Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy
DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle‐derived RNA is an important diagnostic step for patients who have ne...
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| Published in | Human mutation Vol. 43; no. 4; pp. 511 - 528 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
John Wiley & Sons, Inc
01.04.2022
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1059-7794 1098-1004 1098-1004 |
| DOI | 10.1002/humu.24343 |
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| Abstract | DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle‐derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription‐polymerase chain reaction or high‐throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3ʹ‐terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP‐mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full‐length dystrophin expression for some patients.
Intron mutations include the novel mechanism of pseudo‐3'UTR creation, confirmed by RNA Seq. |
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| AbstractList | DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients. DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle‐derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription‐polymerase chain reaction or high‐throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3ʹ‐terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP‐mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full‐length dystrophin expression for some patients. Intron mutations include the novel mechanism of pseudo‐3'UTR creation, confirmed by RNA Seq. DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients. DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle‐derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription‐polymerase chain reaction or high‐throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3ʹ‐terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP‐mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full‐length dystrophin expression for some patients. DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription PCR (RT-PCR) or high-throughput RNA sequencing (RNA-Seq) methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3’-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD . We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients. |
| Author | Udd, Bjarne Dunn, Diane M. Darbro, Benjamin W. Zaidman, Craig M. Statland, Jeff Krzesniak‐Swinarska, Monika A. Day, John W. Drachman, Daniel Wein, Nicolas Finkel, Richard Jokela, Manu Mathews, Katherine D. Habib, Ali A. Connolly, Anne M. Moore, Steven A. Butterfield, Russell J. Waldrop, Megan A. Medne, Livja Collins, James J. Flanigan, Kevin M. Weiss, Robert B. Crawford, Thomas O. Ortiz‐Guerrero, Gloria |
| AuthorAffiliation | 8 Department of Neurology, Washington University, Saint Louis, MO 63110 18 Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112 6 Children’s Hospital of Philadelphia, Philadelphia, PA 19104 9 Johns Hopkins University, Baltimore, MD 21218 1 The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205 13 Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland 10 Columbia University, New York, NY 10032 15 Department of Neurology, University of Minnesota Medical Center, Minneapolis, MN 55454 4 Department of Pathology, The University of Iowa, Iowa City, IA, 52242 11 Department of Neurology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 2 Department of Neurology, The Ohio State University, Columbus, OH 43205 3 Department of Pediatrics, The Ohio State University, Columbus, OH 43205 5 Depatment of Pediatrics, The University of Iowa, Iowa City, IA, 52242 7 Nemours Children’ |
| AuthorAffiliation_xml | – name: 2 Department of Neurology, The Ohio State University, Columbus, OH 43205 – name: 14 Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland – name: 11 Department of Neurology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 – name: 3 Department of Pediatrics, The Ohio State University, Columbus, OH 43205 – name: 12 Department of Pediatric Neurology, Mercy Hospitals, Springfield, MO 65804 – name: 13 Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland – name: 17 Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112 – name: 8 Department of Neurology, Washington University, Saint Louis, MO 63110 – name: 9 Johns Hopkins University, Baltimore, MD 21218 – name: 1 The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205 – name: 6 Children’s Hospital of Philadelphia, Philadelphia, PA 19104 – name: 16 Department of Neurology, University of Kansas, Kansas City, KS – name: 10 Columbia University, New York, NY 10032 – name: 18 Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112 – name: 5 Depatment of Pediatrics, The University of Iowa, Iowa City, IA, 52242 – name: 4 Department of Pathology, The University of Iowa, Iowa City, IA, 52242 – name: 7 Nemours Children’s Hospital, Orlando, FL 32827 – name: 15 Department of Neurology, University of Minnesota Medical Center, Minneapolis, MN 55454 |
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| Keywords | Becker muscular dystrophy deep intronic telescripting Duchenne muscular dystrophy transcription termination pseudoexon |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Current affiliation: University of California, Irvine, CA 92697 Current affiliation: St. Jude Children’s Research Hospital, Memphis TN 38105 Current affiliation: Department of Neurology, Stanford University Medical Center, Palo Alto, CA 94304 Current Affiliation: The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205 Author contributions: MAW, RBW and KMF contributed to the conception and design of study, acquisition and analysis of data and drafting a significant portion of the manuscript or figures. SAM and BWD contributed to acquisition and analysis of data and drafting a significant portion of the manuscript or figures. KDM, LM, RF, AMC, TOC, DD, NW, AH, MAK-S, CMZ, JJC, MJ, BU, JWD, GO-G, JS, RJB and DMD contributed to the acquisition and analysis of data. All authors critically reviewed and revised the manuscript. |
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| Snippet | DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA.... DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA.... |
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| SubjectTerms | Becker muscular dystrophy Becker's muscular dystrophy Biopsy deep intronic DNA-directed RNA polymerase Duchenne muscular dystrophy Dystrophin Dystrophin - genetics Genomics Humans Introns Introns - genetics Muscular dystrophy Muscular Dystrophy, Duchenne - diagnosis Muscular Dystrophy, Duchenne - genetics Muscular Dystrophy, Duchenne - pathology Mutation Patients Polymerase chain reaction pseudoexon Reverse transcription Ribonucleoproteins (small nuclear) RNA polymerase RNA Splice Sites telescripting Transcription termination Translocation |
| Title | Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy |
| URI | https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fhumu.24343 https://www.ncbi.nlm.nih.gov/pubmed/35165973 https://www.proquest.com/docview/2643702702 https://www.proquest.com/docview/2629059647 https://pubmed.ncbi.nlm.nih.gov/PMC9901284 |
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