1
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Djordjevic D, Alawneh I, Amburgey K, Yuki KE, Kyriakopoulou LG, Navickiene V, Stavropoulos J, Yoon G, Dowling JJ, Gonorazky H. A novel deep intronic variant in LAMA2 identified by RNA sequencing. Neuromuscul Disord 2024; 39:19-23. [PMID: 38691940 DOI: 10.1016/j.nmd.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
LAMA2-related muscular dystrophy is caused by pathogenic variants of the alpha2 subunit of Laminin. This common form of muscular dystrophy is characterized by elevated CK >1000IU/L, dystrophic changes on muscle biopsy, complete or partial absence of merosin staining, and both central and peripheral nervous system involvement. Advancements in genomic testing using NGS and wider application of RNA sequencing has expanded our knowledge of novel non-coding pathogenic variants in LAMA2. RNA sequencing is an increasingly utilized technique to directly analyze the transcriptome, through creation of a complementary DNA (cDNA) from the transcript within a tissue sample. Here we describe a homozygous deep intronic variant that produces a novel splice junction in LAMA2 identified by RNA sequencing analysis in a patient with a clinical phenotype in keeping with LAMA2-related muscular dystrophy. Furthermore, in this case merosin staining was retained suggestive of a functional deficit.
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Affiliation(s)
- Djurdja Djordjevic
- Division of Neurology, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Issa Alawneh
- Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Kimberly Amburgey
- Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Canada; Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - Kyoko E Yuki
- Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - Lianna G Kyriakopoulou
- Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - Vilma Navickiene
- Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - Jim Stavropoulos
- Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - Grace Yoon
- Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Canada; Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada
| | - James J Dowling
- Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Canada; Division of Genome Diagnostics, The Hospital for Sick Children. University of Toronto. Toronto, Canada; Program of Genetic and Genome Biology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Hernan Gonorazky
- Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, Canada.
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2
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Geist Hauserman J, Laverty CG, Donkervoort S, Hu Y, Silverstein S, Neuhaus SB, Saade D, Vaughn G, Malicki D, Kaur R, Li Y, Luo Y, Liu P, Burr P, Foley AR, Mohassel P, Bönnemann CG. Clinical, immunohistochemical, and genetic characterization of splice-altering biallelic DES variants: Therapeutic implications. HGG ADVANCES 2024; 5:100274. [PMID: 38358893 PMCID: PMC10876619 DOI: 10.1016/j.xhgg.2024.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Abstract
Pathogenic variants in the DES gene clinically manifest as progressive skeletal muscle weakness, cardiomyopathy with associated severe arrhythmias, and respiratory insufficiency, and are collectively known as desminopathies. While most DES pathogenic variants act via a dominant mechanism, recessively acting variants have also been reported. Currently, there are no effective therapeutic interventions for desminopathies of any type. Here, we report an affected individual with rapidly progressive dilated cardiomyopathy, requiring heart transplantation at age 13 years, in the setting of childhood-onset skeletal muscle weakness. We identified biallelic DES variants (c.640-13 T>A and c.1288+1 G>A) and show aberrant DES gene splicing in the affected individual's muscle. Through the generation of an inducible lentiviral system, we transdifferentiated fibroblast cultures derived from the affected individual into myoblasts and validated this system using RNA sequencing. We tested rationally designed, custom antisense oligonucleotides to screen for splice correction in these transdifferentiated cells and a functional minigene splicing assay. However, rather than correctly redirecting splicing, we found them to induce undesired exon skipping. Our results indicate that, while an individual precision-based molecular therapeutic approach to splice-altering pathogenic variants is promising, careful preclinical testing is imperative for each novel variant to test the feasibility of this type of approach for translation.
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Affiliation(s)
- Janelle Geist Hauserman
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | | | | | - Rupleen Kaur
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Yuesheng Li
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yan Luo
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Patrick Burr
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
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3
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Zhong H, Sian V, Johari M, Katayama S, Oghabian A, Jonson PH, Hackman P, Savarese M, Udd B. Revealing myopathy spectrum: integrating transcriptional and clinical features of human skeletal muscles with varying health conditions. Commun Biol 2024; 7:438. [PMID: 38600180 PMCID: PMC11006663 DOI: 10.1038/s42003-024-06143-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Myopathy refers to a large group of heterogeneous, rare muscle diseases. Bulk RNA-sequencing has been utilized for the diagnosis and research of these diseases for many years. However, the existing valuable sequencing data often lack integration and clinical interpretation. In this study, we integrated bulk RNA-sequencing data from 1221 human skeletal muscles (292 with myopathies, 929 controls) from both databases and our local samples. By applying a method similar to single-cell analysis, we revealed a general spectrum of muscle diseases, ranging from healthy to mild disease, moderate muscle wasting, and severe muscle disease. This spectrum was further partly validated in three specific myopathies (97 muscles) through clinical features including trinucleotide repeat expansion, magnetic resonance imaging fat fraction, pathology, and clinical severity scores. This spectrum helped us identify 234 genuinely healthy muscles as unprecedented controls, providing a new perspective for deciphering the hallmark genes and pathways among different myopathies. The newly identified featured genes of general myopathy, inclusion body myositis, and titinopathy were highly expressed in our local muscles, as validated by quantitative polymerase chain reaction.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Rare Disease Center, Huashan Hospital, Fudan University, Shanghai, China.
| | - Veronica Sian
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, Naples, Italy
| | - Mridul Johari
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Shintaro Katayama
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ali Oghabian
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Tampere Neuromuscular Center, University Hospital, Tampere, Finland
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4
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Pluta N, von Moers A, Pechmann A, Stenzel W, Goebel HH, Atlan D, Wolf B, Nanda I, Zaum AK, Rost S. Whole-Genome Sequencing Identified New Structural Variations in the DMD Gene That Cause Duchenne Muscular Dystrophy in Two Girls. Int J Mol Sci 2023; 24:13567. [PMID: 37686372 PMCID: PMC10488134 DOI: 10.3390/ijms241713567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Dystrophinopathies are the most common muscle diseases, especially in men. In women, on the other hand, a manifestation of Duchenne muscular dystrophy is rare due to X-chromosomal inheritance. We present two young girls with severe muscle weakness, muscular dystrophies, and creatine kinase (CK) levels exceeding 10,000 U/L. In the skeletal muscle tissues, dystrophin staining reaction showed mosaicism. The almost entirely skewed X-inactivation in both cases supported the possibility of a dystrophinopathy. Despite standard molecular diagnostics (including multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing (NGS) gene panel sequencing), the genetic cause of the girls' conditions remained unknown. However, whole-genome sequencing revealed two reciprocal translocations between their X chromosomes and chromosome 5 and chromosome 19, respectively. In both cases, the breakpoints on the X chromosomes were located directly within the DMD gene (in introns 54 and 7, respectively) and were responsible for the patients' phenotypes. Additional techniques such as Sanger sequencing, conventional karyotyping and fluorescence in situ hybridization (FISH) confirmed the disruption of DMD gene in both patients through translocations. These findings underscore the importance of accurate clinical data combined with histopathological analysis in pinpointing the suspected underlying genetic disorder. Moreover, our study illustrates the viability of whole-genome sequencing as a time-saving and highly effective method for identifying genetic factors responsible for complex genetic constellations in Duchenne muscular dystrophy (DMD).
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Affiliation(s)
- Natalie Pluta
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Arpad von Moers
- Department of Pediatrics and Neuropediatrics, DRK Kliniken Berlin, 14050 Berlin, Germany
| | - Astrid Pechmann
- Department of Neuropediatrics and Muscle Disorders, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | - Hans-Hilmar Goebel
- Department of Neuropathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117 Berlin, Germany
| | | | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, 1700 Fribourg, Switzerland
| | - Indrajit Nanda
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Ann-Kathrin Zaum
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Rost
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
- Medical Genetics Center (MGZ), 80335 Munich, Germany
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5
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Ng KWP, Chin HL, Chin AXY, Goh DLM. Using gene panels in the diagnosis of neuromuscular disorders: A mini-review. Front Neurol 2022; 13:997551. [PMID: 36313509 PMCID: PMC9602396 DOI: 10.3389/fneur.2022.997551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023] Open
Abstract
The diagnosis of inherited neuromuscular disorders is challenging due to their genetic and phenotypic variability. Traditionally, neurophysiology and histopathology were primarily used in the initial diagnostic approach to these conditions. Sanger sequencing for molecular diagnosis was less frequently utilized as its application was a time-consuming and cost-intensive process. The advent and accessibility of next-generation sequencing (NGS) has revolutionized the evaluation process of genetically heterogenous neuromuscular disorders. Current NGS diagnostic testing approaches include gene panels, whole exome sequencing (WES), and whole genome sequencing (WGS). Gene panels are often the most widely used, being more accessible due to availability and affordability. In this mini-review, we describe the benefits and risks of clinical genetic testing. We also discuss the utility, benefits, challenges, and limitations of using gene panels in the evaluation of neuromuscular disorders.
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Affiliation(s)
- Kay W. P. Ng
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Hui-Lin Chin
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda X. Y. Chin
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Denise Li-Meng Goh
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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6
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Koczwara KE, Lake NJ, DeSimone AM, Lek M. Neuromuscular disorders: finding the missing genetic diagnoses. Trends Genet 2022; 38:956-971. [PMID: 35908999 DOI: 10.1016/j.tig.2022.07.001] [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: 04/15/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022]
Abstract
Neuromuscular disorders (NMDs) are a wide-ranging group of diseases that seriously affect the quality of life of affected individuals. The development of next-generation sequencing revolutionized the diagnosis of NMD, enabling the discovery of hundreds of NMD genes and many more pathogenic variants. However, the diagnostic yield of genetic testing in NMD cohorts remains incomplete, indicating a large number of genetic diagnoses are not identified through current methods. Fortunately, recent advancements in sequencing technologies, analytical tools, and high-throughput functional screening provide an opportunity to circumvent current challenges. Here, we discuss reasons for missing genetic diagnoses in NMD, how emerging technologies and tools can overcome these hurdles, and examine future approaches to improving diagnostic yields in NMD.
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Affiliation(s)
- Katherine E Koczwara
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Nicole J Lake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Alec M DeSimone
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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7
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Williams K, Yokomori K, Mortazavi A. Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays. Front Genet 2022; 13:835099. [PMID: 35646075 PMCID: PMC9136090 DOI: 10.3389/fgene.2022.835099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) has revolutionized modern genomics, but the large size of myotubes and myofibers has restricted use of scRNA-seq in skeletal muscle. For the study of muscle, single-nucleus RNA-seq (snRNA-seq) has emerged not only as an alternative to scRNA-seq, but as a novel method providing valuable insights into multinucleated cells such as myofibers. Nuclei within myofibers specialize at junctions with other cell types such as motor neurons. Nuclear heterogeneity plays important roles in certain diseases such as muscular dystrophies. We survey current methods of high-throughput single cell and subcellular resolution transcriptomics, including single-cell and single-nucleus RNA-seq and spatial transcriptomics, applied to satellite cells, myoblasts, myotubes and myofibers. We summarize the major myonuclei subtypes identified in homeostatic and regenerating tissue including those specific to fiber type or at junctions with other cell types. Disease-specific nucleus populations were found in two muscular dystrophies, FSHD and Duchenne muscular dystrophy, demonstrating the importance of performing transcriptome studies at the single nucleus level in muscle.
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Affiliation(s)
- Katherine Williams
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, United States
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8
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Waldrop MA, Moore SA, Mathews KD, Darbro BW, Medne L, Finkel R, Connolly AM, Crawford TO, Drachman D, Wein N, Habib AA, Krzesniak-Swinarska MA, Zaidman CM, Collins JJ, Jokela M, Udd B, Day JW, Ortiz-Guerrero G, Statland J, Butterfield RJ, Dunn DM, Weiss RB, Flanigan KM. Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy. Hum Mutat 2022; 43:511-528. [PMID: 35165973 PMCID: PMC9901284 DOI: 10.1002/humu.24343] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/11/2022]
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 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.
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Affiliation(s)
- Megan A. Waldrop
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
| | - Steven A. Moore
- Department of Pathology, The University of Iowa, Iowa City, IA, 52242
| | | | | | - Livja Medne
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Anne M. Connolly
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | | | | | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205
| | | | | | - Craig M. Zaidman
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | - James J. Collins
- Department of Pediatric Neurology, Mercy Hospitals, Springfield, MO 65804
| | - Manu Jokela
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland,Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - John W. Day
- Department of Neurology, University of Minnesota Medical Center, Minneapolis, MN 55454
| | | | - Jeff Statland
- Department of Neurology, University of Kansas, Kansas City, KS
| | - Russell J. Butterfield
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Diane M. Dunn
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Robert B. Weiss
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112,Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Kevin M. Flanigan
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
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9
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Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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11
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Manoharan S, Iyyappan OR. A Hybrid Protocol for Finding Novel Gene Targets for Various Diseases Using Microarray Expression Data Analysis and Text Mining. Methods Mol Biol 2022; 2496:41-70. [PMID: 35713858 DOI: 10.1007/978-1-0716-2305-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The advancement in technology for various scientific experiments and the amount of raw data produced from that is enormous, thus giving rise to various subsets of biologists working with genome, proteome, transcriptome, expression, pathway, and so on. This has led to exponential growth in scientific literature which is becoming beyond the means of manual curation and annotation for extracting information of importance. Microarray data are expression data, analysis of which results in a set of up/downregulated lists of genes that are functionally annotated to ascertain the biological meaning of genes. These genes are represented as vocabularies and/or Gene Ontology terms when associated with pathway enrichment analysis need relational and conceptual understanding to a disease. The chapter deals with a hybrid approach we designed for identifying novel drug-disease targets. Microarray data for muscular dystrophy is explored here as an example and text mining approaches are utilized with an aim to identify promisingly novel drug targets. Our main objective is to give a basic overview from a biologist's perspective for whom text mining approaches of data mining and information retrieval is fairly a new concept. The chapter aims to bridge the gap between biologist and computational text miners and bring about unison for a more informative research in a fast and time efficient manner.
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Affiliation(s)
- Sharanya Manoharan
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, Tamilnadu, India.
| | - Oviya Ramalakshmi Iyyappan
- Department of Sciences, Amrita School of Engineering, Amrita Vishwa Vidyapeetham, Chennai, Tamilnadu, India
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12
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Velluva A, Radtke M, Horn S, Popp B, Platzer K, Gjermeni E, Lin CC, Lemke JR, Garten A, Schöneberg T, Blüher M, Abou Jamra R, Le Duc D. Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies. BMC Genomics 2021; 22:802. [PMID: 34743696 PMCID: PMC8573933 DOI: 10.1186/s12864-021-08125-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/26/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND RNA-seq emerges as a valuable method for clinical genetics. The transcriptome is "dynamic" and tissue-specific, but typically the probed tissues to analyze (TA) are different from the tissue of interest (TI) based on pathophysiology. RESULTS We developed Phenotype-Tissue Expression and Exploration (PTEE), a tool to facilitate the decision about the most suitable TA for RNA-seq. We integrated phenotype-annotated genes, used 54 tissues from GTEx to perform correlation analyses and identify expressed genes and transcripts between TAs and TIs. We identified skeletal muscle as the most appropriate TA to inquire for cardiac arrhythmia genes and skin as a good proxy to study neurodevelopmental disorders. We also explored RNA-seq limitations and show that on-off switching of gene expression during ontogenesis or circadian rhythm can cause blind spots for RNA-seq-based analyses. CONCLUSIONS PTEE aids the identification of tissues suitable for RNA-seq for a given pathology to increase the success rate of diagnosis and gene discovery. PTEE is freely available at https://bioinf.eva.mpg.de/PTEE/.
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Affiliation(s)
- Akhil Velluva
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany.
| | - Maximillian Radtke
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Erind Gjermeni
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, 04289, Leipzig, Germany
- Department of Cardiology, Median Centre for Rehabilitation Schmannewitz, 04774, Dahlen, Germany
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Johannes R Lemke
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Antje Garten
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Diana Le Duc
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany.
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany.
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Multiomic Approaches to Uncover the Complexities of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2021; 22:ijms22168954. [PMID: 34445659 PMCID: PMC8396646 DOI: 10.3390/ijms22168954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Despite major progress in treating skeletal muscle disease associated with dystrophinopathies, cardiomyopathy is emerging as a major cause of death in people carrying dystrophin gene mutations that remain without a targeted cure even with new treatment directions and advances in modelling abilities. The reasons for the stunted progress in ameliorating dystrophin-associated cardiomyopathy (DAC) can be explained by the difficulties in detecting pathophysiological mechanisms which can also be efficiently targeted within the heart in the widest patient population. New perspectives are clearly required to effectively address the unanswered questions concerning the identification of authentic and effectual readouts of DAC occurrence and severity. A potential way forward to achieve further therapy breakthroughs lies in combining multiomic analysis with advanced preclinical precision models. This review presents the fundamental discoveries made using relevant models of DAC and how omics approaches have been incorporated to date.
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14
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Ajiro M, Awaya T, Kim YJ, Iida K, Denawa M, Tanaka N, Kurosawa R, Matsushima S, Shibata S, Sakamoto T, Studer R, Krainer AR, Hagiwara M. Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. Nat Commun 2021; 12:4507. [PMID: 34301951 PMCID: PMC8302731 DOI: 10.1038/s41467-021-24705-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/21/2021] [Indexed: 01/10/2023] Open
Abstract
Approximately half of genetic disease-associated mutations cause aberrant splicing. However, a widely applicable therapeutic strategy to splicing diseases is yet to be developed. Here, we analyze the mechanism whereby IKBKAP-familial dysautonomia (FD) exon 20 inclusion is specifically promoted by a small molecule splice modulator, RECTAS, even though IKBKAP-FD exon 20 has a suboptimal 5' splice site due to the IVS20 + 6 T > C mutation. Knockdown experiments reveal that exon 20 inclusion is suppressed in the absence of serine/arginine-rich splicing factor 6 (SRSF6) binding to an intronic splicing enhancer in intron 20. We show that RECTAS directly interacts with CDC-like kinases (CLKs) and enhances SRSF6 phosphorylation. Consistently, exon 20 splicing is bidirectionally manipulated by targeting cellular CLK activity with RECTAS versus CLK inhibitors. The therapeutic potential of RECTAS is validated in multiple FD disease models. Our study indicates that small synthetic molecules affecting phosphorylation state of SRSFs is available as a new therapeutic modality for mechanism-oriented precision medicine of splicing diseases.
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Affiliation(s)
- Masahiko Ajiro
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobuo Tanaka
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shingo Matsushima
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Saiko Shibata
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tetsunori Sakamoto
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Rolenz Studer
- Center for Stem Cell Biology, Sloan Kettering Institute, New York, NY, USA
| | | | - Masatoshi Hagiwara
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan. .,Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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15
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Zhu F, Zhang F, Hu L, Liu H, Li Y. Integrated Genome and Transcriptome Sequencing to Solve a Neuromuscular Puzzle: Miyoshi Muscular Dystrophy and Early Onset Primary Dystonia in Siblings of the Same Family. Front Genet 2021; 12:672906. [PMID: 34276779 PMCID: PMC8283672 DOI: 10.3389/fgene.2021.672906] [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: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Neuromuscular disorders (NMD), many of which are hereditary, affect muscular function. Due to advances in high-throughput sequencing technologies, the diagnosis of hereditary NMDs has dramatically improved in recent years. METHODS AND RESULTS In this study, we report an family with two siblings exhibiting two different NMD, Miyoshi muscular dystrophy (MMD) and early onset primary dystonia (EOPD). Whole exome sequencing (WES) identified a novel monoallelic frameshift deletion mutation (dysferlin: c.4404delC/p.I1469Sfs∗17) in the Dysferlin gene in the index patient who suffered from MMD. This deletion was inherited from his unaffected father and was carried by his younger sister with EOPD. However, immunostaining staining revealed an absence of dysferlin expression in the proband's muscle tissue and thus suggested the presence of the second underlying mutant allele in dysferlin. Using integrated RNA sequencing (RNA-seq) and whole genome sequencing (WGS) of muscle tissue, a novel deep intronic mutation in dysferlin (dysferlin: c.5341-415A > G) was discovered in the index patient. This mutation caused aberrant mRNA splicing and inclusion of an additional pseudoexon (PE) which we termed PE48.1. This PE was inherited from his unaffected mother. PE48.1 inclusion altered the Dysferlin sequence, causing premature termination of translation. CONCLUSION Using integrated genome and transcriptome sequencing, we discovered hereditary MMD and EOPD affecting two siblings of same family. Our results added further weight to the combined use of RNA-seq and WGS as an important method for detection of deep intronic gene mutations, and suggest that integrated sequencing assays are an effective strategy for the diagnosis of hereditary NMDs.
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Affiliation(s)
- Feng Zhu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengxiao Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lizhi Hu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haowen Liu
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yahua Li
- Department of Respiratory Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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16
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Mullin NK, Voigt AP, Cooke JA, Bohrer LR, Burnight ER, Stone EM, Mullins RF, Tucker BA. Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease. Prog Retin Eye Res 2021; 83:100918. [PMID: 33130253 PMCID: PMC8559964 DOI: 10.1016/j.preteyeres.2020.100918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of inherited retinal disease has benefited immensely from molecular genetic analysis over the past several decades. New technologies that allow for increasingly detailed examination of a patient's DNA have expanded the catalog of genes and specific variants that cause retinal disease. In turn, the identification of pathogenic variants has allowed the development of gene therapies and low-cost, clinically focused genetic testing. Despite this progress, a relatively large fraction (at least 20%) of patients with clinical features suggestive of an inherited retinal disease still do not have a molecular diagnosis today. Variants that are not obviously disruptive to the codon sequence of exons can be difficult to distinguish from the background of benign human genetic variations. Some of these variants exert their pathogenic effect not by altering the primary amino acid sequence, but by modulating gene expression, isoform splicing, or other transcript-level mechanisms. While not discoverable by DNA sequencing methods alone, these variants are excellent targets for studies of the retinal transcriptome. In this review, we present an overview of the current state of pathogenic variant discovery in retinal disease and identify some of the remaining barriers. We also explore the utility of new technologies, specifically patient-derived induced pluripotent stem cell (iPSC)-based modeling, in further expanding the catalog of disease-causing variants using transcriptome-focused methods. Finally, we outline bioinformatic analysis techniques that will allow this new method of variant discovery in retinal disease. As the knowledge gleaned from previous technologies is informing targets for therapies today, we believe that integrating new technologies, such as iPSC-based modeling, into the molecular diagnosis pipeline will enable a new wave of variant discovery and expanded treatment of inherited retinal disease.
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Affiliation(s)
- Nathaniel K Mullin
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jessica A Cooke
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Laura R Bohrer
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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17
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BRCA1 and BRCA2 whole cDNA analysis in unsolved hereditary breast/ovarian cancer patients. Cancer Genet 2021; 258-259:10-17. [PMID: 34237702 DOI: 10.1016/j.cancergen.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022]
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA1/2) explain an important fraction of hereditary breast/ovarian cancer (HBOC) cases. Genetic testing generally involves examining coding regions and exon/intron boundaries, thus the frequency of deleterious variants in non-coding regions is unknown. Here we analysed BRCA1/2 whole cDNA in a large cohort of 320 unsolved high-risk HBOC cases in order to identify potential splicing alterations explained by variants in BRCA1/2 deep intronic regions. Whole RNA splicing profiles were analysed by RT-PCR using Sanger sequencing or high-resolution electrophoresis in a QIAxcel instrument. Known predominant BRCA1/2 alternative splicing events were detected, together with two novel events BRCA1 ▼21 and BRCA2 Δ18q_27p. BRCA2 exon 3 skipping was detected in one patient (male) affected with breast cancer, caused by a known Portuguese founder mutation (c.156_157insAluYa5). An altered BRCA2 splicing pattern was detected in three patients, consisting in the up-regulation of ▼20A, Δ22 and ▼20A+Δ22 transcripts. In silico analysis and semi-quantitative data identified the polymorphism BRCA2 c.8755-66T>C as a potential modifier of Δ22 levels. Our findings suggest that mRNA alterations in BRCA1/2 caused by deep intronic variants are rare in Spanish population. However, RNA analysis complements DNA-based strategies allowing the identification of alterations that could go undetected by conventional testing.
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18
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Nicolau S, Milone M, Liewluck T. Guidelines for genetic testing of muscle and neuromuscular junction disorders. Muscle Nerve 2021; 64:255-269. [PMID: 34133031 DOI: 10.1002/mus.27337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Despite recent advances in the understanding of inherited muscle and neuromuscular junction diseases, as well as the advent of a wide range of genetic tests, patients continue to face delays in diagnosis of sometimes treatable disorders. These guidelines outline an approach to genetic testing in such disorders. Initially, a patient's phenotype is evaluated to identify myopathies requiring directed testing, including myotonic dystrophies, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, mitochondrial myopathies, dystrophinopathies, and oculopharyngodistal myopathy. Initial investigation in the remaining patients is generally a comprehensive gene panel by next-generation sequencing. Broad panels have a higher diagnostic yield and can be cost-effective. Due to extensive phenotypic overlap and treatment implications, genes responsible for congenital myasthenic syndromes should be included when evaluating myopathy patients. For patients whose initial genetic testing is negative or inconclusive, phenotypic re-evaluation is warranted, along with consideration of genes and variants not included initially, as well as their acquired mimickers.
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Affiliation(s)
- Stefan Nicolau
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Teerin Liewluck
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
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19
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Williams ZJ, Velez-Irizarry D, Petersen JL, Ochala J, Finno CJ, Valberg SJ. Candidate gene expression and coding sequence variants in Warmblood horses with myofibrillar myopathy. Equine Vet J 2021; 53:306-315. [PMID: 32453872 PMCID: PMC7864122 DOI: 10.1111/evj.13286] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/18/2020] [Accepted: 05/02/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Myofibrillar myopathy (MFM) of unknown aetiology has recently been identified in Warmblood (WB) horses. In humans, 16 genes have been implicated in various MFM-like disorders. OBJECTIVES To identify variants in 16 MFM candidate genes and compare allele frequencies of all variants between MFM WB and non-MFM WB and coding variants with moderate or severe predicted effects in MFM WB with publicly available data of other breeds. To compare differential gene expression and muscle fibre contractile force between MFM and non-MFM WB. STUDY DESIGN Case-control. ANIMALS 8 MFM WB, 8 non-MFM WB, 33 other WB, 32 Thoroughbreds, 80 Quarter Horses and 77 horses of other breeds in public databases. METHODS Variants were called within transcripts of 16 candidate genes using gluteal muscle mRNA sequences aligned to EquCab3.0 and allele frequencies compared by Fisher's exact test among MFM WB, non-MFM WB and public sequences across breeds. Candidate gene differential expression was determined between MFM and non-MFM WB by fitting a negative binomial generalised log-linear model per gene (false discovery rate <0.05). The maximal isometric force/cross-sectional area generated by isolated membrane-permeabilised muscle fibres was determined. RESULTS None of the 426 variants identified in 16 candidate genes were associated with MFM including 26 missense variants. Breed-specific differences existed in allele frequencies. Candidate gene differential expression and muscle fibre-specific force did not differ between MFM WB (143.1 ± 34.7 kPa) and non-MFM WB (140.2 ± 43.7 kPa) (P = .8). MAIN LIMITATIONS RNA-seq-only assays transcripts expressed in skeletal muscle. Other possible candidate genes were not evaluated. CONCLUSIONS Evidence for association of variants with a disease is essential because coding sequence variants are common in the equine genome. Variants identified in MFM candidate genes, including two coding variants offered as commercial MFM equine genetic tests, did not associate with the WB MFM phenotype.
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Affiliation(s)
- Zoë J. Williams
- Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
| | - Deborah Velez-Irizarry
- Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Julien Ochala
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Carrie J. Finno
- University of California at Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Stephanie J. Valberg
- Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
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20
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Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 2021; 16:1276-1296. [PMID: 33462443 DOI: 10.1038/s41596-020-00462-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 11/06/2020] [Indexed: 12/20/2022]
Abstract
RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-causing gene regulatory defects in individuals affected by genetically undiagnosed rare disorders. Pioneering studies have shown that RNA-seq could increase the diagnosis rates over DNA sequencing alone by 8-36%, depending on the disease entity and tissue probed. To accelerate adoption of RNA-seq by human genetics centers, detailed analysis protocols are now needed. We present a step-by-step protocol that details how to robustly detect aberrant expression levels, aberrant splicing and mono-allelic expression in RNA-seq data using dedicated statistical methods. We describe how to generate and assess quality control plots and interpret the analysis results. The protocol is based on the detection of RNA outliers pipeline (DROP), a modular computational workflow that integrates all the analysis steps, can leverage parallel computing infrastructures and generates browsable web page reports.
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21
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Naber M, Hellebrekers D, Nievelstein RAJ, van Hasselt PM, van Jaarsveld RH, Cuppen I, Oegema R. Deep intronic TIMMDC1 variant delays diagnosis of rapidly progressive complex I deficiency. Eur J Med Genet 2020; 64:104120. [PMID: 33278652 DOI: 10.1016/j.ejmg.2020.104120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 12/25/2022]
Abstract
Complex I deficiency is the most common pediatric mitochondrial disease. It can cause a wide range of clinical disorders, including Leigh syndrome. TIMMDC1 encodes an assembly protein of complex I and has been recently associated with early onset mitochondrial disease in three unrelated families. In all three families the same homozygous deep intronic variant was identified leading to inclusion of a new exon resulting in a frameshift and premature stop codon (c.596 + 2146A > G, p.Gly199_Thr200ins5*). Herein, we describe two brothers of Dutch descent, presenting in infancy with hypotonia and respiratory insufficiency and a rapidly progressive and fatal disease course. Laboratory findings and metabolic investigations revealed no specific abnormalities, notably no raised plasma lactate. MRI showed transient lesions in the basal ganglia of brother 1. A muscle biopsy demonstrated complex I deficiency in brother 2. Exome sequencing yielded a novel heterozygous TIMMDC1 variant: c.385C > T, p.(Arg129*). Targeted sequencing revealed the previously published deep intronic variant c.596 + 2146A > G, p.(Gly199_Thr200ins5*) on the second allele which is not detected by exome sequencing. In summary, we present the fourth family with TIMMDC1-related disease, with a novel nonsense variant. This report illustrates the importance of considering mitochondrial disease even when laboratory findings are normal, and the added value of targeted sequencing of introns.
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Affiliation(s)
- Myrthe Naber
- Department of Genetics, University Medical Center Utrecht, Utrecht University, 3508 AB, Utrecht, the Netherlands
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC), P. Debyelaan 25, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Rutger A J Nievelstein
- Department of Radiology, University Medical Center Utrecht, Utrecht University, 3508 AB, Utrecht, the Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht University, 3508 AB, Utrecht, the Netherlands
| | - Inge Cuppen
- Department of Child Neurology, University Medical Center Utrecht, Utrecht University, 3508 AB, Utrecht, the Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, 3508 AB, Utrecht, the Netherlands.
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22
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Shibata S, Ajiro M, Hagiwara M. Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion. Cell Chem Biol 2020; 27:1472-1482.e6. [DOI: 10.1016/j.chembiol.2020.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
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23
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Abstract
The DMD gene is the largest in the human genome, with a total intron content exceeding 2.2Mb. In the decades since DMD was discovered there have been numerous reported cases of pseudoexons (PEs) arising in the mature DMD transcripts of some individuals, either as the result of mutations or as low-frequency errors of the spliceosome. In this review, I collate from the literature 58 examples of DMD PEs and examine the diversity and commonalities of their features. In particular, I note the high frequency of PEs that arise from deep intronic SNVs and discuss a possible link between PEs induced by distal mutations and the regulation of recursive splicing.
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Affiliation(s)
- Niall P Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University and Perron Institute, Perth, Australia
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24
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Xiao H, Zhou WH. [Application of RNA sequencing in clinical diagnosis of Mendelian disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1138-1142. [PMID: 33059815 PMCID: PMC7568994 DOI: 10.7499/j.issn.1008-8830.2005004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Gene panel and whole exome sequencing are now commonly used to detect Mendelian disease, but the current molecular diagnostic rate of DNA sequencing is only 35%-50%. In recent years, RNA sequencing emerges as a promising diagnostic method. It can detect new pathogenic mutations, and analyze allele-specific expression. This will be helpful to understand the relationship between disease genotype and phenotype, and can complement genome sequencing in order to expand the traditional genomic diagnostic methods of Mendelian disease. RNA sequencing is expected to become a routine tool for diagnosing Mendelian diseases. This article reviews the application of RNA sequencing in the clinical diagnosis of Mendelian disease.
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Affiliation(s)
- Hui Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai 201102, China.
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25
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Beecroft SJ, Lamont PJ, Edwards S, Goullée H, Davis MR, Laing NG, Ravenscroft G. The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders. Mol Diagn Ther 2020; 24:641-652. [PMID: 32997275 DOI: 10.1007/s40291-020-00495-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The impact of high-throughput sequencing in genetic neuromuscular disorders cannot be overstated. The ability to rapidly and affordably sequence multiple genes simultaneously has enabled a second golden age of Mendelian disease gene discovery, with flow-on impacts for rapid genetic diagnosis, evidence-based treatment, tailored therapy development, carrier-screening, and prevention of disease recurrence in families. However, there are likely many more neuromuscular disease genes and mechanisms to be discovered. Many patients and families remain without a molecular diagnosis following targeted panel sequencing, clinical exome sequencing, or even genome sequencing. Here we review how massively parallel, or next-generation, sequencing has changed the field of genetic neuromuscular disorders, and anticipate future benefits of recent technological innovations such as RNA-seq implementation and detection of tandem repeat expansions from short-read sequencing.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | | | - Samantha Edwards
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Hayley Goullée
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Mark R Davis
- Neurogenetic Unit, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.,Neurogenetic Clinic, Royal Perth Hospital, Perth, Australia
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
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Xie Z, Sun C, Liu Y, Yu M, Zheng Y, Meng L, Wang G, Cornejo-Sanchez DM, Bharadwaj T, Yan J, Zhang L, Pineda-Trujillo N, Zhang W, Leal SM, Schrauwen I, Wang Z, Yuan Y. Practical approach to the genetic diagnosis of unsolved dystrophinopathies: a stepwise strategy in the genomic era. J Med Genet 2020; 58:743-751. [PMID: 32978268 DOI: 10.1136/jmedgenet-2020-107113] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/02/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate the diagnostic value of implementing a stepwise genetic testing strategy (SGTS) in genetically unsolved cases with dystrophinopathies. METHODS After routine genetic testing in 872 male patients with highly suspected dystrophinopathies, we identified 715 patients with a pathogenic DMD variant. Of the 157 patients who had no pathogenic DMD variants and underwent a muscle biopsy, 142 patients were confirmed to have other myopathies, and 15 suspected dystrophinopathies remained genetically undiagnosed. These 15 patients underwent a more comprehensive evaluation as part of the SGTS pipeline, which included the stepwise analysis of dystrophin mRNA, short-read whole-gene DMD sequencing, long-read whole-gene DMD sequencing and in silico bioinformatic analyses. RESULTS SGTS successfully yielded a molecular diagnosis of dystrophinopathy in 11 of the 15 genetically unsolved cases. We identified 8 intronic and 2 complex structural variants (SVs) leading to aberrant splicing in 10 of 11 patients, of which 9 variants were novel. In one case, a molecular defect was detected on mRNA and protein level only. Aberrant splicing mechanisms included 6 pseudoexon inclusions and 4 alterations of splice sites and splicing regulatory elements. We showed for the first time the exonisation of a MER48 element as a novel pathogenic mechanism in dystrophinopathies. CONCLUSION Our study highlights the high diagnostic utility of implementing a SGTS pipeline in dystrophinopathies with intronic variants and complex SVs.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chengyue Sun
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yilin Liu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Gao Wang
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Diana M Cornejo-Sanchez
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Jin Yan
- Science and Technology, Beijing Epigen Medical Technology Inc, Beijing, China
| | - Lingxiang Zhang
- Science and Technology, Beijing Epigen Medical Technology Inc, Beijing, China
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
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27
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Xie Z, Sun C, Zhang S, Liu Y, Yu M, Zheng Y, Meng L, Acharya A, Cornejo-Sanchez DM, Wang G, Zhang W, Schrauwen I, Leal SM, Wang Z, Yuan Y. Long-read whole-genome sequencing for the genetic diagnosis of dystrophinopathies. Ann Clin Transl Neurol 2020; 7:2041-2046. [PMID: 32951359 PMCID: PMC7545597 DOI: 10.1002/acn3.51201] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/16/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
The precise genetic diagnosis of dystrophinopathies can be challenging, largely due to rare deep intronic variants and more complex structural variants (SVs). We report on the genetic characterization of a dystrophinopathy patient. He remained without a genetic diagnosis after routine genetic testing, dystrophin protein and mRNA analysis, and short‐ and long‐read whole DMD gene sequencing. We finally identified a novel complex SV in DMD via long‐read whole‐genome sequencing. The variant consists of a large‐scale (~1Mb) inversion/deletion‐insertion rearrangement mediated by LINE‐1s. Our study shows that long‐read whole‐genome sequencing can serve as a clinical diagnostic tool for genetically unsolved dystrophinopathies.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Chengyue Sun
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | | | - Yilin Liu
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Diana M Cornejo-Sanchez
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Gao Wang
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, 100034, China
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Walter MA, Rezaie T, Hufnagel RB, Arno G. Ocular genetics in the genomics age. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:860-868. [PMID: 32896097 DOI: 10.1002/ajmg.c.31844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/29/2022]
Abstract
Current genetic screening methods for inherited eye diseases are concentrated on the coding exons of known disease genes (gene panels, clinical exome). These tests have a variable and often limited diagnostic rate depending on the clinical presentation, size of the gene panel and our understanding of the inheritance of the disorder (with examples described in this issue). There are numerous possible explanations for the missing heritability of these cases including undetected variants within the relevant gene (intronic, up/down-stream and structural variants), variants harbored in genes outside the targeted panel, intergenic variants, variants undetectable by the applied technology, complex/non-Mendelian inheritance, and nongenetic phenocopies. In this article we further explore and review methods to investigate these sources of missing heritability.
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Affiliation(s)
- Michael A Walter
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tayebeh Rezaie
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
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29
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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30
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Barthélémy I, Calmels N, Weiss RB, Tiret L, Vulin A, Wein N, Peccate C, Drougard C, Beroud C, Deburgrave N, Thibaud JL, Escriou C, Punzón I, Garcia L, Kaplan JC, Flanigan KM, Leturcq F, Blot S. X-linked muscular dystrophy in a Labrador Retriever strain: phenotypic and molecular characterisation. Skelet Muscle 2020; 10:23. [PMID: 32767978 PMCID: PMC7412789 DOI: 10.1186/s13395-020-00239-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/09/2020] [Indexed: 12/24/2022] Open
Abstract
Background Canine models of Duchenne muscular dystrophy (DMD) are a valuable tool to evaluate potential therapies because they faithfully reproduce the human disease. Several cases of dystrophinopathies have been described in canines, but the Golden Retriever muscular dystrophy (GRMD) model remains the most used in preclinical studies. Here, we report a new spontaneous dystrophinopathy in a Labrador Retriever strain, named Labrador Retriever muscular dystrophy (LRMD). Methods A colony of LRMD dogs was established from spontaneous cases. Fourteen LRMD dogs were followed-up and compared to the GRMD standard using several functional tests. The disease causing mutation was studied by several molecular techniques and identified using RNA-sequencing. Results The main clinical features of the GRMD disease were found in LRMD dogs; the functional tests provided data roughly overlapping with those measured in GRMD dogs, with similar inter-individual heterogeneity. The LRMD causal mutation was shown to be a 2.2-Mb inversion disrupting the DMD gene within intron 20 and involving the TMEM47 gene. In skeletal muscle, the Dp71 isoform was ectopically expressed, probably as a consequence of the mutation. We found no evidence of polymorphism in either of the two described modifier genes LTBP4 and Jagged1. No differences were found in Pitpna mRNA expression levels that would explain the inter-individual variability. Conclusions This study provides a full comparative description of a new spontaneous canine model of dystrophinopathy, found to be phenotypically equivalent to the GRMD model. We report a novel large DNA mutation within the DMD gene and provide evidence that LRMD is a relevant model to pinpoint additional DMD modifier genes.
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Affiliation(s)
- Inès Barthélémy
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Nadège Calmels
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France.,Laboratoire de Diagnostic Génétique-Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, 1 Place de L'Hôpital, 67091, Strasbourg, France
| | - Robert B Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laurent Tiret
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Adeline Vulin
- SQY Therapeutics, Université de Versailles Saint-Quentin-en-Yvelines, Montigny le Bretonneux, France
| | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Cécile Peccate
- SQY Therapeutics, Université de Versailles Saint-Quentin-en-Yvelines, Montigny le Bretonneux, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, Centre de Recherche en Myologie, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Carole Drougard
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Christophe Beroud
- Aix Marseille Université, INSERM, MMG, Bioinformatics & Genetics, Marseille, France.,APHM, Hôpital Timone Enfants, Laboratoire de Génétique Moléculaire, Marseille, France
| | - Nathalie Deburgrave
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Jean-Laurent Thibaud
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Catherine Escriou
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Isabel Punzón
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France
| | - Luis Garcia
- Université de Versailles Saint-Quentin-en-Yvelines, U1179 INSERM, UFR des Sciences de la Santé, Montigny le Bretonneux, France
| | - Jean-Claude Kaplan
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Kevin M Flanigan
- The Center for Gene Therapy, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - France Leturcq
- Laboratoire de biochimie et génétique moléculaire, hôpital Cochin, AP-HP, université Paris Descartes-Sorbonne Paris Cité, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, Centre de Recherche en Myologie, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Stéphane Blot
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, Ecole nationale vétérinaire d'Alfort, 94700, Maisons-Alfort, France.
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31
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Duchenne Muscular Dystrophy: Journey from Histochemistry to Molecular Diagnosis. Indian Pediatr 2020. [DOI: 10.1007/s13312-020-1919-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Bronstein R, Capowski EE, Mehrotra S, Jansen AD, Navarro-Gomez D, Maher M, Place E, Sangermano R, Bujakowska KM, Gamm DM, Pierce EA. A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families. Hum Mol Genet 2020; 29:967-979. [PMID: 32011687 PMCID: PMC7158377 DOI: 10.1093/hmg/ddaa016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/23/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.
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Affiliation(s)
- Revital Bronstein
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Elizabeth E Capowski
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sudeep Mehrotra
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Alex D Jansen
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Navarro-Gomez
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Mathew Maher
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Riccardo Sangermano
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Kinga M Bujakowska
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, Waisman Center Stem Cell Research Program, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Eric A Pierce
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
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Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med 2020; 22:1181-1190. [PMID: 32225167 DOI: 10.1038/s41436-020-0780-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/14/2023] Open
Abstract
PURPOSE RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing. RNA-seq is typically performed on clinically accessible tissues (CATs) from blood and skin. RNA tissue specificity makes it difficult to identify aberrations in relevant but nonaccessible tissues (non-CATs). We determined how RNA-seq from CATs represent splicing in and across genes and non-CATs. METHODS We quantified RNA splicing in 801 RNA-seq samples from 56 different adult and fetal tissues from Genotype-Tissue Expression Project (GTEx) and ArrayExpress. We identified genes and splicing events in each non-CAT and determined when RNA-seq in each CAT would inadequately represent them. We developed an online resource, MAJIQ-CAT, for exploring our analysis for specific genes and tissues. RESULTS In non-CATs, 40.2% of genes have splicing that is inadequately represented by at least one CAT; 6.3% of genes have splicing inadequately represented by all CATs. A majority (52.1%) of inadequately represented genes are lowly expressed in CATs (transcripts per million (TPM) < 1), but 5.8% are inadequately represented despite being well expressed (TPM > 10). CONCLUSION Many splicing events in non-CATs are inadequately evaluated using RNA-seq from CATs. MAJIQ-CAT allows users to explore which accessible tissues, if any, best represent splicing in genes and tissues of interest.
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O. Mousa N, Osman A, Fahmy N, Abdellatif A, Zada S, El-Fawal H. Duchenne Muscular Dystrophy (DMD) Diagnosis: Past and Present Perspectives. Rare Dis 2020. [DOI: 10.5772/intechopen.90862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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35
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Xu Y, Song T, Li Y, Guo F, Jin X, Cheng L, Zheng J, Li C, Zhang Y, Chen B, Zhang J. Identification of two novel insertion abnormal transcripts in two Chinese families affected with Dystrophinopathy. J Clin Lab Anal 2019; 34:e23142. [PMID: 31793735 PMCID: PMC7171295 DOI: 10.1002/jcla.23142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/12/2019] [Accepted: 11/17/2019] [Indexed: 12/16/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is an X‐linked recessive inheritance muscle dystrophy disease, associated with pathogenic variants in the DMD gene. MLPA, DHPLC and DMD sequence studies fail to found the causative alteration in two cases. This study intends to evaluate the disease‐causing mutations and explains the correlation genotype‐phenotype. Methods The mRNA analysis and Long‐range PCR with sequencing were used for molecular diagnosis. Results In case one, an insertion of 78 nucleotides between exons 40 and 41 (r.5739_5740insMN602429:r415_492) was identified in case one. The insertion sequences were highly homologous to the intron 40 (NG_012232.1:g.1001760_g.1001837). Long‐range PCR with sequencing analysis showed that a novel deep intronic DMD mutation (NG_012232.1:g.1001838A>G) was identified, generating a premature stop codon and terminating protein translation. The likely pathogenic mutation was detected in fetal sample. In case two, an insertion of 74 nucleotides which located inside the consensus sequence AG/GT was detected between exons 2 and 3 (r.93_94insMN584887:r61_134), which resulted in a premature stop codon. The insertion sequences were traceable in the intron 2 of DMD gene (NG_012232.1:g.415926_g.415999). We did not perform prenatal DMD gene diagnosis for case two due to lack of sufficient genetic information. Conclusion These findings clarify importance of proceeding to the mRNA analysis when no causative mutations were found neither by MLPA/DHPLC nor gene sequencing so as to reach the molecular confirmation of DMD and carry out an accurate genetic assessment/ carrier status testing.
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Affiliation(s)
- Ying Xu
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Tingting Song
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu Li
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fenfen Guo
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xin Jin
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lu Cheng
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiao Zheng
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Chunyan Li
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yingqi Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an, China
| | - Biliang Chen
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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36
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Rowlands CF, Baralle D, Ellingford JM. Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. Cells 2019; 8:E1513. [PMID: 31779139 PMCID: PMC6953098 DOI: 10.3390/cells8121513] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
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Affiliation(s)
- Charlie F Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, MP808, Tremona Road, Southampton SO16 6YD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
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37
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Araújo CET, Oliveira CMC, Barbosa JD, Oliveira-Filho JP, Resende LAL, Badial PR, Araujo-Junior JP, McCue ME, Borges AS. A large intragenic deletion in the CLCN1 gene causes Hereditary Myotonia in pigs. Sci Rep 2019; 9:15632. [PMID: 31666547 PMCID: PMC6821760 DOI: 10.1038/s41598-019-51286-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the CLCN1 gene are the primary cause of non-dystrophic Hereditary Myotonia in several animal species. However, there are no reports of Hereditary Myotonia in pigs to date. Therefore, the objective of the present study was to characterize the clinical and molecular findings of Hereditary Myotonia in an inbred pedigree. The clinical, electromyographic, histopathological, and molecular findings were evaluated. Clinically affected pigs presented non-dystrophic recessive Hereditary Myotonia. Nucleotide sequence analysis of the entire coding region of the CLCN1 gene revealed the absence of the exons 15 and 16 in myotonic animals. Analysis of the genomic region flanking the deletion unveiled a large intragenic deletion of 4,165 nucleotides. Interestingly, non-related, non-myotonic pigs expressed transcriptional levels of an alternate transcript (i.e., X2) that was identical to the deleted X1 transcript of myotonic pigs. All myotonic pigs and their progenitors were homozygous recessive and heterozygous, respectively, for the 4,165-nucleotide deletion. This is the first study reporting Hereditary Myotonia in pigs and characterizing its clinical and molecular findings. Moreover, to the best of our knowledge, Hereditary Myotonia has never been associated with a genomic deletion in the CLCN1 gene in any other species.
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Affiliation(s)
- C E T Araújo
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, São Paulo, Brazil
| | - C M C Oliveira
- Instituto de Medicina Veterinária, Universidade Federal do Pará, Campus Castanhal, PA, Brazil
| | - J D Barbosa
- Instituto de Medicina Veterinária, Universidade Federal do Pará, Campus Castanhal, PA, Brazil
| | - J P Oliveira-Filho
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, São Paulo, Brazil
| | - L A L Resende
- São Paulo State University (UNESP), Medical School, Botucatu, Brazil
| | - P R Badial
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Starkville, MS, USA
| | - J P Araujo-Junior
- São Paulo State University (UNESP), Institute of Bioscience, Botucatu, Brazil
| | - M E McCue
- College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - A S Borges
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, São Paulo, Brazil.
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38
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Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA, Relling MV, Rodriguez LL, Tamburro C, Green ED. Opportunities, resources, and techniques for implementing genomics in clinical care. Lancet 2019; 394:511-520. [PMID: 31395439 PMCID: PMC6699751 DOI: 10.1016/s0140-6736(19)31140-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Advances in technologies for assessing genomic variation and an increasing understanding of the effects of genomic variants on health and disease are driving the transition of genomics from the research laboratory into clinical care. Genomic medicine, or the use of an individual's genomic information as part of their clinical care, is increasingly gaining acceptance in routine practice, including in assessing disease risk in individuals and their families, diagnosing rare and undiagnosed diseases, and improving drug safety and efficacy. We describe the major types and measurement tools of genomic variation that are currently of clinical importance, review approaches to interpreting genomic sequence variants, identify publicly available tools and resources for genomic test interpretation, and discuss several key barriers in using genomic information in routine clinical practice.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomic and Precision Medicine, Duke University, Durham, NC, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary V Relling
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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39
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Toksoy G, Durmus H, Aghayev A, Bagirova G, Sevinc Rustemoglu B, Basaran S, Avci S, Karaman B, Parman Y, Altunoglu U, Yapici Z, Tekturk P, Deymeer F, Topaloglu H, Kayserili H, Oflazer-Serdaroglu P, Uyguner ZO. Mutation spectrum of 260 dystrophinopathy patients from Turkey and important highlights for genetic counseling. Neuromuscul Disord 2019; 29:601-613. [DOI: 10.1016/j.nmd.2019.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 12/24/2022]
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40
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Tomar S, Moorthy V, Sethi R, Chai J, Low PS, Hong STK, Lai PS. Mutational spectrum of dystrophinopathies in Singapore: Insights for genetic diagnosis and precision therapy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:230-244. [DOI: 10.1002/ajmg.c.31704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Vikaesh Moorthy
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Josiah Chai
- Department of Neurology, National Neuroscience Institute Singapore
| | - Poh Sim Low
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Stacey Tay Kiat Hong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
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41
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Dominov JA, Uyan Ö, McKenna‐Yasek D, Nallamilli BRR, Kergourlay V, Bartoli M, Levy N, Hudson J, Evangelista T, Lochmuller H, Krahn M, Rufibach L, Hegde M, Brown RH. Correction of pseudoexon splicing caused by a novel intronic dysferlin mutation. Ann Clin Transl Neurol 2019; 6:642-654. [PMID: 31019989 PMCID: PMC6469257 DOI: 10.1002/acn3.738] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 01/12/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Dysferlin is a large transmembrane protein that functions in critical processes of membrane repair and vesicle fusion. Dysferlin-deficiency due to mutations in the dysferlin gene leads to muscular dystrophy (Miyoshi myopathy (MM), limb girdle muscular dystrophy type 2B (LGMD2B), distal myopathy with anterior tibial onset (DMAT)), typically with early adult onset. At least 416 pathogenic dysferlin mutations are known, but for approximately 17% of patients, one or both of their pathogenic variants remain undefined following standard exon sequencing methods that interrogate exons and nearby flanking intronic regions but not the majority of intronic regions. METHODS We sequenced RNA from myogenic cells to identify a novel dysferlin pathogenic variant in two affected siblings that previously had only one disease-causing variant identified. We designed antisense oligonucleotides (AONs) to bypass the effects of this mutation on RNA splicing. RESULTS We identified a new pathogenic point mutation deep within dysferlin intron 50i. This intronic variant causes aberrant mRNA splicing and inclusion of an additional pseudoexon (PE, we term PE50.1) within the mature dysferlin mRNA. PE50.1 inclusion alters the protein sequence, causing premature translation termination. We identified this mutation in 23 dysferlinopathy patients (seventeen families), revealing it to be one of the more prevalent dysferlin mutations. We used AON-mediated exon skipping to correct the aberrant PE50.1 splicing events in vitro, which increased normal mRNA production and significantly restored dysferlin protein expression. INTERPRETATION Deep intronic mutations can be a common underlying cause of dysferlinopathy, and importantly, could be treatable with AON-based exon-skipping strategies.
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Affiliation(s)
- Janice A. Dominov
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Özgün Uyan
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Diane McKenna‐Yasek
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Babi Ramesh Reddy Nallamilli
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgia
- Present address:
Perkin Elmer GenomicsWalthamMassachusetts
| | - Virginie Kergourlay
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
| | - Marc Bartoli
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
| | - Nicolas Levy
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
- Département de Génétique MédicaleAPHMHôpital Timone EnfantsMarseilleFrance
| | - Judith Hudson
- Northern Molecular Genetics ServiceNewcastle upon TyneUnited Kingdom
| | - Teresinha Evangelista
- Newcastle University John Walton Centre for Muscular Dystrophy ResearchMRC Centre for Neuromuscular DiseasesInstitute of Genetic MedicineNewcastle upon TyneUnited Kingdom
| | - Hanns Lochmuller
- Newcastle University John Walton Centre for Muscular Dystrophy ResearchMRC Centre for Neuromuscular DiseasesInstitute of Genetic MedicineNewcastle upon TyneUnited Kingdom
- Department of Neuropediatrics and Muscle DisordersFaculty of MedicineMedical Center–University of FreiburgFreiburgGermany
- Centro Nacional de Análisis Genómico (CNAG‐CRG)Center for Genomic RegulationBarcelona Institute of Science and Technology (BIST)BarcelonaCataloniaSpain
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaCanada
- Division of NeurologyDepartment of MedicineThe Ottawa HospitalOttawaCanada
| | - Martin Krahn
- Marseille Medical Genetics ‐ Translational NeuromyologyAix‐Marseille UnivINSERMMMGMarseilleFrance
- Département de Génétique MédicaleAPHMHôpital Timone EnfantsMarseilleFrance
| | | | - Madhuri Hegde
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgia
| | - Robert H. Brown
- Department of NeurologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
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42
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Gonorazky HD, Naumenko S, Ramani AK, Nelakuditi V, Mashouri P, Wang P, Kao D, Ohri K, Viththiyapaskaran S, Tarnopolsky MA, Mathews KD, Moore SA, Osorio AN, Villanova D, Kemaladewi DU, Cohn RD, Brudno M, Dowling JJ. Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease. Am J Hum Genet 2019; 104:466-483. [PMID: 30827497 PMCID: PMC6407525 DOI: 10.1016/j.ajhg.2019.01.012] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Gene-panel and whole-exome analyses are now standard methodologies for mutation detection in Mendelian disease. However, the diagnostic yield achieved is at best 50%, leaving the genetic basis for disease unsolved in many individuals. New approaches are thus needed to narrow the diagnostic gap. Whole-genome sequencing is one potential strategy, but it currently has variant-interpretation challenges, particularly for non-coding changes. In this study we focus on transcriptome analysis, specifically total RNA sequencing (RNA-seq), by using monogenetic neuromuscular disorders as proof of principle. We examined a cohort of 25 exome and/or panel "negative" cases and provided genetic resolution in 36% (9/25). Causative mutations were identified in coding and non-coding exons, as well as in intronic regions, and the mutational pathomechanisms included transcriptional repression, exon skipping, and intron inclusion. We address a key barrier of transcriptome-based diagnostics: the need for source material with disease-representative expression patterns. We establish that blood-based RNA-seq is not adequate for neuromuscular diagnostics, whereas myotubes generated by transdifferentiation from an individual's fibroblasts accurately reflect the muscle transcriptome and faithfully reveal disease-causing mutations. Our work confirms that RNA-seq can greatly improve diagnostic yield in genetically unresolved cases of Mendelian disease, defines strengths and challenges of the technology, and demonstrates the suitability of cell models for RNA-based diagnostics. Our data set the stage for development of RNA-seq as a powerful clinical diagnostic tool that can be applied to the large population of individuals with undiagnosed, rare diseases and provide a framework for establishing minimally invasive strategies for doing so.
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Affiliation(s)
- Hernan D Gonorazky
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergey Naumenko
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Viswateja Nelakuditi
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Pouria Mashouri
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peiqui Wang
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dennis Kao
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Krish Ohri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Katherine D Mathews
- Departments of Pediatrics and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Andres N Osorio
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Hospital Universitari Sant Joan de Deu, Barcelona 08950, Spain; Center for the Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Barcelona 08950, Spain
| | - David Villanova
- GenomicTales Parc de la Mola, 10, AD700 Escaldes-Engordany, Andorra
| | - Dwi U Kemaladewi
- Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Michael Brudno
- Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5G 0A4, Canada.
| | - James J Dowling
- Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada; Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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43
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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44
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Boisson B, Honda Y, Ajiro M, Bustamante J, Bendavid M, Gennery AR, Kawasaki Y, Ichishima J, Osawa M, Nihira H, Shiba T, Tanaka T, Chrabieh M, Bigio B, Hur H, Itan Y, Liang Y, Okada S, Izawa K, Nishikomori R, Ohara O, Heike T, Abel L, Puel A, Saito MK, Casanova JL, Hagiwara M, Yasumi T. Rescue of recurrent deep intronic mutation underlying cell type-dependent quantitative NEMO deficiency. J Clin Invest 2018; 129:583-597. [PMID: 30422821 DOI: 10.1172/jci124011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/08/2018] [Indexed: 12/20/2022] Open
Abstract
X-linked dominant incontinentia pigmenti (IP) and X-linked recessive anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) are caused by loss-of-function and hypomorphic IKBKG (also known as NEMO) mutations, respectively. We describe a European mother with mild IP and a Japanese mother without IP, whose 3 boys with EDA-ID died from ID. We identify the same private variant in an intron of IKBKG, IVS4+866 C>T, which was inherited from and occurred de novo in the European mother and Japanese mother, respectively. This mutation creates a new splicing donor site, giving rise to a 44-nucleotide pseudoexon (PE) generating a frameshift. Its leakiness accounts for NF-κB activation being impaired but not abolished in the boys' cells. However, aberrant splicing rates differ between cell types, with WT NEMO mRNA and protein levels ranging from barely detectable in leukocytes to residual amounts in induced pluripotent stem cell-derived (iPSC-derived) macrophages, and higher levels in fibroblasts and iPSC-derived neuronal precursor cells. Finally, SRSF6 binds to the PE, facilitating its inclusion. Moreover, SRSF6 knockdown or CLK inhibition restores WT NEMO expression and function in mutant cells. A recurrent deep intronic splicing mutation in IKBKG underlies a purely quantitative NEMO defect in males that is most severe in leukocytes and can be rescued by the inhibition of SRSF6 or CLK.
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Affiliation(s)
- Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Yoshitaka Honda
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiko Ajiro
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Matthieu Bendavid
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Andrew R Gennery
- Institute of Cellular Medicine, Newcastle University and Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Yuri Kawasaki
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Jose Ichishima
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hiroshi Nihira
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Shiba
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Hong Hur
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, USA
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,The Charles Bronfman Institute for Personalized Medicine, and.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yupu Liang
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, USA
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Kazusa DNA Research Institute, Kisarazu, Japan
| | - Toshio Heike
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France.,Howard Hughes Medical Institute (HHMI), New York, New York, USA
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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45
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Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens. J Microbiol Methods 2018; 154:55-62. [PMID: 30332617 DOI: 10.1016/j.mimet.2018.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/12/2018] [Accepted: 10/13/2018] [Indexed: 02/08/2023]
Abstract
With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association pathways of microbial pathogens and their hosts. This approach, therefore, holds promise for applicability in infectious disease diagnostics. A challenge of this approach in the clinical setting is the low amount and quality of RNA, especially microbial RNA in most clinically-infected specimens. Here, we compared two commercially available stranded cDNA library preparation kits, the NuGEN Ovation SoLo RNA-Seq System and the Illumina TruSeq Stranded Total RNA, using RNA extracted from synovial and sonicate fluids from a subject with periprosthetic joint infection. The Ovation SoLo RNA-Seq System provided more useful transcriptomic data for the infecting bacterium, whereas the TruSeq Stranded Total RNA kit provided more useful human transcriptomic data.
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46
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Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. Physiol Genomics 2018; 50:1036-1050. [PMID: 30289745 PMCID: PMC6337024 DOI: 10.1152/physiolgenomics.00044.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log2 fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log2 FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log2 FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log2 FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan.,Department of Population Sciences, University of Minnesota , St. Paul, Minnesota
| | - Sudeep Perumbakkam
- Department of Large Animal Clinical Sciences, Michigan State University , East Lansing, Michigan
| | - Erica C McKenzie
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University , Corvallis, Oregon
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis , Davis, California
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47
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Beecroft SJ, Lombard M, Mowat D, McLean C, Cairns A, Davis M, Laing NG, Ravenscroft G. Genetics of neuromuscular fetal akinesia in the genomics era. J Med Genet 2018; 55:505-514. [PMID: 29959180 DOI: 10.1136/jmedgenet-2018-105266] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/22/2018] [Accepted: 04/19/2018] [Indexed: 12/27/2022]
Abstract
Fetal hypokinesia or akinesia encompasses a broad spectrum of disorders, united by impaired movement in utero. Often, the underlying aetiology is genetic in origin, affecting part of the neuromuscular system. The affordable and high-throughput nature of next-generation DNA sequencing has led to an explosion in disease gene discovery across rare diseases, including fetal akinesias. A genetic diagnosis has clinical utility as it may affect management and prognosis and informs recurrence risk, facilitating family planning decisions. More broadly, knowledge of disease genes increasingly allows population-based preconception carrier screening, which has reduced the incidence of recessive diseases in several populations. Despite gains in knowledge of the genetics of fetal akinesia, many families lack a genetic diagnosis. In this review, we describe the developments in Mendelian genetics of neuromuscular fetal akinesia in the genomics era. We examine genetic diagnoses with neuromuscular causes, specifically including the lower motor neuron, peripheral nerve, neuromuscular junction and muscle.
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Affiliation(s)
- Sarah Jane Beecroft
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Marcus Lombard
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Catriona McLean
- Victorian Neuromuscular Laboratory, Alfred Health, Melbourne, Victoria, Australia
| | - Anita Cairns
- Department of Neurology, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Mark Davis
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
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48
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André LM, Ausems CRM, Wansink DG, Wieringa B. Abnormalities in Skeletal Muscle Myogenesis, Growth, and Regeneration in Myotonic Dystrophy. Front Neurol 2018; 9:368. [PMID: 29892259 PMCID: PMC5985300 DOI: 10.3389/fneur.2018.00368] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/07/2018] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) and 2 (DM2) are autosomal dominant degenerative neuromuscular disorders characterized by progressive skeletal muscle weakness, atrophy, and myotonia with progeroid features. Although both DM1 and DM2 are characterized by skeletal muscle dysfunction and also share other clinical features, the diseases differ in the muscle groups that are affected. In DM1, distal muscles are mainly affected, whereas in DM2 problems are mostly found in proximal muscles. In addition, manifestation in DM1 is generally more severe, with possible congenital or childhood-onset of disease and prominent CNS involvement. DM1 and DM2 are caused by expansion of (CTG•CAG)n and (CCTG•CAGG)n repeats in the 3' non-coding region of DMPK and in intron 1 of CNBP, respectively, and in overlapping antisense genes. This critical review will focus on the pleiotropic problems that occur during development, growth, regeneration, and aging of skeletal muscle in patients who inherited these expansions. The current best-accepted idea is that most muscle symptoms can be explained by pathomechanistic effects of repeat expansion on RNA-mediated pathways. However, aberrations in DNA replication and transcription of the DM loci or in protein translation and proteome homeostasis could also affect the control of proliferation and differentiation of muscle progenitor cells or the maintenance and physiological integrity of muscle fibers during a patient's lifetime. Here, we will discuss these molecular and cellular processes and summarize current knowledge about the role of embryonic and adult muscle-resident stem cells in growth, homeostasis, regeneration, and premature aging of healthy and diseased muscle tissue. Of particular interest is that also progenitor cells from extramuscular sources, such as pericytes and mesoangioblasts, can participate in myogenic differentiation. We will examine the potential of all these types of cells in the application of regenerative medicine for muscular dystrophies and evaluate new possibilities for their use in future therapy of DM.
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Affiliation(s)
- Laurène M André
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - C Rosanne M Ausems
- Department of Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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49
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Teye EK, Sido A, Xin P, Finnberg NK, Gokare P, Kawasawa YI, Salzberg AC, Shimko S, Bayerl M, Ehmann WC, Claxton DF, Rybka WB, Drabick JJ, Wang HG, Abraham T, El-Deiry WS, Brodsky RA, J Hohl R, Pu JJ. PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features. Oncotarget 2018; 8:29887-29905. [PMID: 28187452 PMCID: PMC5444711 DOI: 10.18632/oncotarget.15136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/11/2017] [Indexed: 11/26/2022] Open
Abstract
Previous studies have linked increased frequency of glycosylphosphatidylinositol-anchor protein (GPI-AP) deficiency with genomic instability and the risk of carcinogenesis. However, the underlying mechanism is still not clear. A randomForest analysis of the gene expression array data from 55 MDS patients (GSE4619) demonstrated a significant (p = 0.0007) correlation (Pearson r =-0.4068) between GPI-anchor biosynthesis gene expression and genomic instability, in which PIGN, a gene participating in GPI-AP biosynthesis, was ranked as the third most important in predicting risk of MDS progression. Furthermore, we observed that PIGN gene expression aberrations (increased transcriptional activity but diminished to no protein production) were associated with increased frequency of GPI-AP deficiency in leukemic cells during leukemic transformation/progression. PIGN gene expression aberrations were attributed to partial intron retentions between exons 14 and 15 resulting in frameshifts and premature termination which were confirmed by examining the RNA-seq data from a group of AML patients (phs001027.v1.p1). PIGN gene expression aberration correlated with the elevation of genomic instability marker expression that was independent of the TP53 regulatory pathway. Suppression/elimination of PIGN protein expression caused a similar pattern of genomic instability that was rescued by PIGN restoration. Finally, we found that PIGN bound to the spindle assembly checkpoint protein, MAD1, and regulated its expression during the cell cycle. In conclusion, PIGN gene is crucial in regulating mitotic integrity to maintain chromosomal stability and prevents leukemic transformation/progression.
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Affiliation(s)
- Emmanuel K Teye
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Abigail Sido
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ping Xin
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Niklas K Finnberg
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Prashanth Gokare
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Yuka I Kawasawa
- Institute for Personalized Medicine and Departments of Pharmacology, Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Anna C Salzberg
- Institute for Personalized Medicine and Departments of Pharmacology, Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Sara Shimko
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Michael Bayerl
- Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - W Christopher Ehmann
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - David F Claxton
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Witold B Rybka
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA.,Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Joseph J Drabick
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Hong-Gang Wang
- Department of Pediatrics, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Thomas Abraham
- Department of Neural and Behavioral Science and the Microscopy Imaging Facility, Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Wafik S El-Deiry
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Robert A Brodsky
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raymond J Hohl
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Jeffrey J Pu
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA.,Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
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50
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Clinical Utility Gene Card for: Becker muscular dystrophy. Eur J Hum Genet 2018; 26:1065-1071. [PMID: 29467387 DOI: 10.1038/s41431-017-0064-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/10/2017] [Accepted: 11/23/2017] [Indexed: 12/28/2022] Open
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