Cikes D, Maton L, de Greef JC, Lin IH, Chen YF, Kareem E, Penninger JM, Kessler BM, Raz V. Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability. Sci Rep 2020; 10:17621. [PMID: 33077830 PMCID: PMC7572364 DOI: 10.1038/s41598-020-74676-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/28/2020] [Indexed: 12/30/2022] Open
Abstract
Muscle wasting and atrophy are regulated by multiple molecular processes, including mRNA processing. Reduced levels of the polyadenylation binding protein nucleus 1 (PABPN1), a multifactorial regulator of mRNA processing, cause muscle atrophy. A proteomic study in muscles with reduced PABPN1 levels suggested dysregulation of sarcomeric and cytoskeletal proteins. Here we investigated the hypothesis that reduced PABPN1 levels lead to an aberrant organization of the cytoskeleton. MURC, a plasma membrane-associated protein, was found to be more abundant in muscles with reduced PABPN1 levels, and it was found to be expressed at regions showing regeneration. A polarized cytoskeletal organization is typical for muscle cells, but muscle cells with reduced PABPN1 levels (named as shPAB) were characterized by a disorganized cytoskeleton that lacked polarization. Moreover, cell mechanical features and myogenic differentiation were significantly reduced in shPAB cells. Importantly, restoring cytoskeletal stability, by actin overexpression, was beneficial for myogenesis, expression of sarcomeric proteins and proper localization of MURC in shPAB cell cultures and in shPAB muscle bundle. We suggest that poor cytoskeletal mechanical features are caused by altered expression levels of cytoskeletal proteins and contribute to muscle wasting and atrophy.
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Affiliation(s)
| | - Erik van der Wal
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Domagoj Cikes
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Loes Maton
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessica C de Greef
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - I-Hsuan Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Fan Chen
- College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Elsayad Kareem
- Advanced Microscopy Facility, Vienna Biocenter Core Facilities, Vienna Biocenter (VBC), Vienna, Austria
| | - Josef M Penninger
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield, Department of Medicine, University of Oxford, Oxford, UK
| | - Vered Raz
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands.
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6
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Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020; 10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
A crucial feature of gene expression involves RNA processing to produce 3′ ends through a process termed 3′ end cleavage and polyadenylation (CPA). This ensures the nascent RNA molecule can exit the nucleus and be translated to ultimately give rise to a protein which can execute a function. Further, alternative polyadenylation (APA) can produce distinct transcript isoforms, profoundly expanding the complexity of the transcriptome. CPA is carried out by multi-component protein complexes interacting with multiple RNA motifs and is tightly coupled to transcription, other steps of RNA processing, and even epigenetic modifications. CPA and APA contribute to the maintenance of a multitude of diverse physiological processes. It is therefore not surprising that disruptions of CPA and APA can lead to devastating disorders. Here, we review potential CPA and APA mechanisms involving both loss and gain of function that can have tremendous impacts on health and disease. Ultimately we highlight the emerging diagnostic and therapeutic potential CPA and APA offer.
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Affiliation(s)
- Jamie Nourse
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefano Spada
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, Germany
- Correspondence:
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7
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Ye C, Lin J, Li QQ. Discovery of alternative polyadenylation dynamics from single cell types. Comput Struct Biotechnol J 2020; 18:1012-1019. [PMID: 32382395 PMCID: PMC7200215 DOI: 10.1016/j.csbj.2020.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative polyadenylation (APA) occurs in the process of mRNA maturation by adding a poly(A) tail at different locations, resulting increased diversity of mRNA isoforms and contributing to the complexity of gene regulatory network. Benefit from the development of high-throughput sequencing technologies, we could now delineate APA profiles of transcriptomes at an unprecedented pace. Especially the single cell RNA sequencing (scRNA-seq) technologies provide us opportunities to interrogate biological details of diverse and rare cell types. Despite increasing evidence showing that APA is involved in the cell type-specific regulation and function, efficient and specific laboratory methods for capturing poly(A) sites at single cell resolution are underdeveloped to date. In this review, we summarize existing experimental and computational methods for the identification of APA dynamics from diverse single cell types. A future perspective is also provided.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
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8
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Wang J, Li MY, Yang J, Wang YQ, Wu XY, Huang J, Ying YL, Long YT. Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface. ACS CENTRAL SCIENCE 2020; 6:76-82. [PMID: 31989027 PMCID: PMC6978832 DOI: 10.1021/acscentsci.9b01129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 05/06/2023]
Abstract
DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.
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Affiliation(s)
- Jiajun Wang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Meng-Yin Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
| | - Jie Yang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Xue-Yuan Wu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Jin Huang
- School
of Pharmacy, East China University of Science
and Technology, 200237, Shanghai, China
| | - Yi-Lun Ying
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
| | - Yi-Tao Long
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
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9
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Alonso-Jimenez A, Kroon RHMJM, Alejaldre-Monforte A, Nuñez-Peralta C, Horlings CGC, van Engelen BGM, Olivé M, González L, Verges-Gil E, Paradas C, Márquez C, Garibaldi M, Gallano P, Rodriguez MJ, Gonzalez-Quereda L, Dominguez Gonzalez C, Vissing J, Fornander F, Eisum ASV, García-Sobrino T, Pardo J, García-Figueiras R, Muelas N, Vilchez JJ, Kapetanovic S, Tasca G, Monforte M, Ricci E, Gomez MT, Bevilacqua JA, Diaz-Jara J, Zamorano II, Carlier RY, Laforet P, Pelayo-Negro A, Ramos-Fransi A, Martínez A, Marini-Bettolo C, Straub V, Gutiérrez G, Stojkovic T, Martín MA, Morís G, Fernández-Torrón R, Lopez De Munaín A, Cortes-Vicente E, Querol L, Rojas-García R, Illa I, Diaz-Manera J. Muscle MRI in a large cohort of patients with oculopharyngeal muscular dystrophy. J Neurol Neurosurg Psychiatry 2019; 90:576-585. [PMID: 30530568 DOI: 10.1136/jnnp-2018-319578] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND OBJECTIVE Oculopharyngeal muscular dystrophy (OPMD) is a genetic disorder caused by an abnormal expansion of GCN triplets within the PABPN1 gene. Previous descriptions have focused on lower limb muscles in small cohorts of patients with OPMD, but larger imaging studies have not been performed. Previous imaging studies have been too small to be able to correlate imaging findings to genetic and clinical data. METHODS We present cross-sectional, T1-weighted muscle MRI and CT-scan data from 168 patients with genetically confirmed OPMD. We have analysed the pattern of muscle involvement in the disease using hierarchical analysis and presented it as heatmaps. Results of the scans were correlated with genetic and clinical data. RESULTS Fatty replacement was identified in 96.7% of all symptomatic patients. The tongue, the adductor magnus and the soleus were the most commonly affected muscles. Muscle pathology on MRI correlated positively with disease duration and functional impairment. CONCLUSIONS We have described a pattern that can be considered characteristic of OPMD. An early combination of fat replacement in the tongue, adductor magnus and soleus can be helpful for differential diagnosis. The findings suggest the natural history of the disease from a radiological point of view. The information generated by this study is of high diagnostic value and important for clinical trial development.
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Affiliation(s)
- Alicia Alonso-Jimenez
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain
| | | | | | | | - Corinne G C Horlings
- Neurology Department, Radboud university Medical Center, Nijmegen, The Netherlands
| | | | - Montse Olivé
- Pathology Department (Neuropathology), Neuromuscular Disorders Unit, IDIBELL, Hospital de Bellvitge, Barcelona, Spain
| | - Laura González
- Pathology Department (Neuropathology), Neuromuscular Disorders Unit, IDIBELL, Hospital de Bellvitge, Barcelona, Spain
| | - Enric Verges-Gil
- Pathology Department (Neuropathology), Neuromuscular Disorders Unit, IDIBELL, Hospital de Bellvitge, Barcelona, Spain
| | - Carmen Paradas
- Neuromuscular Disorders Unit, Neurology Department, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla, Sevilla, Spain
| | - Celedonio Márquez
- Neuromuscular Disorders Unit, Neurology Department, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla, Sevilla, Spain
| | - Matteo Garibaldi
- Neuromuscular Disorders Unit, Department of Neurology, Mental Health and Sensory Organs (NESMOS), SAPIENZA University of Rome, Ospedale Sant'Andrea, Rome, Italy
| | - Pía Gallano
- Genetic Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | | | - Lidia Gonzalez-Quereda
- Genetic Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Cristina Dominguez Gonzalez
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain.,Neuromuscular Disorders Unit, Neurology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - John Vissing
- Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Freja Fornander
- Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Sofie Vibæk Eisum
- Copenhagen Neuromuscular Center, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Julio Pardo
- Neurology Department, Hospital Clínico, Santiago de Compostela, Spain
| | | | - Nuria Muelas
- 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, Valencia, Spain
| | - Juan Jesús 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, Valencia, Spain
| | | | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A, Gemelli IRCCS, Roem, Italy
| | - Mauro Monforte
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A, Gemelli IRCCS, Roem, Italy.,Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A, Gemelli IRCCS, Roem, Italy.,Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - María Teresa Gomez
- Neurology Department, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Jorge Alfredo Bevilacqua
- Departamento de Neurología y Neurocirugía, Hospital Clínico Universidad de Chile, Programa de Anatomía y Medicina Legal, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jorge Diaz-Jara
- Centro de imagenología, Hospital Clínico Universidad de Chile, Universidad de Chile, Santiago, Chile
| | - Ivonne Ingrid Zamorano
- Servicio de Neurología, Hospital de Puerto Montt, Servicio de Salud del Reloncavi, Los Lagos Region, Chile
| | - Robert Yves Carlier
- Assistance Publique des Hôpitaux de Paris (AP-HP), Service d'Imagerie Médicale, Pôle Neuro-locomoteur, Hôpital Raymond Poincaré, Garches, Hôpitaux Universitaires Paris-Ile-de-France Ouest, Garches, France
| | - Pascal Laforet
- Assistance Publique des Hôpitaux de Paris (AP-HP), Service de neurologie, Pôle Neuro-locomoteur, Hôpital Raymond Poincaré, Garches, Hôpitaux Universitaires Paris-Ile-de-France Ouest, Garches, France
| | - Ana Pelayo-Negro
- Neurology Department, University Hospital "Marqués de Valdecilla (IDIVAL)", University of Cantabria, and "Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)", Santander, Spain
| | - Alba Ramos-Fransi
- Neurology Department, Hospital Germans Trias I Pujol, Barcelona, Spain
| | | | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gerardo Gutiérrez
- Neurology Department, Hospital Infanta Sofía, San Sebastián de los Reyes, Spain
| | - Tanya Stojkovic
- Institute of Myology, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Germán Morís
- Neurology Department, Hospital Universitario Central de Asturias, Asturias, Spain
| | - Roberto Fernández-Torrón
- Neurology Department, Hospital Donostia, San Sebastián, Spain.,Neuromuscular Area, Neurology Service, Biodonostia Health Research Institute, Donostia University Hospital, Donostia-San Sebastián, Spain
| | - Adolfo Lopez De Munaín
- Neurology Department, Hospital Donostia, San Sebastián, Spain.,Neuromuscular Area, Neurology Service, Biodonostia Health Research Institute, Donostia University Hospital, Donostia-San Sebastián, Spain
| | - Elena Cortes-Vicente
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Luis Querol
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Ricardo Rojas-García
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Isabel Illa
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Jordi Diaz-Manera
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu I Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain .,Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
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10
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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11
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Harish P, Dickson G, Malerba A. Advances in emerging therapeutics for oculopharyngeal muscular dystrophy. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1536542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Pradeep Harish
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - George Dickson
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Alberto Malerba
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
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12
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Raz V, Riaz M, Tatum Z, Kielbasa SM, 't Hoen PAC. The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs. FASEB J 2018; 32:1579-1590. [PMID: 29141996 DOI: 10.1096/fj.201700861r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies among muscles. Muscle-specific molecular mechanisms in healthy and normal conditions could designate changes in physiologic and pathologic conditions. We generated deep mRNA-sequencing data in adult fast and slow mouse muscles, and applying paired analysis, we identified that the muscle-specific signatures are composed of half of the muscle transcriptome. The fast muscles showed a more compact gene network that is concordant with homogenous myofiber typing, compared with the pattern in the slow muscle. The muscle-specific mRNA landscape did not correlate with alternative spicing, alternative polyadenylation, or the expression of muscle transcription factor gene networks. However, we found significant correlation between the differentially expressed noncoding RNAs, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) and their target genes. More than 25% of the genes expressed in a muscle-specific fashion were found to be targets of muscle-specific miRNAs and lncRNAs. We suggest that muscle-specific miRNAs and lncRNAs contribute to the establishment of muscle-specific transcriptomes in adult muscles.-Raz, V., Riaz, M., Tatum, Z., Kielbasa, S. M., 't Hoen, P. A. C. The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.
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Affiliation(s)
- Vered Raz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Muhammad Riaz
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M Kielbasa
- Department of Medical Statistics and Bioinformatics, Bioinformatics Center of Expertise, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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13
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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14
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Raz V, Dickson G, 't Hoen PAC. Dysfunctional transcripts are formed by alternative polyadenylation in OPMD. Oncotarget 2017; 8:73516-73528. [PMID: 29088723 PMCID: PMC5650278 DOI: 10.18632/oncotarget.20640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/03/2017] [Indexed: 11/25/2022] Open
Abstract
Post-transcription mRNA processing in the 3’-untranslated region (UTR) of transcripts alters mRNA landscape. Alternative polyadenylation (APA) utilization in the 3’-UTR often leads to shorter 3’-UTR affecting mRNA stability, a process that is regulated by PABPN1. In skeletal muscles PABPN1 levels reduce with age and a greater decrease in found in Oculopharyngeal muscular dystrophy (OPMD). OPMD is a late onset autosomal dominant myopathy caused by expansion mutation in PABPN1. In OPMD models a shift from distal to proximal polyadenylation site utilization in the 3’-UTR, and PABPN1 was shown to play a prominent role in APA. Whether PABPN1-mediated APA transcripts are functional is not fully understood. We investigate nuclear export and translation efficiency of transcripts in OPMD models. We focused on autophagy-regulated genes (ATGs) with APA utilization in cell models with reduced functional PABPN1. We provide evidence that ATGs transcripts from distal PAS retain in the nucleus and thus have reduced translation efficiency in cells with reduced PABPN1. In contrast, transcripts from proximal PAS showed a higher cytoplasmic abundance but a reduced occupancy in the ribosome. We therefore suggest that in reduced PABPN1 levels ATG transcripts from APA may not effectively translate to proteins. In those conditions we found constitutive autophagosome fusion and reduced autophagy flux. Augmentation of PABPN1 restored autophagosome fusion, suggesting that PABPN1-mediated APA plays a role in autophagy in OPMD and in aging muscles.
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Affiliation(s)
- Vered Raz
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - George Dickson
- School of Biological Science, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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