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Chen K, Wei E, Mitanoska A, Gearhart MD, Kyba M, Bosnakovski D. Dux Is Dispensable for Skeletal Muscle Regeneration: A Study Inspired by a "Red Flagged" Publication and Editorial Oversight. Cells 2025; 14:695. [PMID: 40422198 DOI: 10.3390/cells14100695] [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: 04/17/2025] [Revised: 04/30/2025] [Accepted: 05/07/2025] [Indexed: 05/28/2025] Open
Abstract
Double homeobox (DUX) genes are key embryonic regulators that are silenced after the early cleavage stages of embryogenesis. Aberrant expression of DUX4 in skeletal muscle is linked to facioscapulohumeral muscular dystrophy (FSHD). A recent study reported that Dux, the murine ortholog of DUX4, contributes to the dystrophic phenotype in mdx mice, a Duchenne muscular dystrophy (DMD) model, and that its deletion enhances muscle regeneration by reducing oxidative stress. However, convincing evidence of Dux expression in either intact or injured muscle of wild-type (WT) and mdx mice remains lacking, raising questions about its role in muscle homeostasis. To investigate this, we assessed Dux expression in WT and mdx mice and used Dux knockout (DuxΔ/Δ) mice to evaluate its function during regeneration following cardiotoxin (CTX)-induced injury. Contrary to prior reports, Dux was not expressed in either WT or mdx mice. Moreover, Dux deletion did not enhance muscle regeneration or affect the expression of the oxidative stress regulator Nrf2 following CTX injury. Lastly, we confirmed that neither DUX4 nor its target genes were induced in muscle biopsies from DMD patients, excluding a role for DUX4 in DMD pathology. Collectively, our results demonstrate that Dux does not impact skeletal muscle regeneration or DUX4 contribution to the DMD dystrophic phenotype, directly challenging the conclusions of a previously published study. We comment on issues of editorial oversight that led to the publication of that study and highlight the deleterious impact of the growing wave of fraudulent publications.
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Affiliation(s)
- Kenric Chen
- Department of Pediatrics and Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erdong Wei
- Department of Pediatrics and Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ana Mitanoska
- Department of Pediatrics and Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Micah D Gearhart
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Department of Pediatrics and Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darko Bosnakovski
- Department of Pediatrics and Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
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Eisfeldt J, Ek M, Nordenskjöld M, Lindstrand A. Toward clinical long-read genome sequencing for rare diseases. Nat Genet 2025:10.1038/s41588-025-02160-y. [PMID: 40335760 DOI: 10.1038/s41588-025-02160-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 03/11/2025] [Indexed: 05/09/2025]
Abstract
Genetic diagnostics is driven by technological advances, forming a tight interface between research, clinic and industry, which enables rapid implementation of new technologies. Short-read genome and exome sequencing, the current state of the art in clinical genetics, can detect a broad spectrum of genetic variants across the genome. However, despite these advancements, more than half of individuals with rare diseases remain undiagnosed after genomic investigations. Long-read whole-genome sequencing (LR-WGS) is a promising technology that identifies previously difficult-to-detect variants while also enabling phasing and methylation analysis and has the potential of generating complete personal assemblies. To pave the way for clinical use of LR-WGS, the clinical genomic community must establish standardized protocols and quality parameters while also developing innovative tools for data analysis and interpretation. In this Perspective, we explore the key challenges and benefits in integrating LR-WGS into routine clinical diagnostics.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Marlene Ek
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden.
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Matsumura T, Hashimoto H, Takizawa H, Yoshioka W, Mori-Yoshimura M, Saito Y, Nishino I, Nakamura H. Clinical and genetic characteristics based on the Japanese patient registry for facioscapulohumeral muscular dystrophy: a nationwide analysis. Neuromuscul Disord 2025; 50:105346. [PMID: 40203460 DOI: 10.1016/j.nmd.2025.105346] [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: 12/21/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/11/2025]
Abstract
The Japanese patient registry for facioscapulohumeral muscular dystrophy (FSHD) was launched in September 2020, enrolling patients genetically confirmed to have FSHD. This study aimed to analyze clinical and genetic characteristics based on data from the Japanese FSHD registry. Core items were collected from the TREAT-NMD FSHD dataset, version 1.0. By the end of June 2024, over 200 patients were enrolled, with 161 successfully registered after confirmation. Among them, 156 had FSHD1 and 5 had FSHD2; 81 had affected family members; 116 were ambulatory; 73 had respiratory dysfunction; 22 required mechanical ventilation; 8 had cardiac dysfunction; 4 had retinopathy; and 22 had hearing loss. In patients with FSHD1, the median number of D4Z4 repeats was four, with a low proportion of long repeats. D4Z4 repeat counts influenced age at disease onset, site-specific muscle weakness onset, respiratory function, retinopathy, and hearing loss. Notably, female patients were more likely to have early facial weakness and hearing loss. Our data suggest population diversity in D4Z4 repeat numbers and sex differences. We aim to collaborate with patient groups to enroll more participants and gather more accurate epidemiological data, including cases of FSHD2. Additionally, we plan to investigate racial differences through international collaboration.
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Affiliation(s)
- Tsuyoshi Matsumura
- Department of Neurology, NHO Osaka Toneyama Medical Center, Toneyama 5-1-1, Toyonaka, Osaka 560-8552, Japan.
| | - Hiroya Hashimoto
- Clinical Research Center, NHO Nagoya Medical Center, Sannomaru 4-1-1, Naka-ku, Nagoya, Aichi 460-0001, Japan
| | - Hotake Takizawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
| | - Wakako Yoshioka
- Department of Neuromuscular Research, National Institute of Neuroscience, NCNP, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
| | - Madoka Mori-Yoshimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
| | - Yoshihiko Saito
- Department of Neuromuscular Research, National Institute of Neuroscience, NCNP, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, NCNP, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
| | - Harumasa Nakamura
- Department of Clinical Research Support, NCNP, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8551, Japan
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Xia X, Cheng N, Liu Y, Yue D, Gao M, Hu C, Jiao K, Wang N, Zhu B, Chang X, Zeng M, Song J, Sun C, Yan C, Xi J, Lin J, Luo S, Wang Z, Lu J, Jones PL, Zhao C, Wu Q, Zhu W. 4qA D4Z4 Methylation Test as a Valuable Complement for Differential Diagnosis in Patients with a Facioscapulohumeral Muscular Dystrophy-Like Phenotype. J Mol Diagn 2025; 27:405-418. [PMID: 40113166 DOI: 10.1016/j.jmoldx.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 01/24/2025] [Accepted: 02/12/2025] [Indexed: 03/22/2025] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by pleiotropic contractions of the D4Z4 repeat array on chromosome 4q35 (FSHD1) or by mutations in repressive chromatin regulators of the D4Z4 loci (FSHD2), both resulting in epigenetic dysregulation at the D4Z4 array. DNA methylation of the D4Z4 repeat array has been proposed for diagnosis and prognosis of FSHD disease severity; however, further validation in larger populations is needed. Two hundred forty-seven clinically suspected FSHD cases were retrospectively analyzed with D4Z4 analysis by optical genome mapping or molecular combing and tested the DNA methylation levels for 75 patients and 49 healthy controls. A D4Z4 repeat length-dependent nonlinear increase was observed in both distal and global D4Z4 methylation levels. Distal D4Z4 methylation levels identified patients with FSHD1 with a sensitivity of 100% and a specificity of 97.96% at a cutoff value of 39.66% compared with controls. Distal FSHD1-like hypomethylation was also observed in one subject carrying a special D4Z4 rearrangement, resulting in a proximal contracted array. Clinically, distal methylation levels demonstrated a strong correlation with the age-corrected clinical severity score and onset age. Mediation analysis revealed that the influence of distal methylation on age-corrected clinical severity score was partially mediated by onset age. This study further confirms the distal 4qA D4Z4 methylation analysis as a valuable complement for differential diagnosis in patients with suspected FSHD, including those with complex structural variants.
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Affiliation(s)
- Xingyu Xia
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiqi Liu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chaoping Hu
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China; National Children's Medical Center, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xuechun Chang
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Minghui Zeng
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jie Song
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chong Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chong Yan
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qihan Wu
- Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, National Health Commission Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorder, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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Shams RB, Nieman EL, Perilla-Young Y, Morrell DS, Hildebrandt C. TYMS-ENOSF1 Dyskeratosis Congenita in a Patient With Ring Chromosome 18: A Case Report. Am J Med Genet A 2025:e64081. [PMID: 40207375 DOI: 10.1002/ajmg.a.64081] [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: 02/03/2025] [Revised: 03/11/2025] [Accepted: 03/22/2025] [Indexed: 04/11/2025]
Abstract
Dyskeratosis Congenita (DC) is a rare genetic syndrome due to variants in genes involved in telomeric regulation and maintenance, impacting multiple organ systems. We report a case of DC secondary to TYMS gene deletion in a patient with ring chromosome 18 and related partial monosomy 18p and 18q. TYMS encodes thymidylate synthase, and compound heterozygosity for loss of function variants in TYMS and a specific haplotype of its antisense regulator ENOSFI (enolase super family 1) causes digenic DC. The patient had physical and developmental features of 18p monosomy, including poor growth, feeding issues, distinctive facial features, and strabismus. In early infancy, he developed diffuse hyperpigmentation as well as numerous punctate hypopigmented macules, sparse hair, and nail dystrophy, and diagnosis of DC was confirmed with a telomere length assay. Our case highlights that individuals with deletions at 18p encompassing TYMS should be evaluated for features of digenic dyskeratosis congenita.
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Affiliation(s)
- Rayad B Shams
- University of North Carolina Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Elizabeth L Nieman
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yezmin Perilla-Young
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dean S Morrell
- Department of Dermatology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Clara Hildebrandt
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
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Arends T, Hamm DC, van der Maarel S, Tapscott SJ. Facioscapulohumeral Dystrophy: Molecular Basis and Therapeutic Opportunities. Cold Spring Harb Perspect Biol 2025; 17:a041492. [PMID: 39009417 PMCID: PMC11733064 DOI: 10.1101/cshperspect.a041492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Facioscapulohumeral dystrophy (FSHD) is caused by misexpression of the early embryonic transcription factor Double Homeobox Protein 4 (DUX4) in skeletal muscle. DUX4 is normally expressed at the 4-cell stage of the human embryo and initiates a portion of the first wave of embryonic gene expression that establishes the totipotent cells of the embryo. Following brief expression, the DUX4 locus is suppressed by epigenetic silencing and remains silenced in nearly all somatic cells. Mutations that cause FSHD decrease the efficiency of epigenetic silencing of the DUX4 locus and result in aberrant expression of this transcription factor in skeletal muscles. DUX4 expression in these skeletal muscles reactivates part of the early totipotent program and suppresses the muscle program-resulting in a progressive muscular dystrophy that affects some muscles earlier than others. These advances in understanding the cause of FSHD have led to multiple therapeutic strategies that are now entering clinical trials.
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Affiliation(s)
- Tessa Arends
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Danielle C Hamm
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Silvère van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA
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Paatela EM, St Amant FG, Hamm DC, Bennett SR, Gujral TS, van der Maarel SM, Tapscott SJ. A discrete region of the D4Z4 is sufficient to initiate epigenetic silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.639175. [PMID: 40027792 PMCID: PMC11870474 DOI: 10.1101/2025.02.19.639175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
The DUX4 transcription factor is briefly expressed in the early embryo and is epigenetically repressed in somatic tissues. Loss of epigenetic repression can result in the aberrant expression of DUX4 in skeletal muscle and can cause facioscapulohumeral dystrophy (FSHD). Multiple factors have been identified as necessary to maintain epigenetic silencing of DUX4 in skeletal muscle, but whether specific sequences at the DUX4 locus are sufficient for epigenetic silencing has been unknown. We cloned fragments of the D4Z4 macrosatellite repeat, the DNA region that encompasses the DUX4 retrogene, adjacent to a reporter driven by a constitutive promoter and identified a single fragment sufficient to epigenetically repress reporter gene expression. Previously identified suppressors of DUX4 expression-SETDB1, ATF7IP, SIN3A/B, and LRIF1-were necessary for silencing activity and p38 inhibitors enhanced suppression. These findings identify a key regulatory sequence for D4Z4 epigenetic repression and establish a model system for mechanistic and discovery studies.
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Tan M, Huo H, Feng J, Wang C, Jiang S. Facioscapulohumeral muscular dystrophy type 1 combined with becker muscular dystrophy: a family case report. Front Genet 2025; 15:1522203. [PMID: 39840281 PMCID: PMC11747468 DOI: 10.3389/fgene.2024.1522203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 12/23/2024] [Indexed: 01/23/2025] Open
Abstract
Facioscapulohumeral muscular dystrophy type 1 (FSHD1) and Becker muscular dystrophy (BMD) are distinct disorders caused by different genetic variations and exhibiting different inheritance patterns. The co-occurrence of both conditions within the same family is rare. In this case report, the proband was a 10 year-old boy who presented with eye and mouth orbicular muscles, shoulder and proximal upper and lower limbs weakness. Genetic testing showed that the number of D4Z4 repeat units in the sub-terminal region 4qA of chromosome 4q35 in the proband was only 4 (normal value ≥ 11) and, at the same time, a heterozygous deletion was found in exons 13-29 of DMD gene in the proband, thus the diagnosis was clinically and genetically compatible with both FSHD1 and BMD. Pedigree investigation revealed that his maternal grandmother, mother, aunt and cousin also had muscle weakness in the face, shoulders and limbs. Genetic testing confirmed that each of the four relatives had four D4Z4 repeats in the 4qA region, and all of them carried a heterozygous deletion in exons 13-29 of DMD. Based on the X-linked features of DMD/BMD, the maternal grandmother, mother, and aunt were diagnosed with FSHD1 combined with DMD deletion carriers, and the male cousin was diagnosed with FSHD1 combined with BMD. This study identifies a family with a co-occurrence of clinically overt FSHD1 and BMD, which has important reference value for the diagnosis and treatment of hereditary myopathies.
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Affiliation(s)
| | | | | | | | - Suhua Jiang
- The First People’s Hospital of Foshan, Foshan, China
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Puma A, Tammam G, Ezaru A, Slioui A, Torchia E, Tasca G, Villa L, Cavalli M, Salviati L, van der Vliet PJ, Lemmers RJ, Pini J, van der Maarel SM, Sacconi S. Double trouble: a comprehensive study into unrelated genetic comorbidities in adult patients with Facioscapulohumeral Muscular Dystrophy Type I. Eur J Hum Genet 2025:10.1038/s41431-024-01770-0. [PMID: 39775061 DOI: 10.1038/s41431-024-01770-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 10/22/2024] [Accepted: 12/03/2024] [Indexed: 01/11/2025] Open
Abstract
Facioscapulohumeral dystrophy type 1 (FSHD1) displays prominent intra- and interfamilial variability, which complicates the phenotype-genotype correlation. In this retrospective study, we investigated FSHD1 patients classified as category D according to the Comprehensive Clinical Evaluation Form (CCEF), a category defined by FSHD patients showing uncommon clinical features, to identify genetic causes explaining these uncommon phenotypes. Demographics, clinical data and clinical scales of FSHD1 patients were retrospectively evaluated. Patients were divided into four CCEF categories, and comparisons between groups were performed. In category D, when uncommon features suggested the presence of an unrelated genetic disease, a more extensive collection of data was performed. 157 FSHD1 patients were included in the study (82 males, 75 females) with mean age of 52.1 ± 13.5 years at the time of the study. D4Z4 repeat sizes ranged between 2 and 10 RU. According to the CCEF, 114 patients were classified into category A, 8 into category B and C each, and 27 into category D. In category D, 9 patients presented uncommon features related to commonly acquired comorbidities, whereas in the remaining 18 patients, all but two with upper-sized FSHD1 D4Z4 repeats (7-10 RU), we suspected an unrelated genetic neurological disease based on clinical phenotype. In 14/18 patients, we identified FSHD-unrelated genetic causes, most often unrelated repeat expansion disorders. This emphasizes the need of careful clinical and genetic work-up to avoid confusion between FSHD-intrinsic clinical variability and clinical features unrelated to the disease.
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Affiliation(s)
- Angela Puma
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | - Giulia Tammam
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- IRCCS Mondino Foundation, Pavia, Italy
| | - Andra Ezaru
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | - Abderhmane Slioui
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | | | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Luisa Villa
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | - Michele Cavalli
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | - Leonardo Salviati
- Department of Women's and Children's Health, Clinical Genetics Unit, University of Padova, Padova, Italy
| | | | - Richard Jlf Lemmers
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jonathan Pini
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France
| | | | - Sabrina Sacconi
- Peripheral Nervous System & Muscle Department, Pasteur 2 Hospital, Nice University Hospital, Nice, France.
- Institute for Research on Cancer and Aging of Nice, CNRS, INSERM, Côte d'Azur University, Nice, France.
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Darras BT, Volpe JJ. Muscle Involvement and Restricted Disorders. VOLPE'S NEUROLOGY OF THE NEWBORN 2025:1074-1121.e18. [DOI: 10.1016/b978-0-443-10513-5.00037-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
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11
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Gérard L, Delourme M, Tardy C, Ganne B, Perrin P, Chaix C, Trani JP, Eudes N, Laberthonnière C, Bertaux K, Missirian C, Bassez G, Behin A, Cintas P, Cluse F, De La Cruz E, Delmont E, Evangelista T, Fradin M, Hadouiri N, Kouton L, Laforêt P, Lefeuvre C, Magot A, Manel V, Nectoux J, Pegat A, Sole G, Spinazzi M, Stojkovic T, Svahn J, Tard C, Thauvin C, Verebi C, Salort Campana E, Attarian S, Nguyen K, Badache A, Bernard R, Magdinier F. SMCHD1 genetic variants in type 2 facioscapulohumeral dystrophy and challenges in predicting pathogenicity and disease penetrance. Eur J Hum Genet 2024:10.1038/s41431-024-01781-x. [PMID: 39725690 DOI: 10.1038/s41431-024-01781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 12/09/2024] [Accepted: 12/19/2024] [Indexed: 12/28/2024] Open
Abstract
The molecular diagnosis of type 1 facioscapulohumeral muscular dystrophy (FSHD1) relies on the detection of a shortened D4Z4 array at the 4q35 locus. Until recently, the diagnosis of FSHD2 relied solely on the absence of a shortened D4Z4 allele in clinically affected patients. It is now established that most FSHD2 cases carry a heterozygous variant in the SMCHD1 gene. A decrease in D4Z4 DNA methylation is observed in both FSHD1 and FSHD2 patients. To refine the molecular diagnosis of FSHD2, we performed a molecular diagnosis of SMCHD1 in 54 patients with a clinical diagnosis of FSHD. All patients carry a D4Z4 array of more than 10 D4Z4 units, or a cis-duplication of the locus. Forty-eight of them carry a variant in SMCHD1 and six other cases are hemizygous for the 18p32 locus encompassing SMCHD1. Genetic and epigenetic analyses were considered to assess the pathogenicity of new SMCHD1 variants and of variants previously classified as likely pathogenic. In comparison to the healthy population and FSHD1 patients, we defined a threshold of 40% of methylation at the D4Z4 DR1 site as associated with SMCHD1 variants or SMCHD1 hemizygosity. We also showed that the number of D4Z4 on the shortest 4q allele ranges from 11 up to 35 units in these same patients. Using variant interpretation and protein structure prediction tools, we also highlight the difficulty in interpreting the impact of pathogenic variants on SMCHD1 function. Our study further emphasizes the intriguing relationship between D4Z4 methylation, SMCHD1 variants with SMCHD1 protein structure-function in FSHD.
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Affiliation(s)
- Laurène Gérard
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
| | - Mégane Delourme
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Charlotte Tardy
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Benjamin Ganne
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Pierre Perrin
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Charlene Chaix
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
| | | | - Nathalie Eudes
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | | | - Karine Bertaux
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
- Centre de ressources Biologiques, Biogénopôle, Hôpitaux Universitaires de Marseille, Biogénopôle, 13005, Marseille, France
| | - Chantal Missirian
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Guillaume Bassez
- APHP, Service de Neuromyologie, Institut de Myologie, GH Pitié-Salpêtrière, Paris, France
- Neuromuscular Morphology Unit, Neuromuscular Investigation Center, Institute of Myology, Pitié-Salpêtrière Hospital, Paris, France
| | - Anthony Behin
- APHP, Service de Neuromyologie, Institut de Myologie, GH Pitié-Salpêtrière, Paris, France
| | - Pascal Cintas
- Centre de référence neuromusculaire, CHU Toulouse Purpan, Toulouse, France
| | - Florent Cluse
- Electroneuromyography and Neuromuscular Diseases Unit, Pierre Wertheimer Hospital, Hospices Civils de Lyon, Bron, France
| | - Elisa De La Cruz
- Département de Neurologie, CHU Gui de Chauliac, Montpellier, France
| | - Emilien Delmont
- Centre de références des Maladies neuromusculaires et de la SLA, Hôpitaux Universitaires de Marseille, Hôpital Timone Adulte, Marseille, France
| | - Teresinha Evangelista
- APHP, Service de Neuromyologie, Institut de Myologie, GH Pitié-Salpêtrière, Paris, France
- Neuromuscular Morphology Unit, Neuromuscular Investigation Center, Institute of Myology, Pitié-Salpêtrière Hospital, Paris, France
| | - Mélanie Fradin
- Service de génétique Médicale CHU Rennes, Rennes, Centre de Compétences Maladies Neuromusculaires de Rennes, Rennes, France
| | - Nawale Hadouiri
- INSERM-Université Bourgogne U1231, Equipe GAD Génétique des Anomalies du Développement Dijon, Dijon, France
- Pôle Rééducation-Réadaptation, CHU Dijon-Bourgogne, Dijon, France
| | - Ludivine Kouton
- Centre de références des Maladies neuromusculaires et de la SLA, Hôpitaux Universitaires de Marseille, Hôpital Timone Adulte, Marseille, France
| | - Pascal Laforêt
- Neurology Department, Raymond Poincaré University Hospital, Garches, APHP, Paris, France
- Nord-Est-Ile-de-France Neuromuscular Reference Center, Ile-de-Franc, FHU PHENIX, France
| | - Claire Lefeuvre
- Neurology Department, Raymond Poincaré University Hospital, Garches, APHP, Paris, France
| | - Armelle Magot
- Centre de Référence des Maladies Neuromusculaires AOC, CHU de Nantes, Filnemus, Euro-NMD, Nantes, France
| | - Véronique Manel
- L'Escale, Service de Médecine Physique et de Réadaptation Pédiatrique, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Groupement Est, Bron, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP Centre - Université Paris Cité, Hôpital Cochin, 75014, Paris, France
| | - Antoine Pegat
- Electroneuromyography and Neuromuscular Diseases Unit, Pierre Wertheimer Hospital, Hospices Civils de Lyon, Bron, France
| | - Guilhem Sole
- Centre de Référence des Maladies Neuromusculaires AOC, Service de Neurologie et Maladies Neuromusculaires, FILNEMUS, EURONMD, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Marco Spinazzi
- Neuromuscular Reference Center, Department of Neurology, CHU d'Angers, d'Angers, France
| | - Tanya Stojkovic
- APHP, Service de Neuromyologie, Institut de Myologie, GH Pitié-Salpêtrière, Paris, France
| | - Juliette Svahn
- Electroneuromyography and Neuromuscular Diseases Unit, Pierre Wertheimer Hospital, Hospices Civils de Lyon, Bron, France
| | - Celine Tard
- Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
- Centre de référence des maladies neuromusculaires Nord/Est/Ile- de- France, Lille, France
| | - Christel Thauvin
- INSERM-Université Bourgogne U1231, Equipe GAD Génétique des Anomalies du Développement Dijon, Dijon, France
- Centre de Génétique, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP Centre - Université Paris Cité, Hôpital Cochin, 75014, Paris, France
| | - Emmanuelle Salort Campana
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
- Centre de références des Maladies neuromusculaires et de la SLA, Hôpitaux Universitaires de Marseille, Hôpital Timone Adulte, Marseille, France
| | - Shahram Attarian
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
- Centre de références des Maladies neuromusculaires et de la SLA, Hôpitaux Universitaires de Marseille, Hôpital Timone Adulte, Marseille, France
| | - Karine Nguyen
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Ali Badache
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
| | - Rafaëlle Bernard
- Service de Génétique Médicale, Biogénopôle, Hôpitaux Universitaires de Marseille, Marseille, France
- Aix-Marseille Univ-INSERM, Marseille Medical Genetics, Marseille, France
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12
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Rashnonejad A, Farea M, Amini-Chermahini G, Coulis G, Taylor N, Fowler A, Villalta A, King OD, Harper SQ. Sustained efficacy of CRISPR-Cas13b gene therapy for FSHD is challenged by immune response to Cas13b. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.18.629250. [PMID: 39829765 PMCID: PMC11741234 DOI: 10.1101/2024.12.18.629250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a potentially devastating muscle disease caused by de-repression of the toxic DUX4 gene in skeletal muscle. FSHD patients may benefit from DUX4 inhibition therapies, and although several experimental strategies to reduce DUX4 levels in skeletal muscle are being developed, no approved disease modifying therapies currently exist. We developed a CRISPR-Cas13b system that cleaves DUX4 mRNA and reduces DUX4 protein level, protects cells from DUX4-mediated death, and reduces FSHD-associated biomarkers in vitro . In vivo delivery of the CRISPR-Cas13b system with adeno-associated viral vectors reduced acute damage caused by high DUX4 levels in a mouse model of severe FSHD. However, protection was not sustained over time, with decreases in Cas13b and guide RNA levels between 8 weeks and 6 months after injection. In addition, wild-type mice injected with AAV6.Cas13b showed muscle inflammation with infiltrates containing Cas13b-responsive CD8+ cytotoxic T cells. Our RNA-seq data confirmed that several immune response pathways were significantly increased in human FSHD myoblasts transfected with Cas13b. Overall, our findings suggest that CRISPR-Cas13b is highly effective for DUX4 silencing but successful implementation of CRISPR/Cas13-based gene therapies may require strategies to mitigate immune responses.
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13
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Wang Y, Zhao Z, Meng F, Kong X. Accurate prenatal diagnosis of facioscapulohumeral muscular dystrophy 1 using nanopore sequencing. J Med Genet 2024; 61:1096-1102. [PMID: 39461849 DOI: 10.1136/jmg-2023-109832] [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: 12/20/2023] [Accepted: 10/06/2024] [Indexed: 10/29/2024]
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy 1 (FSHD1) is an autosomal dominant muscular disorder mainly caused by the contraction and hypomethylation of the D4Z4 repeat array in chromosome 4q35. Prenatal diagnosis of FSHD1 is challenging due to the highly repetitive and long genomic structure. In this study, a pregnant woman diagnosed with FSHD1 using optical genome mapping sought assistance for a healthy offspring. METHODS At the 17th week of gestation, she underwent amniocentesis, and genomic DNA (gDNA) was extracted from amniocytes. Whole-genome sequencing of the gDNA was performed using the nanopore MinION platform. RESULTS Despite a sequencing depth of only 7.3×, bioinformatic analyses revealed that the fetus inherited four D4Z4 repeat units with the permissive 4qA from the mother and the eight D4Z4 repeat units with the non-permissive 4qB from the father. To validate the results, SNP-based linkage analyses were conducted with gDNA from the proband, the proband's father and proband's amniocytes. Results indicated that the fetus inherited the maternal pathogenic haplotype based on 144 informative SNPs. Linkage analysis was consistent with the nanopore sequencing. CONCLUSION Nanopore sequencing proves to be an accurate and direct method for genetic testing of monogenic diseases at the single-nucleotide level. This study represents the first application of nanopore sequencing in the prenatal diagnosis of FSHD1, providing a significant advantage for patients with de novo mutations.
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Affiliation(s)
- Yanan Wang
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Meng
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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14
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Capelletti S, García Soto SC, Gonçalves MAFV. On RNA-programmable gene modulation as a versatile set of principles targeting muscular dystrophies. Mol Ther 2024; 32:3793-3807. [PMID: 39169620 PMCID: PMC11573585 DOI: 10.1016/j.ymthe.2024.08.016] [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: 05/05/2024] [Revised: 07/24/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
The repurposing of RNA-programmable CRISPR systems from genome editing into epigenome editing tools is gaining pace, including in research and development efforts directed at tackling human disorders. This momentum stems from the increasing knowledge regarding the epigenetic factors and networks underlying cell physiology and disease etiology and from the growing realization that genome editing principles involving chromosomal breaks generated by programmable nucleases are prone to unpredictable genetic changes and outcomes. Hence, engineered CRISPR systems are serving as versatile DNA-targeting scaffolds for heterologous and synthetic effector domains that, via locally recruiting transcription factors and chromatin remodeling complexes, seek interfering with loss-of-function and gain-of-function processes underlying recessive and dominant disorders, respectively. Here, after providing an overview about epigenetic drugs and CRISPR-Cas-based activation and interference platforms, we cover the testing of these platforms in the context of molecular therapies for muscular dystrophies. Finally, we examine attributes, obstacles, and deployment opportunities for CRISPR-based epigenetic modulating technologies.
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Affiliation(s)
- Sabrina Capelletti
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Sofía C García Soto
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Manuel A F V Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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15
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Padberg GW. 26 th Meryon Lecture St Anne's College, Oxford, 5th July 2024 FSHD: The long road to DUX4. Neuromuscul Disord 2024; 44:104450. [PMID: 39256100 DOI: 10.1016/j.nmd.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Affiliation(s)
- George W Padberg
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands.
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16
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Sohn S, Reid S, Bowen M, Corbex E, Le Gall L, Sidlauskaite E, Hourde C, Morel B, Mariot V, Dumonceaux J. Molecular, Histological, and Functional Changes in Acta1-MCM;FLExDUX4/+ Mice. Int J Mol Sci 2024; 25:11377. [PMID: 39518930 PMCID: PMC11545788 DOI: 10.3390/ijms252111377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 10/15/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024] Open
Abstract
DUX4 is the major gene responsible for facioscapulohumeral dystrophy (FSHD). Several mouse models expressing DUX4 have been developed, the most commonly used by academic laboratories being ACTA1-MCM/FLExDUX4. In this study, molecular and histological modifications in the tibialis anterior and quadriceps muscles were investigated in this model at different time points. We investigated several changes that could be used as markers of therapeutic efficacy. Our results confirm the progressive muscular dystrophy previously described but also highlight biases associated with tamoxifen injections and the complexity of choosing the genes used to calculate a DUX4-pathway gene composite score. We also developed a comprehensive force test that better reflects the movements made in everyday life. This functional force-velocity-endurance model, which describes the force production capacities at all velocity and fatigue levels, was applied on 12-13-week-old animals without tamoxifen. Our data highlight that previously unsuspected muscle properties are also affected by the expression of DUX4, leading to a weaker muscle with a lower initial muscle force but with preserved power and endurance capacity. Importantly, this force-velocity-endurance approach can be used in humans for clinical evaluations.
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Affiliation(s)
- Solene Sohn
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Sophie Reid
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Maximilien Bowen
- Laboratoire Interuniversitaire de Biologie de la Motricité LIBM, EA 7424, Savoie Mont Blanc University, F-7300 Chambéry, France
| | - Emilio Corbex
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Laura Le Gall
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Eva Sidlauskaite
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Christophe Hourde
- Laboratoire Interuniversitaire de Biologie de la Motricité LIBM, EA 7424, Savoie Mont Blanc University, F-7300 Chambéry, France
| | - Baptiste Morel
- Laboratoire Interuniversitaire de Biologie de la Motricité LIBM, EA 7424, Savoie Mont Blanc University, F-7300 Chambéry, France
| | - Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, London WC1N 1EH, UK; (S.S.); (S.R.)
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17
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Strafella C, Megalizzi D, Trastulli G, Proietti Piorgo E, Colantoni L, Tasca G, Monforte M, Zampatti S, Primiano G, Sancricca C, Bortolani S, Torchia E, Ravera B, Torri F, Gadaleta G, Risi B, Caria F, Gerardi F, Carraro E, Gioiosa V, Garibaldi M, Tufano L, Frezza E, Massa R, Caltagirone C, Pennisi EM, Petrucci A, Pane M, Frongia A, Gragnani F, Scutifero M, Mandich P, Grandis M, Maioli MA, Casali C, Manfroi E, Politano L, Passamano L, Petillo R, Rodolico C, Pugliese A, Previtali SC, Sansone V, Vercelli L, Mongini TE, Ricci G, Siciliano G, Filosto M, Ricci E, Cascella R, Giardina E. Integrating D4Z4 methylation analysis into clinical practice: improvement of FSHD molecular diagnosis through distinct thresholds for 4qA/4qA and 4qA/4qB patients. Clin Epigenetics 2024; 16:148. [PMID: 39438900 PMCID: PMC11520157 DOI: 10.1186/s13148-024-01747-2] [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: 06/18/2024] [Accepted: 09/16/2024] [Indexed: 10/25/2024] Open
Abstract
BACKGROUND Facioscapulohumeral dystrophy (FSHD) is a myopathy characterized by the loss of repressive epigenetic features affecting the D4Z4 locus (4q35). The assessment of DNA methylation at two regions (DUX4-PAS and DR1) of D4Z4 locus proved to be an effective method to detect epigenetic signatures compatible with FSHD. The present study aims at validating the employment of this method into clinical practice and improving the protocol by refining the classification thresholds of 4qA/4qA patients. To this purpose, 218 subjects with clinical suspicion of FSHD collected in 2022-2023 were analyzed. Each participant underwent in parallel the traditional FSHD molecular testing (D4Z4 sizing) and the proposed methylation assay. The results provided by both analyses were compared to evaluate the concordance and calculate the performance metrics of the methylation test. RESULTS Among the 218 subjects, the 4q variant type distribution was 54% 4qA/4qA, 43% 4qA/4qB and 3% 4qB/4qB. The methylation analysis was performed only on carriers of at least one 4qA allele. After refining the classification threshold, the test reached the following performance metrics: sensitivity = 0.90, specificity = 1.00 and accuracy = 0.93. These results confirmed the effectiveness of the methylation assay in identifying patients with genetic signature compatible with FSHD1 and FSHD2 based on their DUX4-PAS and DR1 profile, respectively. The methylation data were also evaluated with respect to the clinical information. CONCLUSIONS The study confirmed the ability of the method to accurately identify methylation profiles compatible with FSHD genetic signatures considering the 4q genotype. Moreover, the test allows the detection of hypomethylated profiles in asymptomatic patients, suggesting its potential application in identifying preclinical conditions in patients with positive family history and FSHD genetic signatures. Furthermore, the present work emphasizes the importance of interpreting methylation profiles considering the patients' clinical data.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
- Department of System Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Emma Proietti Piorgo
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Mauro Monforte
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Stefania Zampatti
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
| | - Guido Primiano
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Cristina Sancricca
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Sara Bortolani
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Eleonora Torchia
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Beatrice Ravera
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Francesca Torri
- Department of Clinical and Experimental Medicine, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Giulio Gadaleta
- Presidio Molinette e OIRM (SS Malattie Neuromuscolari e SC Neuropsichiatria Infantile), AOU Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Barbara Risi
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, Via Paolo Richiedei, 16, 25064, Brescia, Italy
| | - Filomena Caria
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, Via Paolo Richiedei, 16, 25064, Brescia, Italy
| | - Francesca Gerardi
- The NEMO Center in Milan, Neurorehabilitation Unit,, University of Milan, ASST Niguarda Hospital, Piazza Dell'Ospedale Maggiore 3, 20161, Milan, Italy
| | - Elena Carraro
- The NEMO Center in Milan, Neurorehabilitation Unit,, University of Milan, ASST Niguarda Hospital, Piazza Dell'Ospedale Maggiore 3, 20161, Milan, Italy
| | - Valeria Gioiosa
- Department of Medico-Surgical Sciences and Biotechnologies, University of Rome Sapienza, Corso Della Repubblica 79, 4100, Latina, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Centre, Sant'Andrea Hospital, Via Di Grottarossa 1035-1039, 00189, Rome, Italy
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, SAPIENZA University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Laura Tufano
- Neuromuscular and Rare Disease Centre, Sant'Andrea Hospital, Via Di Grottarossa 1035-1039, 00189, Rome, Italy
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, SAPIENZA University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Erica Frezza
- Department of Systems Medicine, Neurology Unit, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Roberto Massa
- Department of Systems Medicine, Neurology Unit, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179, Rome, Italy
| | - Elena Maria Pennisi
- UOC of Neurology, San Filippo Neri Hospital, Via Giovanni Martinotti 20, 00135, Rome, Italy
| | - Antonio Petrucci
- Department of Neurology and Neurophysiopathology, Azienda Ospedaliera San Camillo Forlanini, Circonvallazione Gianicolense, 87, 00149, Rome, Italy
| | - Marika Pane
- Pediatric Neurology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
- Centro Clinico Nemo, Fondazione Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Annalia Frongia
- Centro Clinico Nemo, Fondazione Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Francesca Gragnani
- Neurology and Neurophysiopathology Unit, Sandro Pertini Hospital, Via Dei Monti Tiburtini 385, 00157, Rome, Italy
| | - Marianna Scutifero
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Via Santa Maria Di Costantinopoli 16, 80138, Naples, Italy
| | - Paola Mandich
- IRCCS Ospedale Policlinico San Martino - UOC Genetica Medica, Largo R. Benzi 10, 16132, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Largo Paolo Daneo 3, 16132, Genoa, Italy
| | - Marina Grandis
- IRCCS Ospedale Policlinico San Martino - UOC Genetica Medica, Largo R. Benzi 10, 16132, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Health, University of Genova, Largo Paolo Daneo 3, 16132, Genoa, Italy
| | | | - Carlo Casali
- Department of Medico-Surgical Sciences and Biotechnologies, University of Rome Sapienza, Corso Della Repubblica 79, 4100, Latina, Italy
| | - Elisabetta Manfroi
- Department of Neuroscience- Neurogenetics, Santa Maria Hospital, Viale Tristano Di Joannuccio, 05100, Terni, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Via Santa Maria Di Costantinopoli 16, 80138, Naples, Italy
| | - Luigia Passamano
- Cardiomyology and Medical Genetics, University of Campania Luigi Vanvitelli, Via Santa Maria Di Costantinopoli 16, 80138, Naples, Italy
| | - Roberta Petillo
- Medical and Laboratory Genetics Unit, A.O.R.N. 'Antonio Cardarelli', Via A. Cardarelli 9, 80131, Naples, Italy
| | - Carmelo Rodolico
- Department of Clinical and Experimental Medicine, University of Messina, Piazza Pugliatti 1, 98122, Messina, Italy
| | - Alessia Pugliese
- Department of Clinical and Experimental Medicine, University of Messina, Piazza Pugliatti 1, 98122, Messina, Italy
| | - Stefano Carlo Previtali
- Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132, Milan, Italy
| | - Valeria Sansone
- The NEMO Center in Milan, Neurorehabilitation Unit,, University of Milan, ASST Niguarda Hospital, Piazza Dell'Ospedale Maggiore 3, 20161, Milan, Italy
| | - Liliana Vercelli
- Presidio Molinette e OIRM (SS Malattie Neuromuscolari e SC Neuropsichiatria Infantile), AOU Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Tiziana Enrica Mongini
- Presidio Molinette e OIRM (SS Malattie Neuromuscolari e SC Neuropsichiatria Infantile), AOU Città della Salute e della Scienza di Torino, Corso Bramante 88, 10126, Turin, Italy
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Massimiliano Filosto
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, Via Paolo Richiedei, 16, 25064, Brescia, Italy
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
- Istituto Di Neurologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Sheshi Nënë Tereza 4, 1010, Tiranë, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Via Ardeatina 306-354, 00179, Rome, Italy.
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
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18
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Megalizzi D, Trastulli G, Colantoni L, Proietti Piorgo E, Primiano G, Sancricca C, Caltagirone C, Cascella R, Strafella C, Giardina E. Deciphering the Complexity of FSHD: A Multimodal Approach as a Model for Rare Disorders. Int J Mol Sci 2024; 25:10949. [PMID: 39456731 PMCID: PMC11507453 DOI: 10.3390/ijms252010949] [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: 07/31/2024] [Revised: 10/08/2024] [Accepted: 10/09/2024] [Indexed: 10/28/2024] Open
Abstract
Rare diseases are heterogeneous diseases characterized by various symptoms and signs. Due to the low prevalence of such conditions (less than 1 in 2000 people), medical expertise is limited, knowledge is poor and patients' care provided by medical centers is inadequate. An accurate diagnosis is frequently challenging and ongoing research is also insufficient, thus complicating the understanding of the natural progression of the rarest disorders. This review aims at presenting the multimodal approach supported by the integration of multiple analyses and disciplines as a valuable solution to clarify complex genotype-phenotype correlations and promote an in-depth examination of rare disorders. Taking into account the literature from large-scale population studies and ongoing technological advancement, this review described some examples to show how a multi-skilled team can improve the complex diagnosis of rare diseases. In this regard, Facio-Scapulo-Humeral muscular Dystrophy (FSHD) represents a valuable example where a multimodal approach is essential for a more accurate and precise diagnosis, as well as for enhancing the management of patients and their families. Given their heterogeneity and complexity, rare diseases call for a distinctive multidisciplinary approach to enable diagnosis and clinical follow-up.
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Affiliation(s)
- Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
- Department of System Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
| | - Emma Proietti Piorgo
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
| | - Guido Primiano
- Neurophysiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy; (G.P.); (C.S.)
| | - Cristina Sancricca
- Neurophysiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy; (G.P.); (C.S.)
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy;
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
- Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, 1000 Tirana, Albania
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Via Ardeatina 306-354, 00179 Rome, Italy; (D.M.); (G.T.); (L.C.); (E.P.P.); (R.C.); (C.S.)
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
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19
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Findlay AR. Dominantly inherited muscle disorders: understanding their complexity and exploring therapeutic approaches. Dis Model Mech 2024; 17:dmm050720. [PMID: 39501809 PMCID: PMC11574355 DOI: 10.1242/dmm.050720] [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] [Indexed: 11/21/2024] Open
Abstract
Treatments for disabling and life-threatening hereditary muscle disorders are finally close to becoming a reality. Research has thus far focused primarily on recessive forms of muscle disease. The gene replacement strategies that are commonly employed for recessive, loss-of-function disorders are not readily translatable to most dominant myopathies owing to the presence of a normal chromosome in each nucleus, hindering the development of novel treatments for these dominant disorders. This is largely due to their complex, heterogeneous disease mechanisms that require unique therapeutic approaches. However, as viral and RNA interference-based therapies enter clinical use, key tools are now in place to develop treatments for dominantly inherited disorders of muscle. This article will review what is known about dominantly inherited disorders of muscle, specifically their genetic basis, how mutations lead to disease, and the pathomechanistic implications for therapeutic approaches.
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Affiliation(s)
- Andrew R Findlay
- Washington University Saint Louis, Neuromuscular Disease Center, 660 S. Euclid Ave., St Louis, MO 63110, USA
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20
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Xie Q, Ma G, Song Y. Therapeutic Strategy and Clinical Path of Facioscapulohumeral Muscular Dystrophy: Review of the Current Literature. APPLIED SCIENCES 2024; 14:8222. [DOI: 10.3390/app14188222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant genetic disease, which is caused by the mistaken expression of double homeobox protein 4 protein 4 (DUX4) in skeletal muscle. Patients with FSHD are usually accompanied by degenerative changes in the face, shoulders, and upper muscles, gradually accumulating in the lower limb muscles. The severity of patients is quite different, and most patients end up using wheelchairs and losing their self-care ability. At present, the exploration of treatment strategies for FSHD has shifted from relieving symptoms to gene therapy, which brings hope to the future of patients, but the current gene therapy is only in the clinical trial stage. Here, we conducted a comprehensive search of the relevant literature using the keywords FSHD, DUX4, and gene therapy methods including ASOs, CRISPR, and RNAi in the PubMed and Web of Science databases. We discussed the current advancements in treatment strategies for FSHD, as well as ongoing preclinical and clinical trials related to FSHD. Additionally, we evaluated the advantages and limitations of various gene therapy approaches targeting DUX4 aimed at correcting the underlying genetic defect.
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Affiliation(s)
- Qi Xie
- School of Sports Science, Beijing Sport University, Beijing 100084, China
| | - Guangmei Ma
- Department of Physical Education Teaching and Research, Xinjiang University, Wulumuqi 830046, China
| | - Yafeng Song
- China Institute of Sport and Health Science, Beijing Sport University, Beijing 100084, China
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21
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Wong MMK, Hachmer S, Gardner E, Runfola V, Arezza E, Megeney LA, Emerson CP, Gabellini D, Dilworth FJ. SMCHD1 activates the expression of genes required for the expansion of human myoblasts. Nucleic Acids Res 2024; 52:9450-9462. [PMID: 38994563 PMCID: PMC11381350 DOI: 10.1093/nar/gkae600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/01/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
SMCHD1 is an epigenetic regulatory protein known to modulate the targeted repression of large chromatin domains. Diminished SMCHD1 function in muscle fibers causes Facioscapulohumeral Muscular Dystrophy (FSHD2) through derepression of the D4Z4 chromatin domain, an event which permits the aberrant expression of the disease-causing gene DUX4. Given that SMCHD1 plays a broader role in establishing the cellular epigenome, we examined whether loss of SMCHD1 function might affect muscle homeostasis through additional mechanisms. Here we show that acute depletion of SMCHD1 results in a DUX4-independent defect in myoblast proliferation. Genomic and transcriptomic experiments determined that SMCHD1 associates with enhancers of genes controlling cell cycle to activate their expression. Amongst these cell cycle regulatory genes, we identified LAP2 as a key target of SMCHD1 required for the expansion of myoblasts, where the ectopic expression of LAP2 rescues the proliferation defect of SMCHD1-depleted cells. Thus, the epigenetic regulator SMCHD1 can play the role of a transcriptional co-activator for maintaining the expression of genes required for muscle progenitor expansion. This DUX4-independent role for SMCHD1 in myoblasts suggests that the pathology of FSHD2 may be a consequence of defective muscle regeneration in addition to the muscle wasting caused by spurious DUX4 expression.
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Affiliation(s)
- Matthew Man-Kin Wong
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Sarah Hachmer
- Department of Cell and Regenerative Biology, University of Wisconsin; Madison, WI 53705, USA
| | - Ed Gardner
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Valeria Runfola
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - Eric Arezza
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
| | - Lynn A Megeney
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute; Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa; Ottawa, ON K1H 8L6, Canada
- Department of Cell and Regenerative Biology, University of Wisconsin; Madison, WI 53705, USA
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22
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Potabattula R, Durackova J, Kießling S, Michler A, Hahn T, Schorsch M, Trapphoff T, Dieterle S, Haaf T. D4Z4 Hypomethylation in Human Germ Cells. Cells 2024; 13:1497. [PMID: 39273067 PMCID: PMC11394335 DOI: 10.3390/cells13171497] [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: 07/19/2024] [Revised: 08/19/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
Expression of the double homeobox 4 (DUX4) transcription factor is highly regulated in early embryogenesis and is subsequently epigenetically silenced. Ectopic expression of DUX4 due to hypomethylation of the D4Z4 repeat array on permissive chromosome 4q35 alleles is associated with facioscapulohumeral muscular dystrophy (FSHD). In peripheral blood samples from 188 healthy individuals, D4Z4 methylation was highly variable, ranging from 19% to 76%, and was not affected by age. In 48 FSHD2 patients, D4Z4 methylation varied from 3% to 30%. Given that DUX4 is one of the earliest transcribed genes after fertilization, the D4Z4 array is expected to be unmethylated in mature germ cells. Deep bisulfite sequencing of 188 mainly normozoospermic sperm samples revealed an average methylation of 2.5% (range 0.3-22%). Overall, the vast majority (78%) of individual sperm cells displayed no methylation at all. In contrast, only 19 (17.5%) of 109 individual germinal vesicle (GV) oocytes displayed D4Z4 methylation <2.5%. However, it is not unexpected that immature GV oocytes which are not usable for assisted reproduction are endowed with D4Z4 (up to 74%) hypermethylation and/or abnormal (PEG3 and GTL2) imprints. Although not significant, it is interesting to note that the pregnancy rate after assisted reproduction was higher for donors of sperm samples and oocytes with <2.5% methylation.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, 97074 Wuerzburg, Germany; (R.P.); (J.D.); (S.K.); (A.M.)
| | - Jana Durackova
- Institute of Human Genetics, Julius Maximilians University, 97074 Wuerzburg, Germany; (R.P.); (J.D.); (S.K.); (A.M.)
| | - Sarah Kießling
- Institute of Human Genetics, Julius Maximilians University, 97074 Wuerzburg, Germany; (R.P.); (J.D.); (S.K.); (A.M.)
| | - Alina Michler
- Institute of Human Genetics, Julius Maximilians University, 97074 Wuerzburg, Germany; (R.P.); (J.D.); (S.K.); (A.M.)
| | - Thomas Hahn
- Fertility Center Wiesbaden, 65189 Wiesbaden, Germany; (T.H.); (M.S.)
| | - Martin Schorsch
- Fertility Center Wiesbaden, 65189 Wiesbaden, Germany; (T.H.); (M.S.)
| | - Tom Trapphoff
- Fertility Center Dortmund, 44135 Dortmund, Germany; (T.T.); (S.D.)
| | - Stefan Dieterle
- Fertility Center Dortmund, 44135 Dortmund, Germany; (T.T.); (S.D.)
- Division of Reproductive Medicine and Infertility, Department of Obstetrics and Gynecology, Witten/Herdecke University, 44135 Dortmund, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Wuerzburg, Germany; (R.P.); (J.D.); (S.K.); (A.M.)
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23
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Chen JH, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic impacts and evolutionary patterns over time remain elusive in humans due to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, our research shows a gradual rise in disease gene proportion as gene age increases. Logistic regression modeling indicates that this increase in older genes may be related to their longer sequence lengths and higher burdens of deleterious de novo germline variants (DNVs). We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials for phenotypic innovation in young genes compared to older genes, a process that is subject to natural selection. Our study demonstrates that evolutionarily new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jian-Hai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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24
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Hangul C, Ozcan F, Darbas S, Uysal H, Koc AF, Berker Karauzum S. Progesterone may be a regulator and B12 could be an indicator of the proximal D4Z4 repeat methylation status on 4q35ter. J Neurochem 2024; 168:3209-3220. [PMID: 39105526 DOI: 10.1111/jnc.16196] [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: 04/25/2024] [Revised: 07/09/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
Facioscapulohumeral dystrophy (FSHD) has a hypomethylation-related epigenetic background and exhibits a different course in male and female patients. The differences between males and females have been linked to the levels of sex hormones. This study is the first to investigate the possible effect of these hormones on methylation status. We hypothesized that the levels of sex-related hormones, estradiol, testosterone, progesterone, and prolactin might be associated with the methylation status of the proximal part of the D4Z4. We also investigated the effect of fT3, folic acid, and vitamin B12 levels. We collected blood from 28 FSHD patients and 28 controls. DNA was extracted from each individual for bisulfite methylation analysis and serum was separated for biochemical analysis of estradiol, testosterone, progesterone, prolactin, fT3, folic acid, and B12 analysis. Methylation analysis was specified to the DR1, 5P regions and the proximal region covering both DR1 and 5P. Methylation levels were compared between FSHD patients and controls. The correlation of methylation levels with estradiol, testosterone, progesterone, prolactin, fT3, folic acid, and B12 was investigated. We found that the 5P region and the proximal region were significantly hypomethylated in FSHD patients compared to the controls, but not the DR1 region. Male patients exhibited a significant reduction in DNA methylation compared to male controls. Older FSHD patients exhibited a notable decrease in fT3 levels and hypomethylation of the 5P region. Analyses of each CpG revealed seven hypomethylated positions that were significantly different from the control group. Two of the positions demonstrated a correlation with progesterone in the control group. With the exception of one position, the methylation levels were inversely correlated with vitamin B12 in FSHD patients. The results of our study indicate that the methylation of the proximal D4Z4 region, particularly at specific positions, may be associated with progesterone. In addition, vitamin B12 may be an indicator of hypomethylation. We suggest that examining position-specific methylations may be a useful approach for the development of epigenetic treatment modalities.
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Affiliation(s)
- Ceren Hangul
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Filiz Ozcan
- Dialysis Programme, Vocational School of Health Services, Antalya Bilim University, Antalya, Turkey
| | - Sule Darbas
- Tissue Typing Laboratory, Akdeniz University Hospital, Antalya, Turkey
| | - Hilmi Uysal
- Department of Neurology, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Ayse Filiz Koc
- Department of Neurology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Sibel Berker Karauzum
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
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25
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Serrero MC, Paludan SR. Restriction factors regulating human herpesvirus infections. Trends Immunol 2024; 45:662-677. [PMID: 39198098 DOI: 10.1016/j.it.2024.07.010] [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: 07/10/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024]
Abstract
Herpesviruses are DNA viruses and the cause of diseases ranging from mild skin conditions to severe brain diseases. Mammalian antiviral host defense comprises an array of mechanisms, including restriction factors (RFs), which block specific steps in viral replication cycles. In recent years, knowledge of RFs that contribute to controlling herpesvirus infections has expanded significantly, along with a new understanding of viral evasion mechanisms and disease pathogenesis. By integrating findings from human genetics, murine models, and cellular studies, this review provides a current view of RF control of herpesvirus infections. We also explore the regulation of RF expression, discuss the roles of RFs in diseases, and point towards their growing potential as candidate therapeutic targets.
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Affiliation(s)
- Manutea C Serrero
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Immunology of Viral Infections, Aarhus, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Immunology of Viral Infections, Aarhus, Denmark.
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26
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Vishnu VY, Lemmers RJLF, Reyaz A, Mishra R, Ahmad T, van der Vliet PJ, Kretkiewicz MM, Macken WL, Efthymiou S, Dominik N, Morrow JM, Bhatia R, Wilson LA, Houlden H, Hanna MG, Bugiardini E, van der Maarel SM, Srivastava MVP. The first genetically confirmed cohort of Facioscapulohumeral Muscular Dystrophy from Northern India. Eur J Hum Genet 2024; 32:1053-1064. [PMID: 38664571 PMCID: PMC11368952 DOI: 10.1038/s41431-024-01577-z] [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: 07/09/2023] [Revised: 01/12/2024] [Accepted: 02/21/2024] [Indexed: 09/04/2024] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common form of hereditary myopathy. Sixty per cent of the world's population lives in Asia, so a significant percentage of the world's FSHD participants is expected to live there. To date, most FSHD studies have involved individuals of European descent, yet small-scale studies of East-Asian populations suggest that the likelihood of developing FSHD may vary. Here, we present the first genetically confirmed FSHD cohort of Indian ancestry, which suggests a pathogenic FSHD1 allele size distribution intermediate between European and North-East Asian populations and more asymptomatic carriers of 4 unit and 5 unit FSHD1 alleles than observed in European populations. Our data provides important evidence of differences relevant to clinical diagnostics and underscores the need for global FSHD participation in research and trial-ready Indian FSHD cohorts.
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Affiliation(s)
- Venugopalan Y Vishnu
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Alisha Reyaz
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Rinkle Mishra
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Tanveer Ahmad
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Marcelina M Kretkiewicz
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - William L Macken
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | - Natalia Dominik
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | - Jasper M Morrow
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | - Rohit Bhatia
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Lindsay A Wilson
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK.
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK.
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, Queen Square UCL Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK
| | | | - M V Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India.
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Attarian S, Beloribi-Djefaflia S, Bernard R, Nguyen K, Cances C, Gavazza C, Echaniz-Laguna A, Espil C, Evangelista T, Feasson L, Audic F, Zagorda B, Milhe De Bovis V, Stojkovic T, Sole G, Salort-Campana E, Sacconi S. French National Protocol for diagnosis and care of facioscapulohumeral muscular dystrophy (FSHD). J Neurol 2024; 271:5778-5803. [PMID: 38955828 DOI: 10.1007/s00415-024-12538-3] [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] [Received: 03/05/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/04/2024]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common genetically inherited myopathies in adults. It is characterized by incomplete penetrance and variable expressivity. Typically, FSHD patients display asymmetric weakness of facial, scapular, and humeral muscles that may progress to other muscle groups, particularly the abdominal and lower limb muscles. Early-onset patients display more severe muscle weakness and atrophy, resulting in a higher frequency of associated skeletal abnormalities. In these patients, multisystem involvement, including respiratory, ocular, and auditory, is more frequent and severe and may include the central nervous system. Adult-onset FSHD patients may also display some degree of multisystem involvement which mainly remains subclinical. In 95% of cases, FSHD patients carry a pathogenic contraction of the D4Z4 repeat units (RUs) in the subtelomeric region of chromosome 4 (4q35), which leads to the expression of DUX4 retrogene, toxic for muscles (FSHD1). Five percent of patients display the same clinical phenotype in association with a mutation in the SMCHD1 gene located in chromosome 18, inducing epigenetic modifications of the 4q D4Z4 repeated region and expression of DUX4 retrogene. This review highlights the complexities and challenges of diagnosing and managing FSHD, underscoring the importance of standardized approaches for optimal patient outcomes. It emphasizes the critical role of multidisciplinary care in addressing the diverse manifestations of FSHD across different age groups, from skeletal abnormalities in early-onset cases to the often-subclinical multisystem involvement in adults. With no current cure, the focus on alleviating symptoms and slowing disease progression through coordinated care is paramount.
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Affiliation(s)
- Shahram Attarian
- Reference Center for Neuromuscular Disorders and ALS, Timone University Hospital, Aix-Marseille University, Marseille, France.
- FILNEMUS, European Reference Network for Rare Diseases (ERN-NMD), Marseille, France.
- Marseille Medical Genetics, Aix Marseille Université-Inserm UMR_1251, 13005, Marseille, France.
| | - Sadia Beloribi-Djefaflia
- Reference Center for Neuromuscular Disorders and ALS, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Rafaelle Bernard
- Marseille Medical Genetics, Aix Marseille Université-Inserm UMR_1251, 13005, Marseille, France
| | - Karine Nguyen
- Marseille Medical Genetics, Aix Marseille Université-Inserm UMR_1251, 13005, Marseille, France
| | - Claude Cances
- Reference Center for Neuromuscular Disorders, Toulouse Children's Hospital, Toulouse, France
- Pediatric Neurology Department, Toulouse Children's Hospital, Toulouse, France
| | - Carole Gavazza
- Reference Center for Neuromuscular Disorders and ALS, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Andoni Echaniz-Laguna
- Department of Neurology, APHP, CHU de Bicêtre, Le Kremlin Bicêtre, France
- French National Reference Center for Rare Neuropathies (NNERF), Le Kremlin Bicêtre, France
- Inserm U1195, University Paris Saclay, Le Kremlin Bicêtre, France
| | - Caroline Espil
- Reference Center for Neuromuscular Disorders AOC, Children's Hospital, CHU Bordeaux, Bordeaux, France
| | - Teresinha Evangelista
- Institute of Myology, Nord/Est/Ile-de-France Neuromuscular Reference Center, Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Léonard Feasson
- Department of Clinical and Exercise Physiology, University Hospital Center of Saint-Etienne, 42000, Saint-Etienne, France
- Inter-University Laboratory of Human Movement Biology, EA 7424, Jean Monnet University, 42000, Saint-Etienne, France
| | - Frédérique Audic
- Reference Center for Neuromuscular Diseases in Children PACARARE, Neuropediatrics Department, Timone University Children's Hospital, Marseille, France
| | - Berenice Zagorda
- Department of Clinical and Exercise Physiology, University Hospital Center of Saint-Etienne, 42000, Saint-Etienne, France
| | - Virginie Milhe De Bovis
- Reference Center for Neuromuscular Disorders and ALS, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Tanya Stojkovic
- Institute of Myology, Nord/Est/Ile-de-France Neuromuscular Reference Center, Pitié-Salpêtrière Hospital, APHP, Sorbonne University, Paris, France
| | - Guilhem Sole
- Centre de Référence des Maladies Neuromusculaires AOC, FILNEMUS, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Emmanuelle Salort-Campana
- Reference Center for Neuromuscular Disorders and ALS, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Sabrina Sacconi
- Peripheral Nervous System and Muscle Department, Université Côte d'Azur, CHU Nice, Pasteur 2, Nice Hospital, France.
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28
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Beck SL, Yokota T. Oligonucleotide Therapies for Facioscapulohumeral Muscular Dystrophy: Current Preclinical Landscape. Int J Mol Sci 2024; 25:9065. [PMID: 39201751 PMCID: PMC11354670 DOI: 10.3390/ijms25169065] [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: 07/20/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited myopathy, characterized by progressive and asymmetric muscle atrophy, primarily affecting muscles of the face, shoulder girdle, and upper arms before affecting muscles of the lower extremities with age and greater disease severity. FSHD is a disabling condition, and patients may also present with various extramuscular symptoms. FSHD is caused by the aberrant expression of double homeobox 4 (DUX4) in skeletal muscle, arising from compromised epigenetic repression of the D4Z4 array. DUX4 encodes the DUX4 protein, a transcription factor that activates myotoxic gene programs to produce the FSHD pathology. Therefore, sequence-specific oligonucleotides aimed at reducing DUX4 levels in patients is a compelling therapeutic approach, and one that has received considerable research interest over the last decade. This review aims to describe the current preclinical landscape of oligonucleotide therapies for FSHD. This includes outlining the mechanism of action of each therapy and summarizing the preclinical results obtained regarding their efficacy in cellular and/or murine disease models. The scope of this review is limited to oligonucleotide-based therapies that inhibit the DUX4 gene, mRNA, or protein in a way that does not involve gene editing.
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Affiliation(s)
- Samuel L. Beck
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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29
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Santanasto AJ, Acharya S, Wojczynski MK, Cvejkus RK, Lin S, Brent MR, Anema JA, Wang L, Thyagarajan B, Christensen K, Daw EW, Zmuda JM. Whole Genome Linkage and Association Analyses Identify DLG Associated Protein-1 as a Novel Positional and Biological Candidate Gene for Muscle Strength: The Long Life Family Study. J Gerontol A Biol Sci Med Sci 2024; 79:glae144. [PMID: 38808484 PMCID: PMC11226997 DOI: 10.1093/gerona/glae144] [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: 09/20/2023] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults. METHODS Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p (mega-basepair region: 3.4-4.0) linked to grip strength in 3 755 individuals from 582 families aged 64 ± 12 years (range 30-110 years; 55% women). There were 26 families that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 10.94), with 6 families (119 individuals) accounting for most of the linkage signal (LOD = 6.4). In these 6 families, using whole genome sequencing data, we performed association analyses between the 7 312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population substructure. RESULTS We found significant associations between genetic variants (8 SNVs and 4 INDELs, p < 5 × 10-5) in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength. Haplotypes constructed using these variants explained up to 98.1% of the LOD score. Finally, RNAseq data showed that these variants were significantly associated with the expression of nearby Myosin Light Chain 12A (MYL12A), Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1), Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3) genes (p < .0004). CONCLUSIONS The DLGAP1 gene plays an important role in the postsynaptic density of neurons; thus, it is both a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength.
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Affiliation(s)
- Adam J Santanasto
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sandeep Acharya
- Division of Computational and Data Sciences, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ryan K Cvejkus
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shiow Lin
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Michael R Brent
- Division of Computational and Data Sciences, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jason A Anema
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kaare Christensen
- Epidemiology Unit, Institute of Public Health, The Danish Aging Research Center, University of Southern Denmark, Odense, Denmark
| | - E Warwick Daw
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Zmuda
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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30
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Xu T, Yue F, He J, Zhang H, Liu R. Prenatal detection of distal 18p deletion by chromosomal microarray analysis: Three case reports and literature review. Medicine (Baltimore) 2024; 103:e39046. [PMID: 39058883 PMCID: PMC11272248 DOI: 10.1097/md.0000000000039046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Chromosome 18p deletion syndrome is caused by total or partial deletion of the short arm of chromosome 18 and associated with cognitive impairment, growth retardation and mild facial dysmorphism. However, most studies on the genotype-phenotype correlations in the 18p region are diagnosed postnatally. Prenatal reports involving 18p deletions are limited. METHODS Three pregnant women opted for invasive prenatal testing due to noninvasive prenatal testing indicating high risk for chromosome 18 abnormalities. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed simultaneously. The pregnancy outcomes for all cases were followed up. Meanwhile, we also made a literature review on prenatal phenotypes of 18p deletions. RESULTS G-banding analysis showed that 2 fetuses presented abnormal karyotypes: 45,XN,der(18)t(18;21)(p11; q11),-21 (case 2) and 46,XN,18p- (case 3). The karyotype of case 1 was normal. Meanwhile, CMA detected 4.37 Mb (case 1), 7.26 Mb (case 2) and 14.97 Mb (case 3) deletions in chromosome 18p region. All 3 pregnancies were terminated finally according to genetic counseling based upon abnormal CMA results. CONCLUSION Prenatal diagnosis of 18p deletion syndrome is full of challenges due to the phenotypic diversity, incomplete penetrance and lack of prenatal phenotypes. Increased nuchal translucency and holoprosencephaly are common prenatal phenotypes of distal 18p deletion. For fetuses carrying 18p deletions with atypical sonographic phenotypes, noninvasive prenatal testing could be adopted as an effective approach.
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Affiliation(s)
- Tangfei Xu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Fagui Yue
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Jing He
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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31
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Huang Z, Cui W, Ratnayake I, Tawil R, Pfeifer GP. SMCHD1 maintains heterochromatin and genome compartments in human myoblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602392. [PMID: 39026812 PMCID: PMC11257445 DOI: 10.1101/2024.07.07.602392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mammalian genomes are subdivided into euchromatic A compartments that contain mostly active chromatin, and inactive, heterochromatic B compartments. However, it is unknown how A and B genome compartments are established and maintained. Here we studied SMCHD1, an SMC-like protein in human male myoblasts. SMCHD1 colocalizes with Lamin B1 and the heterochromatin mark H3K9me3. Loss of SMCHD1 leads to extensive heterochromatin depletion at the nuclear lamina and acquisition of active chromatin states along all chromosomes. In absence of SMCHD1, long range intra-chromosomal and inter-chromosomal contacts between B compartments are lost while many new TADs and loops are formed. Inactivation of SMCHD1 promotes numerous B to A compartment transitions accompanied by activation of silenced genes. SMCHD1 functions as an anchor for heterochromatin domains ensuring that these domains are inaccessible to epigenome modification enzymes that typically operate in active chromatin. Therefore, A compartments are formed by default when not prevented by SMCHD1.
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32
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Giardina E, Camaño P, Burton-Jones S, Ravenscroft G, Henning F, Magdinier F, van der Stoep N, van der Vliet PJ, Bernard R, Tomaselli PJ, Davis MR, Nishino I, Oflazer P, Race V, Vishnu VY, Williams V, Sobreira CFR, van der Maarel SM, Moore SA, Voermans NC, Lemmers RJLF. Best practice guidelines on genetic diagnostics of facioscapulohumeral muscular dystrophy: Update of the 2012 guidelines. Clin Genet 2024; 106:13-26. [PMID: 38685133 PMCID: PMC11147721 DOI: 10.1111/cge.14533] [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: 12/07/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
The gold standard for facioscapulohumeral muscular dystrophy (FSHD) genetic diagnostic procedures was published in 2012. With the increasing complexity of the genetics of FSHD1 and 2, the increase of genetic testing centers, and the start of clinical trials for FSHD, it is crucial to provide an update on our knowledge of the genetic features of the FSHD loci and renew the international consensus on the molecular testing recommendations. To this end, members of the FSHD European Trial Network summarized the evidence presented during the 2022 ENMC meeting on Genetic diagnosis, clinical outcome measures, and biomarkers. The working group additionally invited genetic and clinical experts from the USA, India, Japan, Australia, South-Africa, and Brazil to provide a global perspective. Six virtual meetings were organized to reach consensus on the minimal requirements for genetic confirmation of FSHD1 and FSHD2. Here, we present the clinical and genetic features of FSHD, specific features of FSHD1 and FSHD2, pros and cons of established and new technologies (Southern blot in combination with either linear or pulsed-field gel electrophoresis, molecular combing, optical genome mapping, FSHD2 methylation analysis and FSHD2 genotyping), the possibilities and challenges of prenatal testing, including pre-implantation genetic testing, and the minimal requirements and recommendations for genetic confirmation of FSHD1 and FSHD2. This consensus is expected to contribute to current clinical management and trial-readiness for FSHD.
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Affiliation(s)
- Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy
- Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Pilar Camaño
- Molecular Diagnostics Platform, Biogipuzkoa Health Research Institute, Hospital Universitario Donostia, San Sebastián, Spain
- CIBERNED, CIBER, Spanish Ministry of Science & Innovation, Carlos III Health Institute, Madrid, Spain
| | | | - Gina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Franclo Henning
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, The Netherlands
| | | | - Rafaëlle Bernard
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille, France
- Centre Hospitalier Universitaire Timone Adultes, Biogénopôle, Service de Génétique Médicale, Marseille, France
| | - Pedro J Tomaselli
- Department of Neurosciences, Division of Neurology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
- Department of Genome Medicine Development, Clinical Genome Analysis, Medical Genome Center (MGC), National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Piraye Oflazer
- Department of Neurology, Koç University Hospital Muscle Center, Koç University Medical Faculty, Istanbul, Turkey
| | - Valerie Race
- Clinical Laboratory Geneticist, Human Genetics, UZ Leuven, Leuven, Belgium
| | - Venugopalan Y Vishnu
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | | | - Cláudia F R Sobreira
- Department of Neurosciences, Division of Neurology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Steve A Moore
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Pathology, Roy J. And Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Nicol C Voermans
- Department of Neurology, Radboud university medical center, Nijmegen, The Netherlands
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33
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Lu-Nguyen N, Snowden S, Popplewell L, Malerba A. Systemic Pharmacotherapeutic Treatment of the ACTA1-MCM/FLExDUX4 Preclinical Mouse Model of FSHD. Int J Mol Sci 2024; 25:6994. [PMID: 39000102 PMCID: PMC11241187 DOI: 10.3390/ijms25136994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/18/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Aberrant expression of the double homeobox 4 (DUX4) gene in skeletal muscle predominantly drives the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD). We recently demonstrated that berberine, an herbal extract known for its ability to stabilize guanine-quadruplex structures, effectively downregulates DUX4 expression in FSHD patient-derived myoblasts and in mice overexpressing exogenous DUX4 after viral vector-based treatment. Here, we sought to confirm berberine's inhibitory efficacy on DUX4 in the widely used FSHD-like transgenic mouse model, ACTA1-MCM/FLExDUX4, where DUX4 is induced at pathogenic levels using tamoxifen. Animals repeatedly treated with berberine via intraperitoneal injections for 4 weeks exhibited significant reductions in both mRNA and protein levels of DUX4, and in mRNA expression of murine DUX4-related genes. This inhibition translated into improved forelimb muscle strength and positive alterations in important FSHD-relevant cellular pathways, although its impact on muscle mass and histopathology was less pronounced. Collectively, our data confirm the efficacy of berberine in downregulating DUX4 expression in the most relevant FSHD mouse model. However, further optimization of dosing regimens and new studies to enhance the bioavailability of berberine in skeletal muscle are warranted to fully leverage its therapeutic potential for FSHD treatment.
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Affiliation(s)
- Ngoc Lu-Nguyen
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK; (N.L.-N.); (S.S.)
| | - Stuart Snowden
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK; (N.L.-N.); (S.S.)
| | - Linda Popplewell
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK; (N.L.-N.); (S.S.)
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Alberto Malerba
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK; (N.L.-N.); (S.S.)
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Chen L, Kong X, Johnston KG, Mortazavi A, Holmes TC, Tan Z, Yokomori K, Xu X. Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome Res 2024; 34:665-679. [PMID: 38777608 PMCID: PMC11216401 DOI: 10.1101/gr.278717.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low percentage of cells, requiring single-cell analysis. However, single-cell/nucleus RNA-seq cannot fully capture the transcriptome of multinucleated large myotubes. To circumvent these issues, we use multiplexed error-robust fluorescent in situ hybridization (MERFISH) spatial transcriptomics that allows profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (MNCs) of control, isogenic D4Z4 contraction mutant and FSHD patient samples, as well as the individual nuclei within them. We find myocyte nuclei segregate into two clusters defined by the expression of DUX4 target genes, which is exclusively found in patient/mutant nuclei, whereas MNCs cluster based on developmental states. Patient/mutant myotubes are found in "FSHD-hi" and "FSHD-lo" states with the former signified by high DUX4 target expression and decreased muscle gene expression. Pseudotime analyses reveal a clear bifurcation of myoblast differentiation into control and FSHD-hi myotube branches, with variable numbers of DUX4 target-expressing nuclei found in multinucleated FSHD-hi myotubes. Gene coexpression modules related to extracellular matrix and stress gene ontologies are significantly altered in patient/mutant myotubes compared with the control. We also identify distinct subpathways within the DUX4 gene network that may differentially contribute to the disease transcriptomic phenotype. Taken together, our MERFISH-based study provides effective gene network profiling of multinucleated cells and identifies FSHD-induced transcriptomic alterations during myoblast differentiation.
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Affiliation(s)
- Lujia Chen
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Ali Mortazavi
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, California 92697, USA
| | - Zhiqun Tan
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA;
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, California 92697, USA;
| | - Xiangmin Xu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
- Center for Neural Circuit Mapping, University of California, Irvine, California 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, California 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California 92697, USA
- Department of Computer Science, University of California, Irvine, California 92697, USA
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Engal E, Sharma A, Aviel U, Taqatqa N, Juster S, Jaffe-Herman S, Bentata M, Geminder O, Gershon A, Lewis R, Kay G, Hecht M, Epsztejn-Litman S, Gotkine M, Mouly V, Eiges R, Salton M, Drier Y. DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis. SCIENCE ADVANCES 2024; 10:eadn7732. [PMID: 38809976 PMCID: PMC11135424 DOI: 10.1126/sciadv.adn7732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is a noncanonical SMC protein and an epigenetic regulator. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy (FSHD), by overexpressing DUX4 in muscle cells. Here, we demonstrate that SMCHD1 is a key regulator of alternative splicing in various cell types. We show how SMCHD1 loss causes splicing alterations of DNMT3B, which can lead to hypomethylation and DUX4 overexpression. Analyzing RNA sequencing data from muscle biopsies of patients with FSHD and Smchd1 knocked out cells, we found mis-splicing of hundreds of genes upon SMCHD1 loss. We conducted a high-throughput screen of splicing factors, revealing the involvement of the splicing factor RBM5 in the mis-splicing of DNMT3B. Subsequent RNA immunoprecipitation experiments confirmed that SMCHD1 is required for RBM5 recruitment. Last, we show that mis-splicing of DNMT3B leads to hypomethylation of the D4Z4 region and to DUX4 overexpression. These results suggest that DNMT3B mis-splicing due to SMCHD1 loss plays a major role in FSHD pathogenesis.
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Affiliation(s)
- Eden Engal
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Aveksha Sharma
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Uria Aviel
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sarah Juster
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mercedes Bentata
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Adi Gershon
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Reyut Lewis
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Merav Hecht
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Marc Gotkine
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112002, Israel
| | - Vincent Mouly
- UPMC University Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Sorbonne University,75252 Paris, France
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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Yang JL, Gu H, Yuan ZZ, Xie XH, Yang YF, Tan ZP. Identification of a pathogenic SMCHD1 variant in a Chinese patient with bosma arhinia microphthalmia syndrome: a case report. BMC Med Genomics 2024; 17:136. [PMID: 38773541 PMCID: PMC11110391 DOI: 10.1186/s12920-024-01907-6] [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: 10/03/2023] [Accepted: 05/13/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Bosma arhinia microphthalmia syndrome (BAMS; MIM603457) is a rare genetic disorder, predominantly autosomal dominant. It is a multi-system developmental disorder characterized by severe hypoplasia of the nose and eyes, and reproductive system defects. BAMS is extremely rare in the world and no cases have been reported in Chinese population so far. Pathogenic variants in the SMCHD1 gene (MIM614982) cause BAMS, while the underlying molecular mechanisms requires further investigation. CASE PRESENTATION In this study, a Chinese girl who has suffered from congenital absence of nose and microphthalmia was enrolled and subsequently submitted to a comprehensive clinical and genetic evaluation. Whole-exome sequencing (WES) was employed to identify the genetic entity of thisgirl. A heterozygous pathogenic variant, NM_015295, c.1025G > C; p. (Trp342Ser) of SMCHD1 was identified. By performing very detailed physical and genetic examinations, the patient was diagnosed as BAMS. CONCLUSION This report is the first description of a variant in SMCHD1 in a Chinese patient affected with BAMS.Our study not only furnished valuable genetic data for counseling of BAMS, but also confirmed the diagnosis of BAMS, which may help the management and prognosis for this patient.
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Affiliation(s)
- Jun-Lin Yang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Heng Gu
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zhuang-Zhuang Yuan
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Xiao-Hui Xie
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yi-Feng Yang
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zhi-Ping Tan
- Department of Cardiovascular Surgery, the Second Xiangya Hospital of Central South University, Changsha, China.
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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Neuhofer CM, Prokisch H. Digenic Inheritance in Rare Disorders and Mitochondrial Disease-Crossing the Frontier to a More Comprehensive Understanding of Etiology. Int J Mol Sci 2024; 25:4602. [PMID: 38731822 PMCID: PMC11083678 DOI: 10.3390/ijms25094602] [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: 02/13/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Our understanding of rare disease genetics has been shaped by a monogenic disease model. While the traditional monogenic disease model has been successful in identifying numerous disease-associated genes and significantly enlarged our knowledge in the field of human genetics, it has limitations in explaining phenomena like phenotypic variability and reduced penetrance. Widening the perspective beyond Mendelian inheritance has the potential to enable a better understanding of disease complexity in rare disorders. Digenic inheritance is the simplest instance of a non-Mendelian disorder, characterized by the functional interplay of variants in two disease-contributing genes. Known digenic disease causes show a range of pathomechanisms underlying digenic interplay, including direct and indirect gene product interactions as well as epigenetic modifications. This review aims to systematically explore the background of digenic inheritance in rare disorders, the approaches and challenges when investigating digenic inheritance, and the current evidence for digenic inheritance in mitochondrial disorders.
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Affiliation(s)
- Christiane M. Neuhofer
- Institute of Human Genetics, University Medical Center, Technical University of Munich, Trogerstr. 32, 81675 Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
- Institute of Human Genetics, Salzburger Landeskliniken, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, 5020 Salzburg, Austria
| | - Holger Prokisch
- Institute of Human Genetics, University Medical Center, Technical University of Munich, Trogerstr. 32, 81675 Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Centre Munich Neuherberg, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
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Kong X, Nguyen NV, Li Y, Sakr JS, Williams K, Sharifi S, Chau J, Bayrakci A, Mizuno S, Takahashi S, Kiyono T, Tawil R, Mortazavi A, Yokomori K. Engineered FSHD mutations results in D4Z4 heterochromatin disruption and feedforward DUX4 network activation. iScience 2024; 27:109357. [PMID: 38510139 PMCID: PMC10951985 DOI: 10.1016/j.isci.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/20/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is linked to contraction of D4Z4 repeats on chromosome 4q with SMCHD1 mutations acting as a disease modifier. D4Z4 heterochromatin disruption and abnormal upregulation of the transcription factor DUX4, encoded in the D4Z4 repeat, are the hallmarks of FSHD. However, defining the precise effect of D4Z4 contraction has been difficult because D4Z4 repeats are primate-specific and DUX4 expression is very rare in highly heterogeneous patient myocytes. We generated isogenic mutant cell lines harboring D4Z4 and/or SMCHD1 mutations in a healthy human skeletal myoblast line. We found that the mutations affect D4Z4 heterochromatin differently, and that SMCHD1 mutation or disruption of DNA methylation stabilizes otherwise variegated DUX4 target activation in D4Z4 contraction mutant cells, demonstrating the critical role of modifiers. Our study revealed amplification of the DUX4 signal through downstream targets, H3.X/Y and LEUTX. Our results provide important insights into how rare DUX4 expression leads to FSHD pathogenesis.
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Affiliation(s)
- Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Nam Viet Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumeng Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jasmine Shaaban Sakr
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kate Williams
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Sheila Sharifi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jonathan Chau
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Altay Bayrakci
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Tohru Kiyono
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ali Mortazavi
- Department of Development and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Dortenzio V, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad DF, O'Donnell-Luria A, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features. HGG ADVANCES 2024; 5:100273. [PMID: 38297832 PMCID: PMC10876629 DOI: 10.1016/j.xhgg.2024.100273] [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: 11/08/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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Affiliation(s)
- Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kamli N W Faour
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA
| | - Akiko Shimamura
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emeline M Kao
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Erica R Denhoff
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Ana Blatnik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Daniel Ben-Isvy
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Lily Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Helen Firth
- Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomy J L de Ravel
- Centre for Human Genetics, UZ Leuven/Leuven University Hospitals, Leuven, Belgium
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital Liverpool, Liverpool, UK
| | | | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - G Christoph Korenke
- Department of Neuropaediatric and Metabolic Diseases, University Children's Hospital Oldenburg, Oldenburg, Germany
| | - Panayiotis Constantinou
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Karen J Low
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK; University of Bristol, Bristol, UK
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | | | | | | | | | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, USA
| | - Wanqing Shao
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Ian Krantz
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maninder Kaur
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Raible
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Moriel Singer-Berk
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sonia Ballal
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Siddharth Srivastava
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Divison of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, Germany; Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Jessica Rzasa
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Philip M Boone
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Sun C, Serra C, Kalicharan BH, Harding J, Rao M. Challenges and Considerations of Preclinical Development for iPSC-Based Myogenic Cell Therapy. Cells 2024; 13:596. [PMID: 38607035 PMCID: PMC11011706 DOI: 10.3390/cells13070596] [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: 02/06/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Cell therapies derived from induced pluripotent stem cells (iPSCs) offer a promising avenue in the field of regenerative medicine due to iPSCs' expandability, immune compatibility, and pluripotent potential. An increasing number of preclinical and clinical trials have been carried out, exploring the application of iPSC-based therapies for challenging diseases, such as muscular dystrophies. The unique syncytial nature of skeletal muscle allows stem/progenitor cells to integrate, forming new myonuclei and restoring the expression of genes affected by myopathies. This characteristic makes genome-editing techniques especially attractive in these therapies. With genetic modification and iPSC lineage specification methodologies, immune-compatible healthy iPSC-derived muscle cells can be manufactured to reverse the progression of muscle diseases or facilitate tissue regeneration. Despite this exciting advancement, much of the development of iPSC-based therapies for muscle diseases and tissue regeneration is limited to academic settings, with no successful clinical translation reported. The unknown differentiation process in vivo, potential tumorigenicity, and epigenetic abnormality of transplanted cells are preventing their clinical application. In this review, we give an overview on preclinical development of iPSC-derived myogenic cell transplantation therapies including processes related to iPSC-derived myogenic cells such as differentiation, scaling-up, delivery, and cGMP compliance. And we discuss the potential challenges of each step of clinical translation. Additionally, preclinical model systems for testing myogenic cells intended for clinical applications are described.
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Affiliation(s)
- Congshan Sun
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
| | - Carlo Serra
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Mahendra Rao
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
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Kim T, Martínez-Bonet M, Wang Q, Hackert N, Sparks JA, Baglaenko Y, Koh B, Darbousset R, Laza-Briviesca R, Chen X, Aguiar VRC, Chiu DJ, Westra HJ, Gutierrez-Arcelus M, Weirauch MT, Raychaudhuri S, Rao DA, Nigrovic PA. Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development. Nat Commun 2024; 15:2150. [PMID: 38459032 PMCID: PMC10923805 DOI: 10.1038/s41467-024-46457-8] [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: 01/27/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells and, in rheumatoid arthritis patients, of blood and joint fluid Tph cells as well as circulating plasmablasts. Correspondingly, ICOS ligation and carriage of the rs117701653 risk allele accelerate T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13. Thus, mechanistic dissection of a functional non-coding variant in human autoimmunity discloses a previously undefined pathway through which ICOS regulates Tph development and abundance.
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Affiliation(s)
- Taehyeung Kim
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marta Martínez-Bonet
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory of Immune-regulation, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Qiang Wang
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicolaj Hackert
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Institute for Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuriy Baglaenko
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Byunghee Koh
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Roxane Darbousset
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Raquel Laza-Briviesca
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Vitor R C Aguiar
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Darren J Chiu
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Harm-Jan Westra
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, The Netherlands
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Divisions of Human Genetics, Biomedical Informatics, and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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42
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Töpf A, Cox D, Zaharieva IT, Di Leo V, Sarparanta J, Jonson PH, Sealy IM, Smolnikov A, White RJ, Vihola A, Savarese M, Merteroglu M, Wali N, Laricchia KM, Venturini C, Vroling B, Stenton SL, Cummings BB, Harris E, Marini-Bettolo C, Diaz-Manera J, Henderson M, Barresi R, Duff J, England EM, Patrick J, Al-Husayni S, Biancalana V, Beggs AH, Bodi I, Bommireddipalli S, Bönnemann CG, Cairns A, Chiew MT, Claeys KG, Cooper ST, Davis MR, Donkervoort S, Erasmus CE, Fassad MR, Genetti CA, Grosmann C, Jungbluth H, Kamsteeg EJ, Lornage X, Löscher WN, Malfatti E, Manzur A, Martí P, Mongini TE, Muelas N, Nishikawa A, O'Donnell-Luria A, Ogonuki N, O'Grady GL, O'Heir E, Paquay S, Phadke R, Pletcher BA, Romero NB, Schouten M, Shah S, Smuts I, Sznajer Y, Tasca G, Taylor RW, Tuite A, Van den Bergh P, VanNoy G, Voermans NC, Wanschitz JV, Wraige E, Yoshimura K, Oates EC, Nakagawa O, Nishino I, Laporte J, Vilchez JJ, MacArthur DG, Sarkozy A, Cordell HJ, Udd B, Busch-Nentwich EM, Muntoni F, Straub V. Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy. Nat Genet 2024; 56:395-407. [PMID: 38429495 PMCID: PMC10937387 DOI: 10.1038/s41588-023-01651-0] [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: 03/29/2021] [Accepted: 12/19/2023] [Indexed: 03/03/2024]
Abstract
In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases.
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Affiliation(s)
- Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Dan Cox
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Irina T Zaharieva
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Valeria Di Leo
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Ian M Sealy
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Andrei Smolnikov
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard J White
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Centre, Tampere University and University Hospital, Tampere, Finland
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Munise Merteroglu
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Laboratory of Angiogenesis and Cancer Metabolism, Department of Biology, University of Padua, Padua, Italy
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | | | - Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Beryl B Cummings
- Laboratory of Angiogenesis and Cancer Metabolism, Department of Biology, University of Padua, Padua, Italy
| | - Elizabeth Harris
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Northern Genetics Service, Institute of Genetics Medicine, Newcastle upon Tyne, UK
| | - Chiara Marini-Bettolo
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jordi Diaz-Manera
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Matt Henderson
- Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jennifer Duff
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jane Patrick
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sundos Al-Husayni
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valerie Biancalana
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Istvan Bodi
- Department of Clinical Neuropathology, King's College Hospital NHS Foundation Trust, London, UK
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, the Children's Hospital at Westmead, the University of Sydney and the Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anita Cairns
- Neurosciences Department, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Mei-Ting Chiew
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Kristl G Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sandra T Cooper
- Kids Neuroscience Centre, the Children's Hospital at Westmead, the University of Sydney and the Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Corrie E Erasmus
- Department of Paediatric Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Casie A Genetti
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carla Grosmann
- Department of Neurology, Rady Children's Hospital University of California San Diego, San Diego, CA, USA
| | - Heinz Jungbluth
- Department of Paediatric Neurology, Neuromuscular Service, Evelina's Children Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
- Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and Medicine (FoLSM), King's College London, London, UK
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Wolfgang N Löscher
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Edoardo Malfatti
- APHP, Neuromuscular Reference Center Nord-Est-Ile-de-France, Henri Mondor Hospital, Université Paris Est, U955, INSERM, Creteil, France
| | - Adnan Manzur
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Pilar Martí
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
| | - Tiziana E Mongini
- Department of Neurosciences Rita Levi Montalcini, Università degli Studi di Torino, Torino, Italy
| | - Nuria Muelas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
- Department of Medicine, Universitat de Valencia, Valencia, Spain
- Neuromuscular Diseases Unit, Neurology Department, Hospital Universitari I Politècnic La Fe, Valencia, Spain
| | - Atsuko Nishikawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | | | - Gina L O'Grady
- Starship Children's Health, Auckland District Health Board, Auckland, New Zealand
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stéphanie Paquay
- Cliniques Universitaires St-Luc, Centre de Référence Neuromusculaire, Université de Louvain, Brussels, Belgium
| | - Rahul Phadke
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Beth A Pletcher
- Division of Clinical Genetics, Department of Pediatrics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Norma B Romero
- Neuromuscular Morphology Unit, Myology Institute, Sorbonne Université, Centre de Référence de Pathologie Neuromusculaire Nord/Est/Ile-de-France (APHP), GH Pitié-Salpêtrière, Paris, France
| | - Meyke Schouten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Snehal Shah
- Department of Neurology, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Yves Sznajer
- Center for Human Genetic, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Allysa Tuite
- Division of Clinical Genetics, Department of Pediatrics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Peter Van den Bergh
- Cliniques Universitaires St-Luc, Centre de Référence Neuromusculaire, Université de Louvain, Brussels, Belgium
| | - Grace VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Julia V Wanschitz
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Elizabeth Wraige
- Evelina's Children Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Emily C Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Juan J Vilchez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Centre, Tampere University and University Hospital, Tampere, Finland
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL & Great Ormond Street Hospital Trust, London, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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43
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Strafella C, Colantoni L, Megalizzi D, Trastulli G, Piorgo EP, Primiano G, Sancricca C, Ricci G, Siciliano G, Caltagirone C, Filosto M, Tasca G, Ricci E, Cascella R, Giardina E. Characterization of D4Z4 alleles and assessment of de novo cases in Facioscapulohumeral dystrophy (FSHD) in a cohort of Italian families. Clin Genet 2024; 105:335-339. [PMID: 38041579 DOI: 10.1111/cge.14466] [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: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant disease, although 10%-30% of cases are sporadic. However, this percentage may include truly de novo patients (carrying a reduced D4Z4 allele that is not present in either of the parents) and patients with apparently sporadic disease resulting from mosaicism, non-penetrance, or complex genetic situations in either patients or parents. In this study, we characterized the D4Z4 Reduced Alleles (DRA) and evaluated the frequency of truly de novo cases in FSHD1 in a cohort of DNA samples received consecutively for FSHD-diagnostic from 100 Italian families. The D4Z4 testing revealed that 60 families reported a DRA compatible with FSHD1 (1-10 RU). The DRA co-segregated with the disease in most cases. Five families with truly de novo cases were identified, suggesting that this condition may be slightly lower (8%) than previously reported. In addition, D4Z4 characterization in the investigated families showed 4% of mosaic cases and 2% with translocations. This study further highlighted the importance of performing family studies for clarifying apparently sporadic FSHD cases, with significant implications for genetic counseling, diagnosis, clinical management, and procreative choices for patients and families.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Luca Colantoni
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
| | | | - Guido Primiano
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Cristina Sancricca
- Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, NeMO-Brescia Clinical Center for Neuromuscular Diseases, Brescia, Italy
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trusts, Newcastle Upon Tyne, UK
| | - Enzo Ricci
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Istituto di Neurologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Biomedicine and Prevention, Medical Genetics Laboratory, Tor Vergata University, Rome, Italy
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44
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Jiang J, Cai X, Qu H, Yao Q, He T, Yang M, Zhou H, Zhang X. Case report: Identification of facioscapulohumeral muscular dystrophy 1 in two siblings with normal phenotypic parents using optical genome mapping. Front Neurol 2024; 15:1258831. [PMID: 38361638 PMCID: PMC10867183 DOI: 10.3389/fneur.2024.1258831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Objective Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is one of the most common forms of autosomal-dominant muscular dystrophies characterized by variable disease penetrance due to shortened D4Z4 repeat units on 4q35. The molecular diagnosis of FSHD1 is usually made by Southern blotting, which is complex, time-consuming, and lacks clinical practicality. Therefore, in this study, optical genome mapping (OGM) is employed for the genetic diagnosis of FSHD1. Furthermore, epigenetic heterogeneity is determined from methylation analysis. Methods Genomic DNA samples from four members of the same family were subjected to whole-exome sequencing. OGM was used to identify structural variations in D4Z4, while sodium bisulfite sequencing helped identify the methylation levels of CpG sites in a region located distally to the D4Z4 array. A multidisciplinary team collected the clinical data, and comprehensive family analyses aided in the assessment of phenotypes and genotypes. Results Whole-exome sequencing did not reveal variants related to clinical phenotypes in the patients. OGM showed that the proband was a compound heterozygote for the 4qA allele with four and eight D4Z4 repeat units, whereas the affected younger brother had only one 4qA allele with four D4Z4 repeat units. Both the proband and her younger brother were found to display asymmetric weakness predominantly involving the facial, shoulder girdle, and upper arm muscles, whereas the younger brother had more severe clinical symptoms. The proband's father, who was found to be normal after a neurological examination, also carried the 4qA allele with eight D4Z4 repeat units. The unaffected mother exhibited 49 D4Z4 repeat units of the 4qA allele and a minor mosaic pattern with four D4Z4 repeat units of the 4qA allele. Consequently, the presence of the 4qA allele in the four D4Z4 repeat units strongly pointed to the occurrence of maternal germline mosaicism. The CpG6 methylation levels were lower in symptomatic patients compared to those in the asymptomatic parents. The older sister had lower clinical scores and ACSS and higher CpG6 methylation levels than that of her younger brother. Conclusions In this study, two siblings with FSHD1 with phenotypically normal parents were identified by OGM. Our findings suggest that the 4qA allele of four D4Z4 repeats was inherited through maternal germline mosaicism. The clinical phenotype heterogeneity is influenced by the CpG6 methylation levels. The results of this study greatly aid in the molecular diagnosis of FSHD1 and in also understanding the clinical phenotypic variability underlying the disease.
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Affiliation(s)
- Jieni Jiang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaotang Cai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Haibo Qu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Radiology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiang Yao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Tiantian He
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Mei Yang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Hui Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xuemei Zhang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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45
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Lemmers RJLF, Butterfield R, van der Vliet PJ, de Bleecker JL, van der Pol L, Dunn DM, Erasmus CE, D'Hooghe M, Verhoeven K, Balog J, Bigot A, van Engelen B, Statland J, Bugiardini E, van der Stoep N, Evangelista T, Marini-Bettolo C, van den Bergh P, Tawil R, Voermans NC, Vissing J, Weiss RB, van der Maarel SM. Autosomal dominant in cis D4Z4 repeat array duplication alleles in facioscapulohumeral dystrophy. Brain 2024; 147:414-426. [PMID: 37703328 PMCID: PMC10834250 DOI: 10.1093/brain/awad312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) has a unique genetic aetiology resulting in partial chromatin relaxation of the D4Z4 macrosatellite repeat array on 4qter. This D4Z4 chromatin relaxation facilitates inappropriate expression of the transcription factor DUX4 in skeletal muscle. DUX4 is encoded by a retrogene that is embedded within the distal region of the D4Z4 repeat array. In the European population, the D4Z4 repeat array is usually organized in a single array that ranges between 8 and 100 units. D4Z4 chromatin relaxation and DUX4 derepression in FSHD is most often caused by repeat array contraction to 1-10 units (FSHD1) or by a digenic mechanism requiring pathogenic variants in a D4Z4 chromatin repressor like SMCHD1, combined with a repeat array between 8 and 20 units (FSHD2). With a prevalence of 1.5% in the European population, in cis duplications of the D4Z4 repeat array, where two adjacent D4Z4 arrays are interrupted by a spacer sequence, are relatively common but their relationship to FSHD is not well understood. In cis duplication alleles were shown to be pathogenic in FSHD2 patients; however, there is inconsistent evidence for the necessity of an SMCHD1 mutation for disease development. To explore the pathogenic nature of these alleles we compared in cis duplication alleles in FSHD patients with or without pathogenic SMCHD1 variant. For both groups we showed duplication-allele-specific DUX4 expression. We studied these alleles in detail using pulsed-field gel electrophoresis-based Southern blotting and molecular combing, emphasizing the challenges in the characterization of these rearrangements. Nanopore sequencing was instrumental to study the composition and methylation of the duplicated D4Z4 repeat arrays and to identify the breakpoints and the spacer sequence between the arrays. By comparing the composition of the D4Z4 repeat array of in cis duplication alleles in both groups, we found that specific combinations of proximal and distal repeat array sizes determine their pathogenicity. Supported by our algorithm to predict pathogenicity, diagnostic laboratories should now be furnished to accurately interpret these in cis D4Z4 repeat array duplications, alleles that can easily be missed in routine settings.
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Affiliation(s)
- Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | | | - Ludo van der Pol
- University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Corrie E Erasmus
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Marc D'Hooghe
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Kristof Verhoeven
- Department of Neurology, Algemeen Ziekenhuis Sint-Jan, 8000, Brugge, Belgium
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Anne Bigot
- Sorbonne Université, Inserm UMRS974, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Baziel van Engelen
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | | | - Enrico Bugiardini
- National Hospital For Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Teresinha Evangelista
- Unité de Morphologie Neuromusculaire, Institut de Myologie, AP-HP, F-75013, Paris, France
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Faculty of Medical Sciences, Newcastle upon Tyne, NE1 3BZ, UK
| | | | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, NY 14642, Rochester, USA
| | - Nicol C Voermans
- Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - John Vissing
- Department of Neurology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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46
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Zheng D, Wondergem A, Kloet S, Willemsen I, Balog J, Tapscott SJ, Mahfouz A, van den Heuvel A, van der Maarel SM. snRNA-seq analysis in multinucleated myogenic FSHD cells identifies heterogeneous FSHD transcriptome signatures associated with embryonic-like program activation and oxidative stress-induced apoptosis. Hum Mol Genet 2024; 33:284-298. [PMID: 37934801 PMCID: PMC10800016 DOI: 10.1093/hmg/ddad186] [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: 02/03/2023] [Revised: 09/22/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
The sporadic nature of DUX4 expression in FSHD muscle challenges comparative transcriptome analyses between FSHD and control samples. A variety of DUX4 and FSHD-associated transcriptional changes have been identified, but bulk RNA-seq strategies prohibit comprehensive analysis of their spatiotemporal relation, interdependence and role in the disease process. In this study, we used single-nucleus RNA-sequencing of nuclei isolated from patient- and control-derived multinucleated primary myotubes to investigate the cellular heterogeneity in FSHD. Taking advantage of the increased resolution in snRNA-sequencing of fully differentiated myotubes, two distinct populations of DUX4-affected nuclei could be defined by their transcriptional profiles. Our data provides insights into the differences between these two populations and suggests heterogeneity in two well-known FSHD-associated transcriptional aberrations: increased oxidative stress and inhibition of myogenic differentiation. Additionally, we provide evidence that DUX4-affected nuclei share transcriptome features with early embryonic cells beyond the well-described cleavage stage, progressing into the 8-cell and blastocyst stages. Altogether, our data suggests that the FSHD transcriptional profile is defined by a mixture of individual and sometimes mutually exclusive DUX4-induced responses and cellular state-dependent downstream effects.
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Affiliation(s)
- Dongxu Zheng
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Annelot Wondergem
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Iris Willemsen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 2628 XE, Delft, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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47
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Bittel AJ, Bittel DC, Gordish-Dressman H, Chen YW. Voluntary wheel running improves molecular and functional deficits in a murine model of facioscapulohumeral muscular dystrophy. iScience 2024; 27:108632. [PMID: 38188524 PMCID: PMC10770537 DOI: 10.1016/j.isci.2023.108632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/11/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Endurance exercise training is beneficial for skeletal muscle health, but it is unclear if this type of exercise can target or correct the molecular mechanisms of facioscapulohumeral muscular dystrophy (FSHD). Using the FLExDUX4 murine model of FSHD characterized by chronic, low levels of pathological double homeobox protein 4 (DUX4) gene expression, we show that 6 weeks of voluntary, free wheel running improves running performance, strength, mitochondrial function, and sarcolemmal repair capacity, while slowing/reversing skeletal muscle fibrosis. These improvements are associated with restored transcriptional activity of gene networks/pathways regulating actin cytoskeletal signaling, vascular remodeling, inflammation, fibrosis, and muscle mass toward wild-type (WT) levels. However, FLExDUX4 mice exhibit blunted increases in mitochondrial content with training and persistent transcriptional overactivation of hypoxia, inflammatory, angiogenic, and cytoskeletal pathways. These results identify exercise-responsive and non-responsive molecular pathways in FSHD, while providing support for the use of endurance-type exercise as a non-invasive treatment option.
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Affiliation(s)
- Adam J. Bittel
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20012, USA
| | - Daniel C. Bittel
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20012, USA
| | | | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20012, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20052, USA
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48
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Engquist EN, Greco A, Joosten LAB, van Engelen BGM, Zammit PS, Banerji CRS. FSHD muscle shows perturbation in fibroadipogenic progenitor cells, mitochondrial function and alternative splicing independently of inflammation. Hum Mol Genet 2024; 33:182-197. [PMID: 37856562 PMCID: PMC10772042 DOI: 10.1093/hmg/ddad175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy. FSHD is highly heterogeneous, with patients following a variety of clinical trajectories, complicating clinical trials. Skeletal muscle in FSHD undergoes fibrosis and fatty replacement that can be accelerated by inflammation, adding to heterogeneity. Well controlled molecular studies are thus essential to both categorize FSHD patients into distinct subtypes and understand pathomechanisms. Here, we further analyzed RNA-sequencing data from 24 FSHD patients, each of whom donated a biopsy from both a non-inflamed (TIRM-) and inflamed (TIRM+) muscle, and 15 FSHD patients who donated peripheral blood mononucleated cells (PBMCs), alongside non-affected control individuals. Differential gene expression analysis identified suppression of mitochondrial biogenesis and up-regulation of fibroadipogenic progenitor (FAP) gene expression in FSHD muscle, which was particularly marked on inflamed samples. PBMCs demonstrated suppression of antigen presentation in FSHD. Gene expression deconvolution revealed FAP expansion as a consistent feature of FSHD muscle, via meta-analysis of 7 independent transcriptomic datasets. Clustering of muscle biopsies separated patients in an unbiased manner into clinically mild and severe subtypes, independently of known disease modifiers (age, sex, D4Z4 repeat length). Lastly, the first genome-wide analysis of alternative splicing in FSHD muscle revealed perturbation of autophagy, BMP2 and HMGB1 signalling. Overall, our findings reveal molecular subtypes of FSHD with clinical relevance and identify novel pathomechanisms for this highly heterogeneous condition.
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Affiliation(s)
- Elise N Engquist
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, 400012, Cluj-Napoca, Romania
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
- The Alan Turing Institute, The British Library, 96 Euston Road, London NW1 2DB, United Kingdom
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49
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Kang PB, Jorand-Fletcher M, Zhang W, McDermott SW, Berry R, Chambers C, Wong KN, Mohamed Y, Thomas S, Venkatesh YS, Westfield C, Whitehead N, Johnson NE. Genetic Patterns of Selected Muscular Dystrophies in the Muscular Dystrophy Surveillance, Tracking, and Research Network. Neurol Genet 2023; 9:e200113. [PMID: 38045992 PMCID: PMC10692796 DOI: 10.1212/nxg.0000000000200113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/29/2023] [Indexed: 12/05/2023]
Abstract
Background and Objectives To report the genetic etiologies of Emery-Dreifuss muscular dystrophy (EDMD), limb-girdle muscular dystrophy (LGMD), congenital muscular dystrophy (CMD), and distal muscular dystrophy (DD) in 6 geographically defined areas of the United States. Methods This was a cross-sectional, population-based study in which we studied the genes and variants associated with muscular dystrophy in individuals who were diagnosed with and received care for EDMD, LGMD, CMD, and DD from January 1, 2008, through December 31, 2016, in the 6 areas of the United States covered by the Muscular Dystrophy Surveillance, Tracking, and Research Network (MD STARnet). Variants of unknown significance (VUSs) from the original genetic test reports were reanalyzed for changes in interpretation. Results Among 243 individuals with definite or probable muscular dystrophy, LGMD was the most common diagnosis (138 cases), followed by CMD (62 cases), DD (22 cases), and EDMD (21 cases). There was a higher proportion of male individuals compared with female individuals, which persisted after excluding X-linked genes (EMD) and autosomal genes reported to have skewed gender ratios (ANO5, CAV3, and LMNA). The most common associated genes were FKRP, CAPN3, ANO5, and DYSF. Reanalysis yielded more definitive variant interpretations for 60 of 144 VUSs, with a mean interval between the original clinical genetic test of 8.11 years for all 144 VUSs and 8.62 years for the 60 reclassified variants. Ten individuals were found to have monoallelic pathogenic variants in genes known to be primarily recessive. Discussion This study is distinct for being an examination of 4 types of muscular dystrophies in selected geographic areas of the United States. The striking proportion of resolved VUSs demonstrates the value of periodic re-examinations of these variants. Such re-examinations will resolve some genetic diagnostic ambiguities before initiating repeat testing or more invasive diagnostic procedures such as muscle biopsy. The presence of monoallelic pathogenic variants in recessive genes in our cohort indicates that some individuals with muscular dystrophy continue to face incomplete genetic diagnoses; further refinements in genetic knowledge and diagnostic approaches will optimize diagnostic information for these individuals.
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Affiliation(s)
- Peter B Kang
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Magali Jorand-Fletcher
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Wanfang Zhang
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Suzanne W McDermott
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Reba Berry
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Chelsea Chambers
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Kristen N Wong
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Yara Mohamed
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Shiny Thomas
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Y Swamy Venkatesh
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Christina Westfield
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Nedra Whitehead
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
| | - Nicholas E Johnson
- From the Paul & Sheila Wellstone Muscular Dystrophy Center (P.B.K.), Department of Neurology, and Institute for Translational Neuroscience, University of Minnesota, Minneapolis; Department of Pediatrics (M.J.-F., Y.M.), University of Florida College of Medicine, Gainesville; Department of Epidemiology and Biostatistics (W.Z.), University of South Carolina, Columbia; Department of Environmental, Occupational, and Geospatial Health Sciences (S.W.M.), Graduate School of Public Health and Health Policy, City University of New York; Division of Population Health Surveillance (R.B., C.W.), Bureau of Maternal and Child Health, South Carolina Department of Health and Environmental Control, Columbia; Department of Human and Molecular Genetics (C.C.), Virginia Commonwealth University, Richmond; Department of Pediatrics (K.N.W.), University of Utah, Salt Lake City; New York State Department of Health (S.T.), Albany; Department of Neurology (Y.S.V.), University of South Carolina, Columbia; RTI International (N.W.), Research Triangle Park, NC; and Department of Neurology (N.E.J.), Virginia Commonwealth University, Richmond
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Guruju NM, Jump V, Lemmers R, Van Der Maarel S, Liu R, Nallamilli BR, Shenoy S, Chaubey A, Koppikar P, Rose R, Khadilkar S, Hegde M. Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy in Patients Clinically Suspected of FSHD Using Optical Genome Mapping. Neurol Genet 2023; 9:e200107. [PMID: 38021397 PMCID: PMC10664978 DOI: 10.1212/nxg.0000000000200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 12/01/2023]
Abstract
Background and Objectives Facioscapulohumeral muscular dystrophy (FSHD) represents the third most common muscular dystrophy in the general population and is characterized by progressive and often asymmetric muscle weakness of the face, upper extremities, arms, lower leg, and hip girdle. In FSHD type 1, contraction of the number of D4Z4 repeats to 1-10 on the chromosome 4-permissive allele (4qA) results in abnormal epigenetic derepression of the DUX4 gene in skeletal muscle. In FSHD type 2, epigenetic derepression of the DUX4 gene on the permissive allele (4qA) with normal-sized D4Z4 repeats (mostly 8-20) is caused by heterozygous pathogenic variants in chromatin modifier genes such as SMCHD1, DNMT3B, or LRIF1. We present validation of the optical genome mapping (OGM) platform for accurate mapping of the D4Z4 repeat size, followed by diagnostic testing of 547 cases with a suspected clinical diagnosis of FSHD and next-generation sequencing (NGS) of the SMCHD1 gene to identify cases with FSHD2. Methods OGM with Bionano Genomics Saphyr and EnFocus FSHD analysis software was used to identify FSHD haplotypes and D4Z4 repeat number and compared with the gold standard of Southern blot-based diagnosis. A custom Agilent SureSelect enrichment kit was used to enrich SMCHD1, followed by NGS on an Illumina system with 100-bp paired-end reads. Copy number variants were assessed using NxClinical software. Results We performed OGM for the diagnosis of FSHD in 547 patients suspected of FSHD between December 2019 and December 2022, including 301 male (55%) and 246 female patients (45%). Overall, 308 of the referred patients were positive for D4Z4 contraction on a permissive haplotype, resulting in a diagnosis of FSHD1. A total of 252 of 547 patients were referred for concurrent testing for FSHD1 and FSHD2. This resulted in the identification of FSHD2 in 9/252 (3.6%) patients. In our FSHD2 cohort, the 4qA allele size ranged from 8 to 18 repeats. Among FSHD1-positive cases, 2 patients had biallelic contraction and 4 patients had homozygous contraction and showed early onset of clinical features. Nine of the 308 patients (3%) positive for 4qA contraction had mosaic 4q alleles with contraction on at least one 4qA allele. The overall diagnostic yield in our cohort was 58%. Discussion A combination of OGM to identify the FSHD haplotype and D4Z4 repeat number and NGS to identify sequence and copy number variants in the SMCHD1 gene is a practical and cost-effective option with increased precision for accurate diagnosis of FSHD types 1 and 2.
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Affiliation(s)
- Naga M Guruju
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Vanessa Jump
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Richard Lemmers
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Silvere Van Der Maarel
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Ruby Liu
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Babi R Nallamilli
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Suresh Shenoy
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Alka Chaubey
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Pratik Koppikar
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Rajiv Rose
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Satish Khadilkar
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
| | - Madhuri Hegde
- From the Revvity Omics (N.M.G., V.J., Ruby Liu, B.R.N., S.S., R.R., M.H.), Pittsburgh, PA; Leiden University Medical Centre (Richard Lemmers, S.V.D.M.), Netherlands; Bionano Genomics (A.C.), San Diego, CA; UT Dallas (P.K.), TX; Bombay Hospital (S.K.), Mumbai, India
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