1
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Bulakh M, Polyakova D, Dadali E, Rudenskaya G, Sharkova I, Markova T, Murtazina A, Demina N, Kurbatov S, Nikitina N, Udalova V, Polyakov A, Ryzhkova O. Genetic spectrum of sarcoglycanopathies in a cohort of Russian patients. Gene 2024; 927:148680. [PMID: 38876406 DOI: 10.1016/j.gene.2024.148680] [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: 11/27/2023] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Sarcoglycanopathies encompass four distinct forms of limb-girdle muscular dystrophies (LGMD), denoted as LGMD R3-R6, arising from mutations within the SGCA, SGCB, SGCG, and SGCD genes. The global prevalence of sarcoglycanopathies is low, making it challenging to study these diseases. The principal objective of this study was to explore the spectrum of mutations in a cohort of Russian patients with sarcoglycanopathies and to ascertain the frequency of these conditions in the Russian Federation. We conducted a retrospective analysis of clinical and molecular genetic data from 49 Russian patients with sarcogycan genes variants. The results indicated that variants in the SGCA gene were found in 71.4 % of cases, with SGCB and SGCG genes each exhibiting variants in 12.2 % of patients. SGCD gene variants were detected in 4.1 % of cases. Bi-allelic pathogenic and likely pathogenic variants were identified in 46 of the 49 cases of sarcoglycanopathies: LGMD R3 (n = 34), LGMD R4 (n = 4), LGMD R5 (n = 6), and LGMD R6 (n = 2). A total of 31 distinct variants were identified, comprising 25 previously reported and 6 novel variants. Two major variants, c.229C > T and c.271G > A, were detected within the SGCA, constituting 61.4 % of all mutant alleles in Russian patients with LGMD R3. Both LGMD R6 cases were caused by the homozygous nonsense variant c.493C > T p.(Arg165Ter) in the SGCD gene. The incidence of sarcoglycanopathies in the Russian Federation was estimated to be at least 1 in 4,115,039, which is lower than the reported incidence in other populations.
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Affiliation(s)
- Maria Bulakh
- the Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Elena Dadali
- the Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Inna Sharkova
- the Research Centre for Medical Genetics, Moscow, Russia.
| | | | | | - Nina Demina
- the Research Centre for Medical Genetics, Moscow, Russia.
| | - Sergei Kurbatov
- Research Institute of Experimental Biology and Medicine, Voronezh State Medical University N.N. Burdenko, Voronezh, Russia; Saratov State Medical University, Saratov, Russia.
| | - Natalia Nikitina
- State Healthcare Institution of Sverdlovsk Region "Clinical Diagnostic Center "Mother's and Child Health Protection", Yekaterinburg, Russia.
| | | | | | - Oxana Ryzhkova
- the Research Centre for Medical Genetics, Moscow, Russia.
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2
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Choi WJ, Kim SH, Lee SR, Oh SH, Kim SW, Shin HY, Park HJ. Global carrier frequency and predicted genetic prevalence of patients with pathogenic sequence variants in autosomal recessive genetic neuromuscular diseases. Sci Rep 2024; 14:3806. [PMID: 38361118 PMCID: PMC10869705 DOI: 10.1038/s41598-024-54413-1] [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: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 02/17/2024] Open
Abstract
Genetic neuromuscular diseases are clinically and genetically heterogeneous genetic disorders that primarily affect the peripheral nerves, muscles, and neuromuscular junctions. This study aimed to identify pathogenic variants, calculate carrier frequency, and predict the genetic prevalence of autosomal recessive neuromuscular diseases (AR-NMDs). We selected 268 AR-NMD genes and analyzed their genetic variants sourced from the gnomAD database. After identifying the pathogenic variants using an algorithm, we calculated the carrier frequency and predicted the genetic prevalence of AR-NMDs. In total, 10,887 pathogenic variants were identified, including 3848 literature verified and 7039 manually verified variants. In the global population, the carrier frequency of AR-NMDs is 32.9%, with variations across subpopulations ranging from 22.4% in the Finnish population to 36.2% in the non-Finnish European population. The predicted genetic prevalence of AR-NMDs was estimated to be 24.3 cases per 100,000 individuals worldwide, with variations across subpopulations ranging from 26.5 to 41.4 cases per 100,000 individuals in the Latino/Admixed American and the Ashkenazi Jewish populations, respectively. The AR-NMD gene with the highest carrier frequency was GAA (1.3%) and the variant with the highest allele frequency was c.-32-13 T>G in GAA with 0.0033 in the global population. Our study revealed a higher-than-expected frequency of AR-NMD carriers, constituting approximately one-third of the global population, highlighting ethnic heterogeneity in genetic susceptibility.
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Affiliation(s)
- Won-Jun Choi
- CHA University School of Medicine, Seongnam, Republic of Korea
| | - Soo-Hyun Kim
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea
| | - Sung Rok Lee
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea
| | - Seung-Hun Oh
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Jun Park
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, Republic of Korea.
- Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
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3
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Dabaj I, Ducatez F, Marret S, Bekri S, Tebani A. Neuromuscular disorders in the omics era. Clin Chim Acta 2024; 553:117691. [PMID: 38081447 DOI: 10.1016/j.cca.2023.117691] [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: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023]
Abstract
Neuromuscular disorders encompass a spectrum of conditions characterized by primary lesions within the peripheral nervous system, which include the anterior horn cell, peripheral nerve, neuromuscular junction, and muscle. In pediatrics, most of these disorders are linked to genetic causes. Despite the considerable progress, the diagnosis of these disorders remains a challenging due to wide clinical presentation, disease heterogeneity and rarity. It is noteworthy that certain neuromuscular disorders, once deemed untreatable, can now be effectively managed through novel therapies. Biomarkers emerge as indispensable tools, serving as objective measures that not only refine diagnostic accuracy but also provide guidance for therapeutic decision-making and the ongoing monitoring of long-term outcomes. Herein a comprehensive review of biomarkers in neuromuscular disorders is provided. We highlight the role of omics-based technologies that further characterize neuromuscular pathophysiology as well as identify potential therapeutic targets to guide treatment strategies.
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Affiliation(s)
- Ivana Dabaj
- Normandie Univ, UNIROUEN, INSERM U1245, Nord/Est/Ile de France Neuromuscular Reference Center CHU Rouen, Department of Neonatalogy, Pediatric Intensive Care, and Neuropediatrics, F-76000 Rouen, France.
| | - Franklin Ducatez
- Normandie Univ, UNIROUEN, INSERM U1245, Nord/Est/Ile de France Neuromuscular Reference Center CHU Rouen, Department of Neonatalogy, Pediatric Intensive Care, and Neuropediatrics, F-76000 Rouen, France
| | - Stéphane Marret
- Normandie Univ, UNIROUEN, INSERM U1245, Nord/Est/Ile de France Neuromuscular Reference Center CHU Rouen, Department of Neonatalogy, Pediatric Intensive Care, and Neuropediatrics, F-76000 Rouen, France
| | - Soumeya Bekri
- Normandie Univ, UNIROUEN, INSERM U1245, CHU Rouen, Department of Metabolic Biochemistry, F-76000 Rouen, France
| | - Abdellah Tebani
- Normandie Univ, UNIROUEN, INSERM U1245, CHU Rouen, Department of Metabolic Biochemistry, F-76000 Rouen, France
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4
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Tran N, Nguyen TA, Ta TD, Tran TH, Nguyen P, Vu CD, Nguyen V, Bui T, Ta TV, Tran VK. Targeted next‐generation sequencing determined a novel SGCG variant that is associated with limb‐girdle muscular dystrophy type 2C: A case report. Clin Case Rep 2023; 11:e7025. [PMID: 36992678 PMCID: PMC10041365 DOI: 10.1002/ccr3.7025] [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: 10/11/2022] [Revised: 12/24/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Limb‐girdle muscular dystrophy‐type 2C (LGMD2C) is caused by mutations in the SGCG gene. Here, we report a case of a 26‐year‐old male who had inactive walking due to proximal muscle weakness. Targeted next‐generation sequencing found a novel variant c.412C > T (Q138*) in the SGCG gene.
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Affiliation(s)
- Nam‐Chung Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Hanoi Medical UniversityHanoiVietnam
- University of Medicine & PharmacyVietnam National UniversityHanoiVietnam
| | | | - Thanh Dat Ta
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Thinh Huy Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Hanoi Medical UniversityHanoiVietnam
| | - Phuoc‐Dung Nguyen
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
| | - Chi Dung Vu
- Department of Medical Genetics, Metabolism &EndocrinologyVietnam National Children's HospitalHanoiVietnam
| | | | - The‐Hung Bui
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Center for Molecular Medicine, Clinical Genetics Unit, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Thanh Van Ta
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
- Hanoi Medical UniversityHanoiVietnam
| | - Van Khanh Tran
- Center for Gene and Protein ResearchHanoi Medical UniversityHanoiVietnam
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5
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Inherited myopathies in the Middle East and North Africa. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Mezzi N, Messaoud O, Mkaouar R, Zitouna N, Romdhane S, Abdessalem G, Charfeddine C, Maazoul F, Ouerteni I, Hamdi Y, Zaouak A, Mrad R, Abdelhak S, Romdhane L. Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved. Genes (Basel) 2021; 12:1820. [PMID: 34828426 PMCID: PMC8617973 DOI: 10.3390/genes12111820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases. Collected data were classified according to the CIM-10 classification and the transmission mode. The spectrum of these diseases is estimated to be 589 entities. This suggests remarkable progress through the development of biomedical health research activities and building capacities. Sixty percent of the reported disorders are autosomal recessive, which could be explained by the high prevalence of endogamous mating. Congenital malformations (29.54%) are the major disease group, followed by metabolic diseases (22%). Sixty percent of the genetic diseases have a known molecular etiology. We also reported additional cases of comorbidity that seem to be a common phenomenon in our population. We also noticed that epidemiological data are scarce. Newborn and carrier screening was only limited to pilot projects for a few genetic diseases. Collected data are being integrated into a database under construction that will be a valuable decision-making tool. This study provides the current situation of genetic diseases in Tunisia and highlights their particularities. Early detection of the disease is important to initiate critical intervention and to reduce morbidity and mortality.
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Affiliation(s)
- Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Nadia Zitouna
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Safa Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana 2080, Tunisia
| | - Faouzi Maazoul
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Ines Ouerteni
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Research Unit Genodermatosis and Cancer LR12SP03, Habib Thameur Hospital, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
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7
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Khaoula R, Cerino M, Da Silva N, Delague V, Nahili H, Kriouile Y, Gorokhova S, Bartoli M, Saïle R, Barakat A, Krahn M. First characterization of congenital myasthenic syndrome type 5 in North Africa. Mol Biol Rep 2021; 48:6999-7006. [PMID: 34553317 DOI: 10.1007/s11033-021-06530-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Congenital myasthenic syndromes (CMS) are associated with defects in the structure and the function of neuromuscular junctions. These rare disorders can result from mutations in the collagenic tail of endplate acetylcholinesterase (COLQ) essentially associated with autosomal recessive inheritance. With the lowered cost of genetic testing and increased access to next-generation sequencing, many mutations have been reported to date. METHODS AND RESULTS In this study we identified the first COLQ homozygous mutation c.1193T>A in the North African population. This study outlines the genetic and phenotypic features of a CMS patient in a Moroccan family. It also describes a novel COLQ missense mutation associated with CMS-5. CONCLUSION COLQ mutations are probably underdiagnosed in these North African populations, this is an issue as CMS-5 may be treated with ephedrine, and albuterol. Indeed, patients can seriously benefit and even recover after the treatment that should be planned according to genetic tests and clinical findings.
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Affiliation(s)
- Rochdi Khaoula
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik, Hassan II University, Casablanca, Morocco. .,Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco.
| | - Mathieu Cerino
- Inserm, U1251-MMG, Marseille Medical Genetics, Aix-Marseille Université, Marseille, France.,Département de Génétique Médicale, APHM, Hôpital Timone Enfants, Marseille, France.,APHM, Hôpital de la Conception, Laboratoire de Biochimie, Marseille, France
| | - Nathalie Da Silva
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Valerie Delague
- INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Halima Nahili
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yamna Kriouile
- Unit of Neuropediatrics and Neurometabolism, Pediatric Department 2, Rabat Children's Hospital, and Faculty of Medicine and Pharmacy of Rabat, University Mohammed V of Rabat, Rabat, Morocco
| | - Svetlana Gorokhova
- Département de Génétique Médicale, APHM, Hôpital Timone Enfants, Marseille, France.,Inserm, U1251-MMG, Marseille Medical Genetics, Aix-Marseille Université, Marseille, France
| | - Marc Bartoli
- Inserm, U1251-MMG, Marseille Medical Genetics, Aix-Marseille Université, Marseille, France
| | - Rachid Saïle
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences Ben M'Sik, Hassan II University, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Martin Krahn
- Département de Génétique Médicale, APHM, Hôpital Timone Enfants, Marseille, France.,Inserm, U1251-MMG, Marseille Medical Genetics, Aix-Marseille Université, Marseille, France
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8
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Abstract
The limb-girdle muscular dystrophies (LGMD) are a collection of genetic diseases united in their phenotypical expression of pelvic and shoulder area weakness and wasting. More than 30 subtypes have been identified, five dominant and 26 recessive. The increase in the characterization of new genotypes in the family of LGMDs further adds to the heterogeneity of the disease. Meanwhile, better understanding of the phenotype led to the reconsideration of the disease definition, which resulted in eight old subtypes to be no longer recognized officially as LGMD and five new diseases to be added to the LGMD family. The unique variabilities of LGMD stem from genetic mutations, which then lead to protein and ultimately muscle dysfunction. Herein, we review the LGMD pathway, starting with the genetic mutations that encode proteins involved in muscle maintenance and repair, and including the genotype–phenotype relationship of the disease, the epidemiology, disease progression, burden of illness, and emerging treatments.
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9
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The ties that bind: functional clusters in limb-girdle muscular dystrophy. Skelet Muscle 2020; 10:22. [PMID: 32727611 PMCID: PMC7389686 DOI: 10.1186/s13395-020-00240-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
The limb-girdle muscular dystrophies (LGMDs) are a genetically pleiomorphic class of inherited muscle diseases that are known to share phenotypic features. Selected LGMD genetic subtypes have been studied extensively in affected humans and various animal models. In some cases, these investigations have led to human clinical trials of potential disease-modifying therapies, including gene replacement strategies for individual subtypes using adeno-associated virus (AAV) vectors. The cellular localizations of most proteins associated with LGMD have been determined. However, the functions of these proteins are less uniformly characterized, thus limiting our knowledge of potential common disease mechanisms across subtype boundaries. Correspondingly, broad therapeutic strategies that could each target multiple LGMD subtypes remain less developed. We believe that three major "functional clusters" of subcellular activities relevant to LGMD merit further investigation. The best known of these is the glycosylation modifications associated with the dystroglycan complex. The other two, mechanical signaling and mitochondrial dysfunction, have been studied less systematically but are just as promising with respect to the identification of significant mechanistic subgroups of LGMD. A deeper understanding of these disease pathways could yield a new generation of precision therapies that would each be expected to treat a broader range of LGMD patients than a single subtype, thus expanding the scope of the molecular medicines that may be developed for this complex array of muscular dystrophies.
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10
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Jamaleddine M, Harris MS, Liyanage L, Cook GA. Expression, purification, and structural analysis of the full-length human integral membrane protein γ-sarcoglycan. Protein Expr Purif 2019; 167:105525. [PMID: 31682967 DOI: 10.1016/j.pep.2019.105525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022]
Abstract
Mutation of the gene encoding γ-sarcoglycan (SGCG), an integral membrane protein responsible for maintaining the integrity of the muscle cell sarcolemma, results in Limb-Girdle Muscular Dystrophy (LGMD), a congenital disease with no current treatment options. This member of the sarcoglycan glycoprotein family is a vital component of the Dystrophin Complex, which together facilitate normal muscle function. However, very little is known about the structure and dynamics of these proteins, and of membrane glycoproteins in general. This is due to a number of factors, including their complexity, heterogeneity and highly-specific native environments. The expression, purification, and structural study of membrane proteins is further impeded by their hydrophobic nature and consequent propensity to aggregate in aqueous solutions. Here, we report the first successful expression and purification of milligram quantities of full-length recombinant SGCG, utilizing fusion protein-guided overexpression to inclusion bodies in Escherichia coli. Purification of SGCG from the fusion protein, TrpΔLE, was facilitated using chemical cleavage. Cleavage products were then isolated by size-exclusion chromatography. Successful purification of the protein was confirmed using SDS-PAGE and mass spectroscopy. Finally, solution nuclear magnetic resonance spectroscopy of uniformly 15N-labeled SGCG in detergent environments was performed, yielding the first spectra of the full-length membrane glycoprotein, SGCG. These results represent the initial structural studies of SGCG, laying the foundation for further investigation on the interaction and dynamics of other integral membrane proteins. More specifically, this data allows for opportunities in the future for enhanced treatment modalities and cures for LGMD.
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Affiliation(s)
- Michael Jamaleddine
- Oklahoma State University, Department of Chemistry, 107 Physical Science, Stillwater, OK, 74074, USA
| | - Michael S Harris
- Oklahoma State University, Department of Chemistry, 107 Physical Science, Stillwater, OK, 74074, USA
| | - Leshani Liyanage
- Oklahoma State University, Department of Chemistry, 107 Physical Science, Stillwater, OK, 74074, USA
| | - Gabriel A Cook
- Oklahoma State University, Department of Chemistry, 107 Physical Science, Stillwater, OK, 74074, USA.
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11
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Liu W, Pajusalu S, Lake NJ, Zhou G, Ioannidis N, Mittal P, Johnson NE, Weihl CC, Williams BA, Albrecht DE, Rufibach LE, Lek M. Estimating prevalence for limb-girdle muscular dystrophy based on public sequencing databases. Genet Med 2019; 21:2512-2520. [PMID: 31105274 DOI: 10.1038/s41436-019-0544-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/02/2019] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Limb-girdle muscular dystrophies (LGMD) are a genetically heterogeneous category of autosomal inherited muscle diseases. Many genes causing LGMD have been identified, and clinical trials are beginning for treatment of some genetic subtypes. However, even with the gene-level mechanisms known, it is still difficult to get a robust and generalizable prevalence estimation for each subtype due to the limited amount of epidemiology data and the low incidence of LGMDs. METHODS Taking advantage of recently published exome and genome sequencing data from the general population, we used a Bayesian method to develop a robust disease prevalence estimator. RESULTS This method was applied to nine recessive LGMD subtypes. The estimated disease prevalence calculated by this method was largely comparable with published estimates from epidemiological studies; however, it highlighted instances of possible underdiagnosis for LGMD2B and 2L. CONCLUSION The increasing size of aggregated population variant databases will allow for robust and reproducible prevalence estimates of recessive disease, which is critical for the strategic design and prioritization of clinical trials.
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Affiliation(s)
- Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Sander Pajusalu
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Geyu Zhou
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Nilah Ioannidis
- Jain Foundation, Seattle, WA, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Plavi Mittal
- Jain Foundation, Seattle, WA, USA.,In-Depth Genomics, Bellevue, WA, USA
| | - Nicholas E Johnson
- Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis,, MO, USA
| | | | | | | | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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12
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Nazari-Ghadikolaei A, Mehrabani-Yeganeh H, Miarei-Aashtiani SR, Staiger EA, Rashidi A, Huson HJ. Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat. Front Genet 2018; 9:105. [PMID: 29670642 PMCID: PMC5893768 DOI: 10.3389/fgene.2018.00105] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.
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Affiliation(s)
- Anahit Nazari-Ghadikolaei
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hassan Mehrabani-Yeganeh
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed R. Miarei-Aashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Amir Rashidi
- Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan, Sanandaj, Iran
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
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Bulakh MV, Ryzhkova OP, Polyakov AV. Sarcoglycanopathies: Clinical, Molecular and Genetic Characteristics, Epidemiology, Diagnostics and Treatment Options. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418020059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Angelini C, Fanin M. Limb girdle muscular dystrophies: clinical-genetical diagnostic update and prospects for therapy. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1367283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Corrado Angelini
- Department of Neurodegenerative Disorders, Neuromuscular Center, San Camillo Hospital IRCCS, Venice, Italy
| | - Marina Fanin
- Department of Neurosciences, University of Padova, Padova, Italy
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15
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Dalichaouche I, Sifi Y, Roudaut C, Sifi K, Hamri A, Rouabah L, Abadi N, Richard I. γ-sarcoglycan and dystrophin mutation spectrum in an Algerian cohort. Muscle Nerve 2017; 56:129-135. [DOI: 10.1002/mus.25443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Imene Dalichaouche
- Laboratory of Molecular and Cellular Biology, Faculty of Natural Sciences and Life; University 1 of Constantine; Algeria
| | - Yamina Sifi
- Service of Neurology CHU of Constantine; Algeria
- Laboratory of Biology and Molecular Genetics CHU and University 3 of Constantine; Algeria
| | - Carinne Roudaut
- INSERM, U951, INTEGRARE research unit; Evry F-91002 France
- Généthon, R&D Department; Evry F-91002 France
| | - Karima Sifi
- Laboratory of Biology and Molecular Genetics CHU and University 3 of Constantine; Algeria
- Laboratory of Biochemistry CHU of Constantine; Algeria
| | - Abdelmadjid Hamri
- Service of Neurology CHU of Constantine; Algeria
- Laboratory of Biology and Molecular Genetics CHU and University 3 of Constantine; Algeria
| | - Leila Rouabah
- Laboratory of Molecular and Cellular Biology, Faculty of Natural Sciences and Life; University 1 of Constantine; Algeria
| | - Noureddine Abadi
- Laboratory of Biology and Molecular Genetics CHU and University 3 of Constantine; Algeria
- Laboratory of Biochemistry CHU of Constantine; Algeria
| | - Isabelle Richard
- INSERM, U951, INTEGRARE research unit; Evry F-91002 France
- Généthon, R&D Department; Evry F-91002 France
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16
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Pantoja-Melendez CA, Miranda-Duarte A, Roque-Ramirez B, Zenteno JC. Epidemiological and Molecular Characterization of a Mexican Population Isolate with High Prevalence of Limb-Girdle Muscular Dystrophy Type 2A Due to a Novel Calpain-3 Mutation. PLoS One 2017; 12:e0170280. [PMID: 28103310 PMCID: PMC5245889 DOI: 10.1371/journal.pone.0170280] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 01/03/2017] [Indexed: 01/07/2023] Open
Abstract
Limb-Girdle Muscular Dystrophy type 2 (LGMD2) is a group of autosomally recessive inherited disorders defined by weakness and wasting of the shoulder and pelvic girdle muscles. In the past, several population isolates with high incidence of LGMD2 arising from founder mutation effects have been identified. The aim of this work is to describe the results of clinical, epidemiologic, and molecular studies performed in a Mexican village segregating numerous cases of LGMD2. A population census was conducted in the village to identify all LGMD affected patients. Molecular analysis included genome wide homozygosity mapping using a 250K SNP Affymetrix microarray followed by PCR amplification and direct nucleotide sequencing of the candidate gene. In addition, DNA from 401 randomly selected unaffected villagers was analyzed to establish the carrier frequency of the LGMD2 causal mutation. A total of 32 LGMD2 patients were identified in the village, rendering a disease prevalence of 4.3 (CI: 2.9–5.9) cases per 1,000 habitants (1 in 232). Genome wide homozygosity mapping revealed that affected individuals shared a 6.6 Mb region of homozygosity at chromosome 15q15. The identified homozygous interval contained CAPN3, the gene responsible for LGMD2 type A (LGMD2A). Direct sequencing of this gene revealed homozygosity for a novel c.348C>A mutation (p.Ala116Asp) in DNA from all 20 affected subjects available for genetic screening, except one which was heterozygous for the mutation. In such patient, a heterozygous c.2362AG>TCATCT deletion/insertion was recognized as the second CAPN3 mutation. Western blot and autocatalytic activity analyses in protein lysates from skeletal muscle biopsy obtained from a p.Ala116Asp homozygous patient suggested that this particular mutation increased the autocatalytic activity of CAPN3. Thirty eigth heterozygotes of the p.Ala116Asp mutation were identified among 401 genotyped unaffected villagers, yielding a population carrier frequency of 1 in 11. This study demonstrates that a cluster of patients with LGMD2A in a small Mexican village arises from a novel CAPN3 founder mutation. Evidence of allelic heterogeneity is demonstrated by the recognition of an additional CAPN3 mutation in a single affected. Our study provides an additional example of genetic isolation causing a high prevalence of LGMD and of successful molecular characterization of the disease by means of homozygosity mapping. The identification of a very high carrier frequency of the LGMD2-causing mutation has implications for more rational genetic counseling in this community.
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Affiliation(s)
- Carlos A. Pantoja-Melendez
- Department of Genetics-Research Unit, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | | | | | - Juan C. Zenteno
- Department of Genetics-Research Unit, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
- * E-mail:
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18
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Akinyemi RO, Owolabi MO, Oyeniyi T, Ovbiagele B, Arnett DK, Tiwari HK, Walker R, Ogunniyi A, Kalaria RN. Neurogenomics in Africa: Perspectives, progress, possibilities and priorities. J Neurol Sci 2016; 366:213-223. [PMID: 27288810 DOI: 10.1016/j.jns.2016.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022]
Abstract
The understanding of the genetic basis of neurological disorders has grown rapidly in the last two decades. Despite the genomic heterogeneity within African populations, large-scale candidate gene or linkage and exome studies are lacking. However, current knowledge on neurogenetics in African populations is limited and geographically very uneven. Isolated reports indicate the existence of autosomal dominant or recessive conditions incorporating cerebrovascular, movement, neuromuscular, seizure and motor neuron disorders in Africans. In addition, few African families with neurodegenerative disorders associated with dementia have been characterized in North, West and South Africa. The current insurgency in genomic research triggered by among others the Human Health and Heredity (H3) Africa Initiative indicates that there are unique opportunities to advance our knowledge and understanding of the influence of genomic variation on the pattern, presentations and prognosis of neurological disorders in Africa. These have enormous potential to unmask novel genes and molecular pathways germane to the neurobiology of brain disorders. It would facilitate the development of novel diagnostics, preventative and targeted treatments in the new paradigm of precision medicine. Nevertheless, it is crucial to strike a balance between effective traditional public health strategies and personalized genome based care. The translational barriers can be overcome through robust stakeholder engagement and sustainable multilevel, multigenerational and multidisciplinary capacity building and infrastructural development for genomic medicine in Africa.
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Affiliation(s)
- Rufus O Akinyemi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria; Institute of Neuroscience, Newcastle University, UK.
| | - Mayowa O Owolabi
- Department of Medicine, College of Medicine, University of Ibadan, Nigeria
| | | | - Bruce Ovbiagele
- Department of Neurosciences, Medical University of South Carolina, USA
| | - Donna K Arnett
- School of Public Health, University of Alabama at Birmingham, USA
| | - Hemant K Tiwari
- School of Public Health, University of Alabama at Birmingham, USA
| | - Richard Walker
- Institute of Health and Society, Newcastle University, UK
| | - Adesola Ogunniyi
- Department of Medicine, College of Medicine, University of Ibadan, Nigeria
| | - Raj N Kalaria
- Institute of Neuroscience, Newcastle University, UK.
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Where do we stand in trial readiness for autosomal recessive limb girdle muscular dystrophies? Neuromuscul Disord 2015; 26:111-25. [PMID: 26810373 DOI: 10.1016/j.nmd.2015.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/27/2015] [Accepted: 11/29/2015] [Indexed: 12/20/2022]
Abstract
Autosomal recessive limb girdle muscular dystrophies (LGMD2) are a group of genetically heterogeneous diseases that are typically characterised by progressive weakness and wasting of the shoulder and pelvic girdle muscles. Many of the more than 20 different conditions show overlapping clinical features with other forms of muscular dystrophy, congenital, myofibrillar or even distal myopathies and also with acquired muscle diseases. Although individually extremely rare, all types of LGMD2 together form an important differential diagnostic group among neuromuscular diseases. Despite improved diagnostics and pathomechanistic insight, a curative therapy is currently lacking for any of these diseases. Medical care consists of the symptomatic treatment of complications, aiming to improve life expectancy and quality of life. Besides well characterised pre-clinical tools like animal models and cell culture assays, the determinants of successful drug development programmes for rare diseases include a good understanding of the phenotype and natural history of the disease, the existence of clinically relevant outcome measures, guidance on care standards, up to date patient registries, and, ideally, biomarkers that can help assess disease severity or drug response. Strong patient organisations driving research and successful partnerships between academia, advocacy, industry and regulatory authorities can also help accelerate the elaboration of clinical trials. All these determinants constitute aspects of translational research efforts and influence patient access to therapies. Here we review the current status of determinants of successful drug development programmes for LGMD2, and the challenges of translating promising therapeutic strategies into effective and accessible treatments for patients.
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