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Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
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2
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Pickart AM, Martin AS, Gross BN, Dellefave-Castillo LM, McCallen LM, Nagaraj CB, Rippert AL, Schultz CP, Ulm EA, Armstrong N. Genetic counseling for the dystrophinopathies-Practice resource of the National Society of Genetic Counselors. J Genet Couns 2024. [PMID: 38682751 DOI: 10.1002/jgc4.1892] [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: 05/23/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 05/01/2024]
Abstract
The dystrophinopathies encompass the phenotypically variable forms of muscular dystrophy caused by pathogenic variants in the DMD gene. The dystrophinopathies include the most common inherited muscular dystrophy among 46,XY individuals, Duchenne muscular dystrophy, as well as Becker muscular dystrophy and other less common phenotypic variants. With increased access to and utilization of genetic testing in the diagnostic and carrier setting, genetic counselors and clinicians in diverse specialty areas may care for individuals with and carriers of dystrophinopathy. This practice resource was developed as a tool for genetic counselors and other health care professionals to support counseling regarding dystrophinopathies, including diagnosis, health risks and management, psychosocial needs, reproductive options, clinical trials, and treatment. Genetic testing efforts have enabled genotype/phenotype correlation in the dystrophinopathies, but have also revealed unexpected findings, further complicating genetic counseling for this group of conditions. Additionally, the therapeutic landscape for dystrophinopathies has dramatically changed with several FDA-approved therapeutics, an expansive research pathway, and numerous clinical trials. Genotype-phenotype correlations are especially complex and genetic counselors' unique skill sets are useful in exploring and explaining this to families. Given the recent advances in diagnostic testing and therapeutics related to dystrophinopathies, this practice resource is a timely update for genetic counselors and other healthcare professionals involved in the diagnosis and care of individuals with dystrophinopathies.
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Affiliation(s)
- Angela M Pickart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
| | - Brianna N Gross
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Leslie M McCallen
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Chinmayee B Nagaraj
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Elizabeth A Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Niki Armstrong
- Parent Project Muscular Dystrophy, Washington, District of Columbia, USA
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3
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Gatto F, Benemei S, Piluso G, Bello L. The complex landscape of DMD mutations: moving towards personalized medicine. Front Genet 2024; 15:1360224. [PMID: 38596212 PMCID: PMC11002111 DOI: 10.3389/fgene.2024.1360224] [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: 12/22/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disorder characterized by progressive muscle degeneration, with respiratory and cardiac complications, caused by mutations in the DMD gene, encoding the protein dystrophin. Various DMD mutations result in different phenotypes and disease severity. Understanding genotype/phenotype correlations is essential to optimize clinical care, as mutation-specific therapies and innovative therapeutic approaches are becoming available. Disease modifier genes, trans-active variants influencing disease severity and phenotypic expressivity, may modulate the response to therapy, and become new therapeutic targets. Uncovering more disease modifier genes via extensive genomic mapping studies offers the potential to fine-tune prognostic assessments for individuals with DMD. This review provides insights into genotype/phenotype correlations and the influence of modifier genes in DMD.
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Affiliation(s)
| | | | - Giulio Piluso
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Luca Bello
- Department of Neurosciences DNS, University of Padova, Padova, Italy
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4
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Muto H, Yu Y, Chambers JK, Coghill LM, Nakamura Y, Uchida K, Lyons LA. Association of a novel dystrophin (DMD) genetic nonsense variant in a cat with X-linked muscular dystrophy with a mild clinical course. J Vet Intern Med 2024; 38:1160-1166. [PMID: 38415938 PMCID: PMC10937502 DOI: 10.1111/jvim.17024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
X-linked muscular dystrophy in cats (FXMD) is an uncommon disease, with few reports describing its pathogenic genetic variants. A 9-year-old castrated male domestic shorthair cat was presented with persistent muscle swelling and breathing difficulty from 3 years of age. Serum activity of alanine aminotransferase, aspartate transaminase, and creatine kinase were abnormally high. Physical and neurological examinations showed muscle swelling in the neck and proximal limb, slow gait, and occasional breathing difficulties. Electromyography showed pseudomyotonic discharges and complex repetitive discharges with a "dive-bomber" sound. Histopathology revealed muscle necrosis and regeneration. Whole-genome sequencing identified a novel and unique hemizygous nonsense genetic variant, c.8333G > A in dystrophin (DMD), potentially causing a premature termination codon (p.Trp2778Ter). Based on a combination of clinical and histological findings and the presence of the DMD nonsense genetic variant, this case was considered FXMD, which showed mild clinical signs and long-term survival, even though immunohistochemical characterization was lacking.
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Affiliation(s)
| | - Yoshihiko Yu
- Laboratory of Veterinary RadiologyNippon Veterinary and Life Science UniversityTokyoJapan
- Present address:
MitakaTokyoJapan
| | - James K. Chambers
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Lyndon M. Coghill
- Department of Veterinary PathobiologyCollege of Veterinary Medicine, University of MissouriColumbiaMissouriUSA
| | | | - Kazuyuki Uchida
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Leslie A. Lyons
- Department of Veterinary PathobiologyCollege of Veterinary Medicine, University of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and SurgeryCollege of Veterinary Medicine, University of MissouriColumbiaMissouriUSA
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5
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d'Apolito M, Ranaldi A, Santoro F, Cannito S, Gravina M, Santacroce R, Ragnatela I, Margaglione A, D'Andrea G, Casavecchia G, Brunetti ND, Margaglione M. De Novo p.Asp3368Gly Variant of Dystrophin Gene Associated with X-Linked Dilated Cardiomyopathy and Skeletal Myopathy: Clinical Features and In Silico Analysis. Int J Mol Sci 2024; 25:2787. [PMID: 38474032 DOI: 10.3390/ijms25052787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Dystrophin (DMD) gene mutations are associated with skeletal muscle diseases such as Duchenne and Becker Muscular Dystrophy (BMD) and X-linked dilated cardiomyopathy (XL-DCM). To investigate the molecular basis of DCM in a 37-year-old woman. Clinical and genetic investigations were performed. Genetic testing was performed with whole exome sequencing (WES) using the Illumina platform. According to the standard protocol, a variant found by WES was confirmed in all available members of the family by bi-directional capillary Sanger resequencing. The effect of the variant was investigated by using an in silico prediction of pathogenicity. The index case was a 37-year-old woman diagnosed with DCM at the age of 33. A germline heterozygous A>G transversion at nucleotide 10103 in the DMD gene, leading to an aspartic acid-glycine substitution at the amino acid 3368 of the DMD protein (c.10103A>G p.Asp3368Gly), was identified and confirmed by PCR-based Sanger sequencing of the exon 70. In silico prediction suggests that this variant could have a deleterious impact on protein structure and functionality (CADD = 30). The genetic analysis was extended to the first-degree relatives of the proband (mother, father, and sister) and because of the absence of the variant in both parents, the p.Asp3368Gly substitution was considered as occurring de novo. Then, the direct sequencing analysis of her 8-year-old son identified as hemizygous for the same variant. The young patient did not present any signs or symptoms attributable to DCM, but reported asthenia and presented with bilateral calf hypertrophy at clinical examination. Laboratory testing revealed increased levels of creatinine kinase (maximum value of 19,000 IU/L). We report an early presentation of dilated cardiomyopathy in a 33-year-old woman due to a de novo pathogenic variant of the dystrophin (DMD) gene (p.Asp3368Gly). Genetic identification of this variant allowed an early diagnosis of a skeletal muscle disease in her son.
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Affiliation(s)
- Maria d'Apolito
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Alessandra Ranaldi
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Francesco Santoro
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Cardiology Unit, University Polyclinic Hospital of Foggia, 71122 Foggia, Italy
| | - Sara Cannito
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Matteo Gravina
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Rosa Santacroce
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Ilaria Ragnatela
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | | | - Giovanna D'Andrea
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Grazia Casavecchia
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Cardiology Unit, University Polyclinic Hospital of Foggia, 71122 Foggia, Italy
| | - Natale Daniele Brunetti
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
- Cardiology Unit, University Polyclinic Hospital of Foggia, 71122 Foggia, Italy
| | - Maurizio Margaglione
- Medical Genetics, Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
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Wahyuni DK, Indriati DT, Ilham M, Murtadlo AAA, Purnobasuki H, Junairiah, Purnama PR, Ikram NKK, Samian MZ, Subramaniam S. Morpho-anatomical characterization and DNA barcoding of Artemesia vulgaris L. BRAZ J BIOL 2024; 84:e278393. [PMID: 38422290 DOI: 10.1590/1519-6984.278393] [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: 09/11/2023] [Accepted: 01/06/2024] [Indexed: 03/02/2024] Open
Abstract
Artemisia vulgaris L. belongs to Asteraceae, is a herbal plant that has various benefits in the medical field, so that its use in the medical field can be explored optimally, the plant must be thoroughly identified. This study aims to identify A. vulgaris both in terms of descriptive morpho-anatomy and DNA barcoding using BLAST and phylogenetic tree reconstruction. The morpho-anatomical character was observed on root, stem, and leaf. DNA barcoding analysis was carried out through amplification and alignment of the rbcL and matK genes. All studies were conducted on three samples from Taman Husada (Medicinal Plant Garden) Graha Famili Surabaya, Indonesia. The anatomical slide was prepared by the paraffin method. Morphological studies revealed that the leaves of A. vulgaris both on the lower-middle part and on the upper part of the stem have differences, especially in the character of the stipules, petioles, and incisions they have. Meanwhile, from the study of anatomy, A. vulgaris has an anomocytic type of stomata and its distribution is mostly on the ventral part of the leaves. Through the BLAST process and phylogenetic tree reconstruction, the plant sequences being studied are closely related to several species of the genus Artemisia as indicated by a percentage identity above 98% and branch proximity between taxa in the reconstructed phylogenetic tree.
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Affiliation(s)
- D K Wahyuni
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - D T Indriati
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - M Ilham
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - A A A Murtadlo
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - H Purnobasuki
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - Junairiah
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
| | - P R Purnama
- Chulalongkorn University, Faculty of Science, Graduate Program in Bioinformatics and Computational Biology, Bangkok, Thailand
| | - N K K Ikram
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - M Z Samian
- Universiti Malaya, Faculty of Science, Institute of Biological Sciences, Kuala Lumpur, Malaysia
- Universiti Malaya, Centre for Research in Biotechnology for Agriculture - CEBAR, Kuala Lumpur, Malaysia
| | - S Subramaniam
- Universitas Airlangga, Faculty of Science and Technology, Department of Biology, Surabaya, East Java, Indonesia
- Universiti Sains Malaysia, School of Biological Science, Georgetown, Malaysia
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7
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Ricci G, Govoni A, Torri F, Astrea G, Buchignani B, Marinella G, Battini R, Manca ML, Castiglione V, Giannoni A, Emdin M, Siciliano G. Characterization of Phenotypic Variability in Becker Muscular Dystrophy for Clinical Practice and Towards Trial Readiness: A Two-Years Follow up Study. J Neuromuscul Dis 2024; 11:375-387. [PMID: 38189759 DOI: 10.3233/jnd-221513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Background Becker muscular dystrophy (BMD) is a dystrophinopathy due to in-frame mutations in the dystrophin gene (DMD) which determines a reduction of dystrophin at muscle level. BMD has a wide spectrum of clinical variability with different degrees of disability. Studies of natural history are needed also in view of up-coming clinical trials. Objectives From an initial cohort of 32 BMD adult subjects, we present a detailed phenotypic characterization of 28 patients, then providing a description of their clinical natural history over the course of 12 months for 18 and 24 months for 13 of them. Methods Each patient has been genetically characterized. Baseline, and 1-year and 2 years assessments included North Star Ambulatory Assessment (NSAA), timed function tests (time to climb and descend four stairs), 6-minute walk test (6MWT), Walton and Gardner-Medwin Scale and Medical Research Council (MRC) scale. Muscle magnetic resonance imaging (MRI) was acquired at baseline and in a subgroup of 9 patients after 24 months. Data on cardiac function (electrocardiogram, echocardiogram, and cardiac MRI) were also collected. Results and conclusions Among the clinical heterogeneity, a more severe involvement is often observed in patients with 45-X del, with a disease progression over two years. The 6MWT appears sensitive to detect modification from baseline during follow up while no variation was observed by MRC testing. Muscle MRI of the lower limbs correlates with clinical parameters.Our study further highlights how the phenotypic variability of BMD adult patients makes it difficult to describe an uniform course and substantiates the need to identify predictive parameters and biomarkers to stratify patients.
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Affiliation(s)
- Giulia Ricci
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Alessandra Govoni
- Neuromuscular and Rare Disease Unit, La Fondazione IRCCS Ca' Granda Ospedale Maggiore di Milano Policlinico, Milano, Italy
| | - Francesca Torri
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Guja Astrea
- Department of Developmental Neuroscience, IRCCS Stella Maris, Calambrone, Pisa, Italy
| | - Bianca Buchignani
- Department of Developmental Neuroscience, IRCCS Stella Maris, Calambrone, Pisa, Italy
- Department of Translational Research and of New Surgical and Medical Technologies Pisa University, Pisa, Italy
| | - Gemma Marinella
- Department of Developmental Neuroscience, IRCCS Stella Maris, Calambrone, Pisa, Italy
| | - Roberta Battini
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
- Department of Developmental Neuroscience, IRCCS Stella Maris, Calambrone, Pisa, Italy
| | - Maria Laura Manca
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
- Department of Mathematics, University of Pisa, Pisa, Italy
| | - Vincenzo Castiglione
- Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
- Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Alberto Giannoni
- Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
- Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Michele Emdin
- Health Science Interdisciplinary Center, Scuola Superiore Sant'Anna, Pisa, Italy
- Fondazione Toscana Gabriele Monasterio, Pisa, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
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McFadden A, Martin K, Foster G, Vierra M, Lundquist EW, Everts RE, Martin E, Volz E, McLoone K, Brooks SA, Lafayette C. Two Novel Variants in MITF and PAX3 Associated With Splashed White Phenotypes in Horses. J Equine Vet Sci 2023; 128:104875. [PMID: 37406837 DOI: 10.1016/j.jevs.2023.104875] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Mutations causing depigmentation are relatively common in Equus caballus (horse). Over 40 alleles in multiple genes are associated with increased white spotting (as of February 2023). The splashed white phenotype, a coat spotting pattern described as appearing like the horse has been splashed with white paint, was previously associated with variants in the PAX3 and MITF genes. Both genes encode transcription factors known to control melanocyte migration and pigmentation. We report two novel mutations, a stop-gain mutation in PAX3 (XM_005610643.3:c.927C>T, ECA6:11,196,181, EquCab3.0) and a missense mutation in a binding domain of MITF (NM_001163874.1:c.993A>T, ECA16:21,559,940, EquCab3.0), each with a strong association with increased depigmentation in Pura Raza Española horses (P = 1.144E-11, N = 30, P = 4.441E-16, N = 39 respectively). Using a quantitative method to score depigmentation, the PAX3 and MITF mutations were found to have average white scores of 25.50 and 24.45, respectively, compared to the average white coat spotting score of 1.89 in the control set. The functional impact for each mutation was predicted to be moderate to extreme (I-TASSER, SMART, Variant Effect Predictor, SIFT). We propose to designate the MITF mutant allele as Splashed White 9 and the PAX3 mutant allele as Splashed White 10 per convention.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Samantha A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL
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9
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Bello L, Hoffman EP, Pegoraro E. Is it time for genetic modifiers to predict prognosis in Duchenne muscular dystrophy? Nat Rev Neurol 2023; 19:410-423. [PMID: 37308617 DOI: 10.1038/s41582-023-00823-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Patients with Duchenne muscular dystrophy (DMD) show clinically relevant phenotypic variability, despite sharing the same primary biochemical defect (dystrophin deficiency). Factors contributing to this clinical variability include allelic heterogeneity (specific DMD mutations), genetic modifiers (trans-acting genetic polymorphisms) and variations in clinical care. Recently, a series of genetic modifiers have been identified, mostly involving genes and/or proteins that regulate inflammation and fibrosis - processes increasingly recognized as being causally linked with physical disability. This article reviews genetic modifier studies in DMD to date and discusses the effect of genetic modifiers on predicting disease trajectories (prognosis), clinical trial design and interpretation (inclusion of genotype-stratified subgroup analyses) and therapeutic approaches. The genetic modifiers identified to date underscore the importance of progressive fibrosis, downstream of dystrophin deficiency, in driving the disease process. As such, genetic modifiers have shown the importance of therapies aimed at slowing this fibrotic process and might point to key drug targets.
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Affiliation(s)
- Luca Bello
- Department of Neurosciences (DNS), University of Padova, Padova, Italy
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University (State University of New York), Binghamton, NY, USA
| | - Elena Pegoraro
- Department of Neurosciences (DNS), University of Padova, Padova, Italy.
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10
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Andrews JG, Galindo MK, Thomas S, Mathews KD, Whitehead N. DMD Gene and Dystrophinopathy Phenotypes Associated With Mutations: A Systematic Review for Clinicians. J Clin Neuromuscul Dis 2023; 24:171-187. [PMID: 37219861 DOI: 10.1097/cnd.0000000000000436] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
ABSTRACT The diagnosis of Duchenne and Becker muscular dystrophy (DBMD) is made by genetic testing in approximately 95% of cases. Although specific mutations can be associated with skeletal muscle phenotype, pulmonary and cardiac comorbidities (leading causes of death in Duchenne) have not been associated with Duchenne muscular dystrophy mutation type or location and vary within families. Therefore, identifying predictors for phenotype severity beyond frameshift prediction is important clinically. We performed a systematic review assessing research related to genotype-phenotype correlations in DBMD. While there are severity differences across the spectrum and within mild and severe forms of DBMD, few protective or exacerbating mutations within the dystrophin gene were reported. Except for intellectual disability, clinical test results reporting genotypic information are insufficient for clinical prediction of severity and comorbidities and the predictive validity is too low to be useful when advising families. Including expanded information coupled with proposed severity predictions in clinical genetic reports for DBMD is critical for improving anticipatory guidance.
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Affiliation(s)
- Jennifer G Andrews
- Department of Pediatrics, College of Medicine, University of Arizona, Tucson, AZ
| | | | | | - Katherine D Mathews
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA; and
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11
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Torella A, Budillon A, Zanobio M, Del Vecchio Blanco F, Picillo E, Politano L, Nigro V, Piluso G. Alu-Mediated Insertions in the DMD Gene: A Difficult Puzzle to Interpret Clinically. Int J Mol Sci 2023; 24:ijms24119241. [PMID: 37298193 DOI: 10.3390/ijms24119241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Disrupting variants in the DMD gene are associated with Duchenne or Becker muscular dystrophy (DMD/BMD) or with hyperCKemia, all of which present very different degrees of clinical severity. The clinical phenotypes of these disorders could not be distinguished in infancy or early childhood. Accurate phenotype prediction based on DNA variants may therefore be required in addition to invasive tests, such as muscle biopsy. Transposon insertion is one of the rarest mutation types. Depending on their position and characteristics, transposon insertions may affect the quality and/or quantity of dystrophin mRNA, leading to unpredictable alterations in gene products. Here, we report the case of a three-year-old boy showing initial skeletal muscle involvement in whom we characterized a transposon insertion (Alu sequence) in exon 15 of the DMD gene. In similar cases, the generation of a null allele is predicted, resulting in a DMD phenotype. However, mRNA analysis of muscle biopsy tissue revealed skipping of exon 15, which restored the reading frame, thus predicting a milder phenotype. This case is similar to very few others already described in the literature. This case further enriches our knowledge of the mechanisms perturbing splicing and causing exon skipping in DMD, helping to properly guide clinical diagnosis.
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Affiliation(s)
- Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Alberto Budillon
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Zanobio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Francesca Del Vecchio Blanco
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Esther Picillo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Luisa Politano
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
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Chkioua L, Amri Y, Sahli C, Rhouma FB, Chehida AB, Tebib N, Messaoud T, Abdennebi HB, Laradi S. Identification of mutations that causes glucose-6-phosphate transporter defect in tunisian patients with glycogenosis type 1b. Diabetol Metab Syndr 2023; 15:86. [PMID: 37118808 PMCID: PMC10142411 DOI: 10.1186/s13098-023-01065-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Glycogen storage disease type 1b (GSD1b) is an autosomal recessive lysosomal storage disease caused by defective glucose-6-phosphate transporter encoded by SLC37A4 leading to the accumulation of glycogen in various tissues. The high rate of consanguineous marriages in Tunisian population provides an ideal environment to facilitate the identification of homozygous pathogenic mutations. We aimed to determine the clinical and genetic profiles of patients with GSD1b to evaluate SLC37A4 mutations spectrum in Tunisian patients. METHODS All exons and flanking intron regions of SLC37A4 gene were screened by direct sequencing to identify mutations and polymorphisms in three unrelated families with GSD1b. Bioinformatics tools were then used to predict the impacts of identified mutations on the structure and function of protein in order to propose a function-structure relationship of the G6PT1 protein. RESULTS Three patients (MT, MB and SI) in Families I, II and III who had the severe phenotype were homoallelic for the two identified mutations: p.R300H (famillies I, II) and p.W393X (Family III), respectively. One of the alterations was a missense mutation p.R300H of exon 6 in SLC37A4 gene. The analysis of the protein structure flexibility upon p.R300H mutation using DynaMut tool and CABS-flex 2.0 server showed that the reported mutation increase the molecule flexibility of in the cytosol region and would probably lead to significant conformational changes. CONCLUSION This is the first Tunisian report of SLC37A4 mutations identified in Tunisia causing the glycogenosis type Ib disease. Bioinformatics analysis allowed us to establish an approximate structure-function relationship for the G6PT1 protein, thereby providing better genotype/phenotype correlation knowledge.
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Affiliation(s)
- Latifa Chkioua
- Research Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.
- Faculty of Pharmacy, University of Monastir, Street Avicenne, Monastir, 5000, Tunisia.
| | - Yessine Amri
- Biochemistry Laboratory (LR 00SP03), Bechir Hamza Children's Hospital, Tunis, Tunisia
- Department of Educational Sciences, Higher Institute of Applied Studies in Humanity, University of Jendouba, Le Kef, Tunis, Tunisia
| | - Chayma Sahli
- Biochemistry Laboratory (LR 00SP03), Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Ferdawes Ben Rhouma
- Research Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Amel Ben Chehida
- Pediatrics Department, La Rabta Hospital, Tunis, Tunisia
- Research Laboratory: LR12SPO2 Investigation and Management of Inherited Metabolic Diseases, Faculty of Medicine of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Neji Tebib
- Pediatrics Department, La Rabta Hospital, Tunis, Tunisia
| | - Taieb Messaoud
- Biochemistry Laboratory (LR 00SP03), Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Hassen Ben Abdennebi
- Research Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Sandrine Laradi
- The Auvergne-Rhône-Alpes Regional Branch of the French National Blood System EFS/GIMAP, EA 3064, Saint Etienne, 42100, France
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Viggiano E, Picillo E, Passamano L, Onore ME, Piluso G, Scutifero M, Torella A, Nigro V, Politano L. Spectrum of Genetic Variants in the Dystrophin Gene: A Single Centre Retrospective Analysis of 750 Duchenne and Becker Patients from Southern Italy. Genes (Basel) 2023; 14:214. [PMID: 36672955 PMCID: PMC9859256 DOI: 10.3390/genes14010214] [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: 11/07/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Dystrophinopathies are X-linked recessive muscle disorders caused by mutations in the dystrophin (DMD) gene that include deletions, duplications, and point mutations. Correct diagnosis is important for providing adequate patient care and family planning, especially at this time when mutation-specific therapies are available. We report a large single-centre study on the spectrum of DMD gene variants observed in 750 patients analyzed for suspected Duchenne (DMD) or Becker (BMD) muscular dystrophy, over the past 30 years, at the Cardiomyology and Medical Genetics of the University of Campania. We found 534 (71.21%) large deletions, 73 (9.73%) large duplications, and 112 (14.93%) point mutations, of which 44 (5.9%) were small ins/del causing frame-shifts, 57 (7.6%) nonsense mutations, 8 (1.1%) splice site and 3 (0.4%) intronic mutations, and 31 (4.13%) non mutations. Moreover, we report the prevalence of the different types of mutations in patients with DMD and BMD according to their decade of birth, from 1930 to 2020, and correlate the data to the different techniques used over the years. In the most recent decades, we observed an apparent increase in the prevalence of point mutations, probably due to the use of Next-Generation Sequencing (NGS). In conclusion, in southern Italy, deletions are the most frequent variation observed in DMD and BMD patients followed by point mutations and duplications, as elsewhere in the world. NGS was useful to identify point mutations in cases of strong suspicion of DMD/BMD negative on deletions/duplications analyses. In the era of personalized medicine and availability of new causative therapies, a collective effort is necessary to enable DMD and BMD patients to have timely genetic diagnoses and avoid late implementation of standard of care and late initiation of appropriate treatment.
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Affiliation(s)
- Emanuela Viggiano
- Department of Prevention, Hygiene and Public Health Service, ASL Roma 2, 00157 Rome, Italy
| | - Esther Picillo
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Luigia Passamano
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Maria Elena Onore
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Giulio Piluso
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Marianna Scutifero
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Annalaura Torella
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Vincenzo Nigro
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
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Barnard AM, Hammers DW, Triplett WT, Kim S, Forbes SC, Willcocks RJ, Daniels MJ, Senesac CR, Lott DJ, Arpan I, Rooney WD, Wang RT, Nelson SF, Sweeney HL, Vandenborne K, Walter GA. Evaluating Genetic Modifiers of Duchenne Muscular Dystrophy Disease Progression Using Modeling and MRI. Neurology 2022; 99:e2406-e2416. [PMID: 36240102 PMCID: PMC9687406 DOI: 10.1212/wnl.0000000000201163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Duchenne muscular dystrophy (DMD) is a progressive muscle degenerative disorder with a well-characterized disease phenotype but considerable interindividual heterogeneity that is not well understood. The aim of this study was to evaluate the effects of dystrophin variations and genetic modifiers of DMD on rate and age of muscle replacement by fat. METHODS One hundred seventy-five corticosteroid treated participants from the ImagingDMD natural history study underwent repeated magnetic resonance spectroscopy (MRS) of the vastus lateralis (VL) and soleus (SOL) to determine muscle fat fraction (FF). MRS was performed annually in most instances; however, some individuals had additional visits at 3 or 6 monthss intervals. FF changes over time were modeled using nonlinear mixed effects to estimate disease trajectories based on the age that the VL or SOL reached half-maximum change in FF (mu) and the time required for FF change (sigma). Computed mu and sigma values were evaluated for dystrophin variations that have demonstrated the ability to lead to a mild phenotype as well as compared between different genetic polymorphism groups. RESULTS Participants with dystrophin gene deletions amenable to exon 8 skipping (n = 4) had minimal increases in SOL FF and had an increase in VL mu value by 4.4 years compared with a reference cohort (p = 0.039). Participants with nonsense variations within exons that may produce milder phenotypes (n = 11) also had minimal increases in SOL and VL FFs. No differences in estimated FF trajectories were seen for individuals amenable to exon 44 skipping (n = 10). Modeling of the SPP1, LTBP4, and thrombospondin-1 (THBS1) genetic modifiers did not result in significant differences in muscle FF trajectories between genotype groups (p > 0.05); however, trends were noted for the polymorphisms associated with long-range regulation of LTBP4 and THBS1 that deserve further follow-up. DISCUSSION The results of this study link the historically mild phenotypes seen in individuals amenable to exon 8 skipping and with certain nonsense variations with alterations in trajectories of lower extremity muscle replacement by fat.
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Affiliation(s)
- Alison M Barnard
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - David W Hammers
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - William T Triplett
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Sarah Kim
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Sean C Forbes
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Rebecca J Willcocks
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Michael J Daniels
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Claudia R Senesac
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Donovan J Lott
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Ishu Arpan
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - William D Rooney
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Richard T Wang
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Stanley F Nelson
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - H Lee Sweeney
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Krista Vandenborne
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville
| | - Glenn A Walter
- From the Department of Physical Therapy (A.M.B., W.T.T., S.C.F., R.J.W., C.R.S., D.J.L., K.V.) Pharmacology and Therapeutics (D.W.H., H.L.S.), University of Florida, Gainesville; Center for Pharmacometrics and Systems Pharmacology (S.K.), Department of Pharmaceutics, College of Pharmacy, University of Florida, Orlando; Department of Statistics (M.J.D.), University of Florida, Gainesville; Department of Neurology (I.A.), Oregon Health & Science University, Portland; Advanced Imaging Research Center (W.D.R.), Oregon Health & Science University, Portland; Department of Human Genetics (R.T.W., S.F.N.), University of California Los Angeles, CA; and Department of Physiology and Functional Genomics (G.A.W.), University of Florida, Gainesville.
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Gan S, Liu S, Yang H, Wu L. Clinical and genetic characteristics of Chinese Duchenne/Becker muscular dystrophy patients with small mutations. Front Neurosci 2022; 16:992546. [DOI: 10.3389/fnins.2022.992546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
BackgroundDuchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are amongst the inherited neuromuscular diseases with the highest incidence. Small mutations are less common and therefore have been poorly studied in China.Materials and methodsThe clinical data of 150 patients diagnosed with DMD/BMD by genetic analysis in Hunan Children’s Hospital from 2009 to 2021 were analyzed. The patients were followed up for an average of 3.42 years and their clinical characteristics were collected. Loss of ambulation (LOA) was used to evaluate the severity of disease progression. The correlation among clinical features, different variants, and glucocorticoid (GC) treatment was analyzed by Cox regression analysis.Results150 different variants were detected in this study, including 21 (14%) novel mutations, 88 (58.7%) non-sense mutations, 33 (22.0%) frameshift mutations, 22 (14.7%) splicing mutations, and 7 (4.7%) missense mutations. Single-exon skipping and single- or double-exon (double/single-exon) skipping strategies covered more than 90% of patients with small mutations. A case with frameshift mutation combined with Klinefelter’s syndrome (47, XXY) and another one with missense mutation combined with epilepsy was found in our study. De novo mutations accounted for 30.0% of all patients. The mean onset age was 4.19 ± 1.63 years old, and the mean diagnosed age was 5.60 ± 3.13 years old. The mean age of LOA was 10.4 years old (40 cases). 60.7% of them received GC treatment at 7.0 ± 2.7 years old. The main causes of complaints were muscle weakness, high creatine kinase (CK), motor retardation, and family history. The risk factors of LOA were positive family history (HR 5.52, CI 1.26–24.18), short GC treatment duration (HR 0.54, CI 0.36–0.82) and frameshift mutation (HR 14.58, CI 1.74–121.76). DMD patients who treated with GC after 7 years old had a higher risk of earlier LOA compared to those receiving treatment before the age of 7 (HR 0.083, CI 0.009–0.804). Moreover, an earlier onset age, a higher CK value, and a larger LOA population were found in the DMD patients compared to the BMD ones. Finally, the locations of the most frequent mutation were in exon 70 and exon 22.ConclusionIn conclusion, 150 small mutations were identified in this study, and 21 of them were discovered for the first time. We found the hotspots of small mutations were in exon 70 and exon 20. Also, the analysis showed that positive family history, frameshift mutation, short duration of GC treatment, and delayed GC treatment resulted in earlier LOA for the DMD patients. Taken together, our findings complement the mutation spectrum of DMD/BMD, benefit us understanding to the DMD disease, and lay foundations for the clinical trials.
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A Nonsense Variant in the DMD Gene Causes X-Linked Muscular Dystrophy in the Maine Coon Cat. Animals (Basel) 2022; 12:ani12212928. [PMID: 36359052 PMCID: PMC9653713 DOI: 10.3390/ani12212928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Feline dystrophin-deficient muscular dystrophy (ddMD) is a fatal disease characterized by progressive weakness and degeneration of skeletal muscles and is caused by variants in the DMD gene. To date, only two feline causal variants have been identified. This study reports two cases of male Maine coon siblings that presented with muscular hypertrophy, growth retardation, weight loss, and vomiting. (2) Both cats were clinically examined and histopathology and immunofluorescent staining of the affected muscle was performed. DMD mRNA was sequenced to identify putative causal variants. (3) Both cats showed a significant increase in serum creatine kinase activity. Electromyography and histopathological examination of the muscle samples revealed abnormalities consistent with a dystrophic phenotype. Immunohistochemical testing revealed the absence of dystrophin, confirming the diagnosis of dystrophin-deficient muscular dystrophy. mRNA sequencing revealed a nonsense variant in exon 11 of the feline DMD gene, NC_058386.1 (XM_045050794.1): c.1180C > T (p.(Arg394*)), which results in the loss of the majority of the dystrophin protein. Perfect X-linked segregation of the variant was established in the pedigree. (4) ddMD was described for the first time in the Maine coon and the c.1180C>T variant was confirmed as the causal variant.
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Zinina E, Bulakh M, Chukhrova A, Ryzhkova O, Sparber P, Shchagina O, Polyakov A, Kutsev S. Specificities of the DMD Gene Mutation Spectrum in Russian Patients. Int J Mol Sci 2022; 23:ijms232112710. [PMID: 36361501 PMCID: PMC9658738 DOI: 10.3390/ijms232112710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022] Open
Abstract
Duchenne/Becker muscular dystrophy (DMD/BMD) is the most common form of muscular dystrophy, accounting for over 50% of all cases. In this regard, in Russia we carry out a program of selective screening for DMD/BMD, which mainly involves male patients. The main inclusion criteria are an increase in the level of creatine phosphokinase (>2000 U/L) or an established clinical diagnosis. At the first stage of screening, patients are scanned for extended deletions and duplications in the DMD gene using multiplex ligase-dependent probe amplification (MLPA SALSA P034 and P035 DMD probemix, MRC-Holland). The second stage is the search for small mutations using a custom NGS panel, which includes 31 genes responsible for various forms of limb-girdle muscular dystrophy. In a screening of 1025 families with a referral Duchenne/Becker diagnosis, pathogenic and likely pathogenic variants in the DMD gene were found in 788 families (in 76.9% of cases). In the current study, we analyzed the mutation spectrum of the DMD gene in Russian patients and noted certain differences between the examined cohort and the multi-ethnic cohort. The analysis of the DMD gene mutation spectrum is essential for patients with DMD/BMD because the exact mutation type determines the application of a specific therapeutic method.
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Rare and population-specific functional variation across pig lines. Genet Sel Evol 2022; 54:39. [PMID: 35659233 PMCID: PMC9164375 DOI: 10.1186/s12711-022-00732-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. METHODS We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (FST), individual load, and association to production traits. RESULTS Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site FST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. CONCLUSIONS Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.
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19
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Gruber D, Lloyd‐Puryear M, Armstrong N, Scavina M, Tavakoli NP, Brower AM, Caggana M, Chung WK. Newborn screening for Duchenne muscular dystrophy-early detection and diagnostic algorithm for female carriers of Duchenne muscular dystrophy. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:197-205. [PMID: 36152336 PMCID: PMC9826042 DOI: 10.1002/ajmg.c.32000] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
Duchenne muscular dystrophy (DMD) is the most common pediatric-onset form of muscular dystrophy, occurring in 1 in 5,000 live male births. DMD is a multi-system disease resulting in muscle weakness with progressive deterioration of skeletal, heart, and smooth muscle, and learning disabilities. Pathogenic/likely pathogenic (P/LP) variants in the DMD gene, which encodes dystrophin protein, cause dystrophinopathy. All males with a P/LP variant in the X-linked DMD gene are expected to be affected. Two to 20% of female heterozygotes with a P/LP variant develop symptoms of dystrophinopathy ranging from mild muscle weakness to significant disability similar to Becker muscular dystrophy. Recently, with improvements in therapies and testing methodology, there is stronger evidence supporting newborn screening (NBS) for DMD for males and females because females may also develop symptoms. A consented pilot study to screen newborns for DMD was initiated in New York State (NYS) and conducted from 2019 to 2021. The identification of female carriers and the realization of the subsequent uncertainty of providers concerning follow-up during the pilot led to the development of algorithms for screening and diagnosis of carrier females, including both NBS and cascade molecular testing of family members.
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Affiliation(s)
- Dorota Gruber
- Department of PediatricsCohen Children's Medical Center, Northwell HealthNew Hyde ParkNew YorkUSA,Departments of Pediatrics and CardiologyDonald and Barbara Zucker School of Medicine at Hofstra/NorthwellHempsteadNew YorkUSA
| | - Michele Lloyd‐Puryear
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (Retired), National Institutes of HealthBethesdaMarylandUSA
| | - Niki Armstrong
- Parent Project Muscular DystrophyWashingtonDistrict of ColumbiaUSA
| | - Mena Scavina
- Parent Project Muscular DystrophyWashingtonDistrict of ColumbiaUSA,Nemours Children's Health, DelawareWilmingtonDelawareUSA
| | - Norma P. Tavakoli
- Division of Genetics, Wadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Amy M. Brower
- American College of Medical Genetics and GenomicsBethesdaMarylandUSA
| | - Michele Caggana
- Division of Genetics, Wadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Wendy K. Chung
- Department of PediatricsColumbia University Irving Medical CenterNew YorkNew YorkUSA
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20
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Potapova NA. Nonsense Mutations in Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:400-412. [PMID: 35790376 DOI: 10.1134/s0006297922050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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21
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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22
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Eintracht J, Forsythe E, May-Simera H, Moosajee M. Translational readthrough of ciliopathy genes BBS2 and ALMS1 restores protein, ciliogenesis and function in patient fibroblasts. EBioMedicine 2021; 70:103515. [PMID: 34365092 PMCID: PMC8353411 DOI: 10.1016/j.ebiom.2021.103515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Ciliary dysfunction underlies a range of genetic disorders collectively termed ciliopathies, for which there are no treatments available. Bardet-Biedl syndrome (BBS) is characterised by multisystemic involvement, including rod-cone dystrophy and renal abnormalities. Together with Alström syndrome (AS), they are known as the 'obesity ciliopathies' due to their common phenotype. Nonsense mutations are responsible for approximately 11% and 40% of BBS and AS cases, respectively. Translational readthrough inducing drugs (TRIDs) can restore full-length protein bypassing in-frame premature termination codons, and are a potential therapeutic approach for nonsense-mediated ciliopathies. METHODS Patient fibroblasts harbouring nonsense mutations from two different ciliopathies (Bardet-Biedl Syndrome and Alström Syndrome) were treated with PTC124 (ataluren) or amlexanox. Following treatment, gene expression, protein levels and ciliogenesis were evaluated. The expression of intraflagellar transport protein IFT88 and G-protein coupled receptor SSTR3 was investigated as a readout of ciliary function. FINDINGS mRNA expression was significantly increased in amlexanox-treated patient fibroblasts, and full-length BBS2 or ALMS1 protein expression was restored in PTC124- and amlexanox-treated fibroblasts. Treatment with TRIDs significantly improved ciliogenesis defects in BBS2Y24*/R275* fibroblasts. Treatment recovered IFT88 expression and corrected SSTR3 mislocalisation in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts, suggesting rescue of ciliary function. INTERPRETATION The recovery of full-length BBS2 and ALMS1 expression and correction of anatomical and functional ciliary defects in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts suggest TRIDs are a potential therapeutic option for the treatment of nonsense-mediated ciliopathies. FUNDING Wellcome Trust 205174/Z/16/Z, National Centre for the Replacement, Refinement & Reduction of Animals in Research. Deutsche Forschungsgemeinschaft SPP2127 (DFG Grant MA 6139/3-1).
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Affiliation(s)
| | - Elizabeth Forsythe
- Clinical Genetics Unit, Great Ormond Street Hospital; Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health
| | - Helen May-Simera
- Institute of Molecular Physiology, Johannes Gutenburg University, Mainz
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, United Kingdom; The Francis Crick Institute, London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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23
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Luce L, Carcione M, Mazzanti C, Buonfiglio PI, Dalamón V, Mesa L, Dubrovsky A, Corderí J, Giliberto F. Theragnosis for Duchenne Muscular Dystrophy. Front Pharmacol 2021; 12:648390. [PMID: 34149409 PMCID: PMC8209366 DOI: 10.3389/fphar.2021.648390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Dystrophinopathies cover a spectrum of rare progressive X-linked muscle diseases, arising from DMD mutations. They are among the most common pediatric muscular dystrophies, being Duchenne muscular dystrophy (DMD) the most severe form. Despite the fact that there is still no cure for these serious diseases, unprecedented advances are being made for the development of therapies for DMD. Some of which are already conditionally approved: exon skipping and premature stop codon read-through. The present work aimed to characterize the mutational spectrum of DMD in an Argentinian cohort, to identify candidates for available pharmacogenetic treatments and finally, to conduct a comparative analysis of the Latin American (LA) frequencies of mutations amenable for available DMD therapies. We studied 400 patients with clinical diagnosis of dystrophinopathy, implementing a diagnostic molecular algorithm including: MLPA/PCR/Sanger/Exome and bioinformatics. We also performed a meta-analysis of LA's metrics for DMD available therapies. The employed algorithm resulted effective for the achievement of differential diagnosis, reaching a detection rate of 97%. Because of this, corticosteroid treatment was correctly indicated and validated in 371 patients with genetic confirmation of dystrophinopathy. Also, 20 were eligible for exon skipping of exon 51, 21 for exon 53, 12 for exon 45 and another 70 for premature stop codon read-through therapy. We determined that 87.5% of DMD patients will restore the reading frame with the skipping of only one exon. Regarding nonsense variants, UGA turned out to be the most frequent premature stop codon observed (47%). According to the meta-analysis, only four LA countries (Argentina, Brazil, Colombia and Mexico) provide the complete molecular algorithm for dystrophinopathies. We observed different relations among the available targets for exon skipping in the analyzed populations, but a more even proportion of nonsense variants (∼40%). In conclusion, this manuscript describes the theragnosis carried out in Argentinian dystrophinopathy patients. The implemented molecular algorithm proved to be efficient for the achievement of differential diagnosis, which plays a crucial role in patient management, determination of the standard of care and genetic counseling. Finally, this work contributes with the international efforts to characterize the frequencies and variants in LA, pillars of drug development and theragnosis.
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Affiliation(s)
- Leonela Luce
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carcione
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Chiara Mazzanti
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula I Buonfiglio
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Viviana Dalamón
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Lilia Mesa
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Alberto Dubrovsky
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - José Corderí
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Florencia Giliberto
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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24
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Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement. Genes (Basel) 2021; 12:genes12020133. [PMID: 33494189 PMCID: PMC7909759 DOI: 10.3390/genes12020133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 01/25/2023] Open
Abstract
Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16–29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a “non-carrier” status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1–15 and 30–34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16–29 deletion, while the second allele showed a 1–34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16–29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.
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25
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Zimowski JG, Purzycka J, Pawelec M, Ozdarska K, Zaremba J. Small mutations in Duchenne/Becker muscular dystrophy in 164 unrelated Polish patients. J Appl Genet 2021; 62:289-295. [PMID: 33420945 DOI: 10.1007/s13353-020-00605-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
In the 164 patients with Duchenne/Becker muscular dystrophy, we found 142 different small mutations including 51 novel mutations not listed in the LOVD, the UMD-DMD, the ClinVar, and the HGMD databases. Among all mutations, nonsense mutations occurred in 45.7%, frameshift mutations in 32.9%, and splicing mutations in 19.5%. Small mutations were distributed throughout the whole dystrophin gene. Splicing mutations were twice more common in BMD patients than in DMD patients. Eighty-two percent of mothers of the males affected with DMD/BMD were found to be carriers of small mutations.
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Affiliation(s)
- Janusz G Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland. .,, Warsaw, Poland.
| | - Joanna Purzycka
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Magdalena Pawelec
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Katarzyna Ozdarska
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
| | - Jacek Zaremba
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957, Sobieskiego 9, Warsaw, Poland
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