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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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Salari M, Etemadifar M, Rashedi R, Mardani S. A Review of Ocular Movement Abnormalities in Hereditary Cerebellar Ataxias. CEREBELLUM (LONDON, ENGLAND) 2024; 23:702-721. [PMID: 37000369 DOI: 10.1007/s12311-023-01554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Cerebellar ataxias are a wide heterogeneous group of disorders that may present with fine motor deficits as well as gait and balance disturbances that have a significant influence on everyday activities. To review the ocular movements in cerebellar ataxias in order to improve the clinical knowledge of cerebellar ataxias and related subtypes. English papers published from January 1990 to May 2022 were selected by searching PubMed services. The main search keywords were ocular motor, oculomotor, eye movement, eye motility, and ocular motility, along with each ataxia subtype. The eligible papers were analyzed for clinical presentation, involved mutations, the underlying pathology, and ocular movement alterations. Forty-three subtypes of spinocerebellar ataxias and a number of autosomal dominant and autosomal recessive ataxias were discussed in terms of pathology, clinical manifestations, involved mutations, and with a focus on the ocular abnormalities. A flowchart has been made using ocular movement manifestations to differentiate different ataxia subtypes. And underlying pathology of each subtype is reviewed in form of illustrated models to reach a better understanding of each disorder.
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Affiliation(s)
- Mehri Salari
- Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Etemadifar
- Department of Functional Neurosurgery, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ronak Rashedi
- Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sayna Mardani
- Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Chen X, Zhang F, Shi Y, Wang H, Chen M, Yang D, Wang L, Liu P, Xie F, Chen J, Fu A, Hu B, Wang B, Ouyang Z, Wu S, Lin Z, Cen Z, Luo W. Origin and evolution of pentanucleotide repeat expansions at the familial cortical myoclonic tremor with epilepsy type1 - SAMD12 locus. Eur J Hum Genet 2024:10.1038/s41431-024-01586-y. [PMID: 38467733 DOI: 10.1038/s41431-024-01586-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
Familial cortical myoclonic tremor with epilepsy type 1 (FCMTE1) is caused by (TTTTA)exp(TTTCA)exp repeat expansions in SAMD12, while pure (TTTTA)exp is polymorphic. Our investigation focused on the origin and evolution of pure (TTTTA)exp and (TTTTA)exp(TTTCA)exp at this locus. We observed a founder effect between them. The phylogenetic analysis suggested that the (TTTTA)exp(TTTCA)exp might be generated from pure (TTTTA)exp through infrequent transformation events. Long-read sequencing revealed somatic generation of (TTTTA)exp(TTTCA)exp from pure (TTTTA)exp, likely via long segment (TTTCA) repeats insertion. Our findings indicate close relationships between the non-pathogenic (TTTTA)exp and the pathogenic (TTTTA)exp(TTTCA)exp, with dynamic interconversions. This sheds light on the genesis of pathogenic repeat expansions from ancestral premutation alleles. Our results may guide future studies in detecting novel repeat expansion disorders and elucidating repeat expansion mutational processes, thereby enhancing our understanding of human genomic variation.
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Affiliation(s)
- Xinhui Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Fan Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yihua Shi
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Haotian Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Miao Chen
- Department of Neurology, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Dehao Yang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Lebo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Peng Liu
- Department of Neurology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, Zhejiang, China
| | - Jiawen Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co., Ltd. Wuhan, Wuhan, 430075, China
| | - Ben Hu
- Center for Tumor Precision Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430062, China
| | - Bo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiyuan Ouyang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Sheng Wu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiru Lin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhidong Cen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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Sanchez-Flores M, Corral-Juan M, Gasch-Navalón E, Cirillo D, Sanchez I, Matilla-Dueñas A. Novel genotype-phenotype correlations, differential cerebellar allele-specific methylation, and a common origin of the (ATTTC) n insertion in spinocerebellar ataxia type 37. Hum Genet 2024; 143:211-232. [PMID: 38396267 PMCID: PMC11043136 DOI: 10.1007/s00439-024-02644-7] [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: 08/26/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
Spinocerebellar ataxia subtype 37 (SCA37) is a rare disease originally identified in ataxia patients from the Iberian Peninsula with a pure cerebellar syndrome. SCA37 patients carry a pathogenic intronic (ATTTC)n repeat insertion flanked by two polymorphic (ATTTT)n repeats in the Disabled-1 (DAB1) gene leading to cerebellar dysregulation. Herein, we determine the precise configuration of the pathogenic 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n SCA37 alleles by CRISPR-Cas9 and long-read nanopore sequencing, reveal their epigenomic signatures in SCA37 lymphocytes, fibroblasts, and cerebellar samples, and establish new molecular and clinical correlations. The 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n pathogenic allele configurations revealed repeat instability and differential methylation signatures. Disease age of onset negatively correlated with the (ATTTC)n, and positively correlated with the 3'(ATTTT)n. Geographic origin and gender significantly correlated with age of onset. Furthermore, significant predictive regression models were obtained by machine learning for age of onset and disease evolution by considering gender, the (ATTTC)n, the 3'(ATTTT)n, and seven CpG positions differentially methylated in SCA37 cerebellum. A common 964-kb genomic region spanning the (ATTTC)n insertion was identified in all SCA37 patients analysed from Portugal and Spain, evidencing a common origin of the SCA37 mutation in the Iberian Peninsula originating 859 years ago (95% CI 647-1378). In conclusion, we demonstrate an accurate determination of the size and configuration of the regulatory 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n repeat tract, avoiding PCR bias amplification using CRISPR/Cas9-enrichment and nanopore long-read sequencing, resulting relevant for accurate genetic diagnosis of SCA37. Moreover, we determine novel significant genotype-phenotype correlations in SCA37 and identify differential cerebellar allele-specific methylation signatures that may underlie DAB1 pathogenic dysregulation.
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Affiliation(s)
- Marina Sanchez-Flores
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Marc Corral-Juan
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Esther Gasch-Navalón
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | | | - Ivelisse Sanchez
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Antoni Matilla-Dueñas
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain.
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Joly-Amado A, Kulkarni N, Nash KR. Reelin Signaling in Neurodevelopmental Disorders and Neurodegenerative Diseases. Brain Sci 2023; 13:1479. [PMID: 37891846 PMCID: PMC10605156 DOI: 10.3390/brainsci13101479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Reelin is an extracellular matrix glycoprotein involved in neuronal migration during embryonic brain development and synaptic plasticity in the adult brain. The role of Reelin in the developing central nervous system has been extensively characterized. Indeed, a loss of Reelin or a disruption in its signaling cascade leads to neurodevelopmental defects and is associated with ataxia, intellectual disability, autism, and several psychiatric disorders. In the adult brain, Reelin is critically involved in neurogenesis and synaptic plasticity. Reelin's signaling potentiates glutamatergic and GABAergic neurotransmission, induces synaptic maturation, and increases AMPA and NMDA receptor subunits' expression and activity. As a result, there is a growing literature reporting that a loss of function and/or reduction of Reelin is implicated in numerous neurodegenerative diseases. The present review summarizes the current state of the literature regarding the implication of Reelin and Reelin-mediated signaling during aging and neurodegenerative disorders, highlighting Reelin as a possible target in the prevention or treatment of progressive neurodegeneration.
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Affiliation(s)
- Aurelie Joly-Amado
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL 33612, USA; (N.K.); (K.R.N.)
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Cuccurullo C, Striano P, Coppola A. Familial Adult Myoclonus Epilepsy: A Non-Coding Repeat Expansion Disorder of Cerebellar-Thalamic-Cortical Loop. Cells 2023; 12:1617. [PMID: 37371086 DOI: 10.3390/cells12121617] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Familial adult myoclonus Epilepsy (FAME) is a non-coding repeat expansion disorder that has been reported under different acronyms and initially linked to four main loci: FAME1 (8q23.3-q24.1), FAME 2 (2p11.1-q12.1), FAME3 (5p15.31-p15.1), and FAME4 (3q26.32-3q28). To date, it is known that the genetic mechanism underlying FAME consists of the expansion of similar non-coding pentanucleotide repeats, TTTCA and TTTTA, in different genes. FAME is characterized by cortical tremor and myoclonus usually manifesting within the second decade of life, and infrequent seizures by the third or fourth decade. Cortical tremor is the core feature of FAME and is considered part of a spectrum of cortical myoclonus. Neurophysiological investigations as jerk-locked back averaging (JLBA) and corticomuscular coherence analysis, giant somatosensory evoked potentials (SEPs), and the presence of long-latency reflex I (or C reflex) at rest support cortical tremor as the result of the sensorimotor cortex hyperexcitability. Furthermore, the application of transcranial magnetic stimulation (TMS) protocols in FAME patients has recently shown that inhibitory circuits are also altered within the primary somatosensory cortex and the concomitant involvement of subcortical networks. Moreover, neuroimaging studies and postmortem autoptic studies indicate cerebellar alterations and abnormal functional connectivity between the cerebellum and cerebrum in FAME. Accordingly, the pathophysiological mechanism underlying FAME has been hypothesized to reside in decreased sensorimotor cortical inhibition through dysfunction of the cerebellar-thalamic-cortical loop, secondary to primary cerebellar pathology. In this context, the non-coding pentameric expansions have been proposed to cause cerebellar damage through an RNA-mediated toxicity mechanism. The elucidation of the underlying pathological mechanisms of FAME paves the way to novel therapeutic possibilities, such as RNA-targeting treatments, possibly applicable to other neurodegenerative non-coding disorders.
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Affiliation(s)
- Claudia Cuccurullo
- Department of Neuroscience, Reproductive Sciences and Odontostomatology, Federico II University of Naples, 80131 Naples, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, 16126 Genova, Italy
| | - Antonietta Coppola
- Department of Neuroscience, Reproductive Sciences and Odontostomatology, Federico II University of Naples, 80131 Naples, Italy
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Rosenbohm A, Pott H, Thomsen M, Rafehi H, Kaya S, Szymczak S, Volk AE, Mueller K, Silveira I, Weishaupt JH, Tönnies H, Seibler P, Zschiedrich K, Schaake S, Westenberger A, Zühlke C, Depienne C, Trinh J, Ludolph AC, Klein C, Bahlo M, Lohmann K. Familial Cerebellar Ataxia and Amyotrophic Lateral Sclerosis/Frontotemporal Dementia with DAB1 and C9ORF72 Repeat Expansions: An 18-Year Study. Mov Disord 2022; 37:2427-2439. [PMID: 36148898 PMCID: PMC10900262 DOI: 10.1002/mds.29221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Coding and noncoding repeat expansions are an important cause of neurodegenerative diseases. OBJECTIVE This study determined the clinical and genetic features of a large German family that has been followed for almost 2 decades with an autosomal dominantly inherited spinocerebellar ataxia (SCA) and independent co-occurrence of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). METHODS We carried out clinical examinations and telephone interviews, reviewed medical records, and performed magnetic resonance imaging and positron emission tomography scans of all available family members. Comprehensive genetic investigations included linkage analysis, short-read genome sequencing, long-read sequencing, repeat-primed polymerase chain reaction, and Southern blotting. RESULTS The family comprises 118 members across seven generations, 30 of whom were definitely and five possibly affected. In this family, two different pathogenic mutations were found, a heterozygous repeat expansion in C9ORF72 in four patients with ALS/FTD and a heterozygous repeat expansion in DAB1 in at least nine patients with SCA, leading to a diagnosis of DAB1-related ataxia (ATX-DAB1; SCA37). One patient was affected by ALS and SCA and carried both repeat expansions. The repeat in DAB1 had the same configuration but was larger than those previously described ([ATTTT]≈75 [ATTTC]≈40-100 [ATTTT]≈415 ). Clinical features in patients with SCA included spinocerebellar symptoms, sometimes accompanied by additional ophthalmoplegia, vertical nystagmus, tremor, sensory deficits, and dystonia. After several decades, some of these patients suffered from cognitive decline and one from additional nonprogressive lower motor neuron affection. CONCLUSION We demonstrate genetic and clinical findings during an 18-year period in a unique family carrying two different pathogenic repeat expansions, providing novel insights into their genotypic and phenotypic spectrums. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Hendrik Pott
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Mirja Thomsen
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Haloom Rafehi
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Sabine Kaya
- Institute of Human GeneticsUniversity Hospital EssenEssenGermany
| | - Silke Szymczak
- Insitute of Medical Biometry and StatisticsUniversity of LübeckLübeckGermany
| | - Alexander E. Volk
- Institute of Human GeneticsUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | | | - Isabel Silveira
- i3S‐Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
| | - Jochen H. Weishaupt
- Division of Neurodegeneration, Neurology DepartmentUniversity Medicine Mannheim, Heidelberg UniversityMannheimGermany
| | - Holger Tönnies
- Institute of Human GeneticsChristian‐Albrechts‐UniversityKielGermany
| | - Philip Seibler
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Susen Schaake
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | | | | | - Joanne Trinh
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Albert C. Ludolph
- Department of NeurologyUniversity of UlmUlmGermany
- German Center for Neurodegenerative Diseases, Site UlmUlmGermany
| | | | - Melanie Bahlo
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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Baviera-Muñoz R, Carretero-Vilarroig L, Vázquez-Costa JF, Morata-Martínez C, Campins-Romeu M, Muelas N, Sastre-Bataller I, Martínez-Torres I, Pérez-García J, Sivera R, Sevilla T, Vilchez JJ, Jaijo T, Espinós C, Millán JM, Bataller L, Aller E. Diagnostic Efficacy of Genetic Studies in a Series of Hereditary Cerebellar Ataxias in Eastern Spain. NEUROLOGY GENETICS 2022; 8:e200038. [DOI: 10.1212/nxg.0000000000200038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Background and ObjectivesTo determine the diagnostic efficacy of clinical exome-targeted sequencing (CES) and spinocerebellar ataxia 36 (SCA36) screening in a real-life cohort of patients with cerebellar ataxia (CA) from Eastern Spain.MethodsA total of 130 unrelated patients with CA, negative for common trinucleotide repeat expansions (SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA12, SCA17, dentatorubral pallidoluysian atrophy [DRPLA], and Friedreich ataxia), were studied with CES. Bioinformatic and genotype-phenotype analyses were performed to assess the pathogenicity of the variants encountered. Copy number variants were analyzed when appropriate. In undiagnosed dominant and sporadic cases, repeat primed PCR was used to screen for the presence of a repeat expansion in theNOP56gene.ResultsCES identified pathogenic or likely pathogenic variants in 50 families (39%), including 23 novel variants. Overall, there was a high genetic heterogeneity, and the most frequent genetic diagnosis wasSPG7(n = 15), followed bySETX(n = 6),CACNA1A(n = 5),POLR3A(n = 4), andSYNE1(n = 3). In addition, 17 families displayed likely pathogenic/pathogenic variants in 14 different genes:KCND3(n = 2),KIF1C(n = 2),CYP27A1A(n = 2),AFG3L2(n = 1),ANO10(n = 1),CAPN1(n = 1),CWF19L1(n = 1),ITPR1(n = 1),KCNA1(n = 1),OPA1(n = 1),PNPLA6(n = 1),SPG11(n = 1),SPTBN2(n = 1), andTPP1(n = 1). Twenty-two novel variants were characterized. SCA36 was diagnosed in 11 families, all with autosomal dominant (AD) presentation. SCA36 screening increased the total diagnostic rate to 47% (n = 61/130). Ultimately, undiagnosed patients showed delayed age at onset (p< 0.05) and were more frequently sporadic.DiscussionOur study provides insight into the genetic landscape of CA in Eastern Spain. Although CES was an effective approach to capture genetic heterogeneity, most patients remained undiagnosed. SCA36 was found to be a relatively frequent form and, therefore, should be tested prior to CES in familial AD presentations in particular geographical regions.
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ATTCT and ATTCC repeat expansions in the ATXN10 gene affect disease penetrance of spinocerebellar ataxia type 10. HGG ADVANCES 2022; 3:100137. [PMID: 36092952 PMCID: PMC9460507 DOI: 10.1016/j.xhgg.2022.100137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is an autosomal-dominant disorder caused by an expanded pentanucleotide repeat in the ATXN10 gene. This repeat expansion, when fully penetrant, has a size of 850–4,500 repeats. It has been shown that the repeat composition can be a modifier of disease, e.g., seizures. Here, we describe a Mexican kindred in which we identified both pure (ATTCT)n and mixed (ATTCT)n-(ATTCC)n expansions in the same family. We used amplification-free targeted sequencing and optical genome mapping to decipher the composition of these repeat expansions. We found a considerable degree of mosaicism of the repeat expansion. This mosaicism was confirmed in skin fibroblasts from individuals with ATXN10 expansions with RNAScope in situ hybridization. All affected family members with the mixed ATXN10 repeat expansion showed typical clinical signs of spinocerebellar ataxia and epilepsy. In contrast, individuals with the pure ATXN10 expansion present with Parkinson's disease or are unaffected, even in individuals more than 20 years older than the average age at onset for SCA10. Our findings suggest that the pure (ATTCT)n expansion is non-pathogenic, while repeat interruptions, e.g., (ATTCC)n, are necessary to cause SCA10. This mechanism has been recently described for several other repeat expansions including SCA31 (BEAN1), SCA37 (DAB1), and three loci for benign adult familial myoclonic epilepsy BAFME (SAMD12, TNRC6A, RAPGEF2). Therefore, long-read sequencing and optical genome mapping of the entire genomic structure of repeat expansions are critical for clinical practice and genetic counseling, as variations in the repeat can affect disease penetrance, symptoms, and disease trajectory.
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Loureiro JR, Castro AF, Figueiredo AS, Silveira I. Molecular Mechanisms in Pentanucleotide Repeat Diseases. Cells 2022; 11:cells11020205. [PMID: 35053321 PMCID: PMC8773600 DOI: 10.3390/cells11020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
The number of neurodegenerative diseases resulting from repeat expansion has increased extraordinarily in recent years. In several of these pathologies, the repeat can be transcribed in RNA from both DNA strands producing, at least, one toxic RNA repeat that causes neurodegeneration by a complex mechanism. Recently, seven diseases have been found caused by a novel intronic pentanucleotide repeat in distinct genes encoding proteins highly expressed in the cerebellum. These disorders are clinically heterogeneous being characterized by impaired motor function, resulting from ataxia or epilepsy. The role that apparently normal proteins from these mutant genes play in these pathologies is not known. However, recent advances in previously known spinocerebellar ataxias originated by abnormal non-coding pentanucleotide repeats point to a gain of a toxic function by the pathogenic repeat-containing RNA that abnormally forms nuclear foci with RNA-binding proteins. In cells, RNA foci have been shown to be formed by phase separation. Moreover, the field of repeat expansions has lately achieved an extraordinary progress with the discovery that RNA repeats, polyglutamine, and polyalanine proteins are crucial for the formation of nuclear membraneless organelles by phase separation, which is perturbed when they are expanded. This review will cover the amazing advances on repeat diseases.
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Affiliation(s)
- Joana R. Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana F. Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana S. Figueiredo
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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Wang ZW, Wang LP, Du Y, Liu Q. Mutations in NOTCH3 Gene may Promote the Clinical Presentation of Spinocerebellar Ataxia Type 37 Caused by Mutations in DAB1 Gene. Front Mol Biosci 2021; 8:668312. [PMID: 34222332 PMCID: PMC8243652 DOI: 10.3389/fmolb.2021.668312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Autosomal dominant spinocerebellar ataxia type 37 (SCA37) and Cerebral autosomal dominant arteriopathy with subcortical infarct and leukoencephalopathy (CADASIL) result from DAB1 and NOTCH3 gene mutations, respectively. Methods: In addition to conventional diagnostic methods, next-generation sequencing (NGS) and Sanger sequencing were performed to define and confirm the DAB1 and NOTCH3 gene mutation for a Chinese pedigree. Bioinformatics analysis was also applied for the mutated DAB1 and NOTCH3 protein using available software tools. Results: Brain magnetic resonance imaging shows diffuse leukoencephalopathy and cerebellar atrophy in the proband. NGS and Sanger sequencing identified two novel heterozygous mutations: NM_021080:c.318T > G (p.H106Q) in the DAB1 gene and NM_000435:c.3298C > T (p.R1100C) in the NOTCH3 gene. Bioinformatics analysis suggested that the DAB1 and NOTCH3 gene mutations are disease-causing and may be responsible for the phenotypes. Conclusion: This is the first report of a pedigree with both SAC37 and CADASIL phenotypes carrying corresponding gene mutations. Mutations in the NOTCH3 gene may promote the clinical presentation of spinocerebellar ataxia type 37 caused by mutations in the DAB1 gene. In addition to general examinations, it is vital for physicians to apply molecular genetics to get an accurate diagnosis in the clinic, especially for rare diseases.
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Affiliation(s)
- Zhao-Wei Wang
- Department of Neurology, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Li-Ping Wang
- Department of Neurology, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Ye Du
- Department of Neurology, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Qi Liu
- Department of Transfusion, Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
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12
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Depienne C, Mandel JL. 30 years of repeat expansion disorders: What have we learned and what are the remaining challenges? Am J Hum Genet 2021; 108:764-785. [PMID: 33811808 PMCID: PMC8205997 DOI: 10.1016/j.ajhg.2021.03.011] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Tandem repeats represent one of the most abundant class of variations in human genomes, which are polymorphic by nature and become highly unstable in a length-dependent manner. The expansion of repeat length across generations is a well-established process that results in human disorders mainly affecting the central nervous system. At least 50 disorders associated with expansion loci have been described to date, with half recognized only in the last ten years, as prior methodological difficulties limited their identification. These limitations still apply to the current widely used molecular diagnostic methods (exome or gene panels) and thus result in missed diagnosis detrimental to affected individuals and their families, especially for disorders that are very rare and/or clinically not recognizable. Most of these disorders have been identified through family-driven approaches and many others likely remain to be identified. The recent development of long-read technologies provides a unique opportunity to systematically investigate the contribution of tandem repeats and repeat expansions to the genetic architecture of human disorders. In this review, we summarize the current and most recent knowledge about the genetics of repeat expansion disorders and the diversity of their pathophysiological mechanisms and outline the perspectives of developing personalized treatments in the future.
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Affiliation(s)
- Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, 75013 Paris, France.
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR 7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France; USIAS University of Strasbourg Institute of Advanced study, 67000 Strasbourg, France.
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13
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Mizuguchi T, Toyota T, Miyatake S, Mitsuhashi S, Doi H, Kudo Y, Kishida H, Hayashi N, Tsuburaya RS, Kinoshita M, Fukuyama T, Fukuda H, Koshimizu E, Tsuchida N, Uchiyama Y, Fujita A, Takata A, Miyake N, Kato M, Tanaka F, Adachi H, Matsumoto N. Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment. Brain 2021; 144:1103-1117. [PMID: 33791773 DOI: 10.1093/brain/awab021] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/14/2022] Open
Abstract
A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy. Although the precise determination of the entire SAMD12 repeat sequence is important for molecular diagnosis and research, obtaining this sequence remains challenging when using conventional genomic/genetic methods, and even short-read and long-read next-generation sequencing technologies have been insufficient. Incomplete information regarding expanded repeat sequences may hamper our understanding of the pathogenic roles played by varying numbers of repeat units, genotype-phenotype correlations, and mutational mechanisms. Here, we report a new approach for the precise determination of the entire expanded repeat sequence and present a workflow designed to improve the diagnostic rates in various repeat expansion diseases. We examined 34 clinically diagnosed benign adult familial myoclonic epilepsy patients, from 29 families using repeat-primed PCR, Southern blot, and long-read sequencing with Cas9-mediated enrichment. Two cases with questionable results from repeat-primed PCR and/or Southern blot were confirmed as pathogenic using long-read sequencing with Cas9-mediated enrichment, resulting in the identification of pathogenic SAMD12 repeat expansions in 76% of examined families (22/29). Importantly, long-read sequencing with Cas9-mediated enrichment was able to provide detailed information regarding the sizes, configurations, and compositions of the expanded repeats. The inserted TTTCA repeat size and the proportion of TTTCA sequences among the overall repeat sequences were highly variable, and a novel repeat configuration was identified. A genotype-phenotype correlation study suggested that the insertion of even short (TTTCA)14 repeats contributed to the development of benign adult familial myoclonic epilepsy. However, the sizes of the overall TTTTA and TTTCA repeat units are also likely to be involved in the pathology of benign adult familial myoclonic epilepsy. Seven unsolved SAMD12-negative cases were investigated using whole-genome long-read sequencing, and infrequent, disease-associated, repeat expansions were identified in two cases. The strategic workflow resolved two questionable SAMD12-positive cases and two previously SAMD12-negative cases, increasing the diagnostic yield from 69% (20/29 families) to 83% (24/29 families). This study indicates the significant utility of long-read sequencing technologies to explore the pathogenic contributions made by various repeat units in complex repeat expansions and to improve the overall diagnostic rate.
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Affiliation(s)
- Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tomoko Toyota
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu 807-8555, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Medical Research Institute Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yosuke Kudo
- Department of Neurology, Yokohama Brain and Spine Center, Yokohama 235-0012, Japan
| | - Hitaru Kishida
- Department of Neurology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Noriko Hayashi
- Department of Neurology, Yamato Municipal Hospital, Yamato 242-8602, Japan
| | - Rie S Tsuburaya
- Department of Pediatric Neurology, National Hospital Organization Utano National Hospital, Kyoto 616-8255, Japan
| | - Masako Kinoshita
- Department of Neurology, National Hospital Organization Utano National Hospital, Kyoto 616-8255, Japan
| | - Tetsuhiro Fukuyama
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto 390-8621, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo 142-8666, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiroaki Adachi
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu 807-8555, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
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14
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Smits DJ, Schot R, Wilke M, van Slegtenhorst M, de Wit MCY, Dremmen MHG, Dobyns WB, Barkovich AJ, Mancini GMS. Biallelic DAB1 Variants Are Associated With Mild Lissencephaly and Cerebellar Hypoplasia. NEUROLOGY-GENETICS 2021; 7:e558. [PMID: 33928188 PMCID: PMC7830234 DOI: 10.1212/nxg.0000000000000558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/02/2020] [Indexed: 11/15/2022]
Abstract
Objective We aimed to identify pathogenic variants in a girl with epilepsy,
developmental delay, cerebellar ataxia, oral motor difficulty, and
structural brain abnormalities with the use of whole-exome sequencing. Methods Whole-exome trio analysis and molecular functional studies were performed in
addition to the clinical findings and neuroimaging studies. Results Brain MRI showed mild pachygyria, hypoplasia of the cerebellar vermis, and
abnormal foliation of the cerebellar vermis, suspected for a variant in one
of the genes of the Reelin pathway. Trio whole-exome sequencing and
additional functional studies were performed to identify the pathogenic
variants. Trio whole-exome sequencing revealed compound heterozygous splice
variants in DAB1, both affecting the highly conserved
functional phosphotyrosine-binding domain. Expression studies in
patient-derived cells showed loss of normal transcripts, confirming
pathogenicity. Conclusions We conclude that these variants are very likely causally related to the
cerebral phenotype and propose to consider loss-of-function
DAB1 variants in patients with RELN-like cortical
malformations.
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Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Rachel Schot
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Marie Claire Y de Wit
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Marjolein H G Dremmen
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - William B Dobyns
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - A James Barkovich
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics (D.J.S., R.S., M.W., M.S., G.M.S.M.), ErasmusMC University Medical Center Rotterdam; Department of Child Neurology (M.C.Y.W.) and Department of Radiology (M.H.G.D.), Sophia Children's Hospital, ErasmusMC University Medical Center Rotterdam, the Netherlands; Department of Pediatrics (W.B.D.), University of Washington; Department of Neurology (W.B.D.), University of Washington, Seattle; Center for Integrative Brain Research (W.B.D.), Seattle Children's Research Institute, WA; Department of Human Genetics (W.B.D.), University of Minnesota, Minneapolis; Department of Radiology and Biomedical Imaging (A.J.B.), University of California, San Francisco; and ENCORE Expertise Center for Neurodevelopmental Disorders (M.C.Y.W., M.H.G.D., G.M.S.M.), ErasmusMC University Medical Center, Rotterdam, the Netherlands
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15
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Brown RE, Freudenreich CH. Structure-forming repeats and their impact on genome stability. Curr Opin Genet Dev 2020; 67:41-51. [PMID: 33279816 DOI: 10.1016/j.gde.2020.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
Repetitive sequences throughout the genome are a major source of endogenous DNA damage, due to the propensity of many of them to form alternative non-B DNA structures that can interfere with replication, transcription, and DNA repair. These repetitive sequences are prone to breakage (fragility) and instability (changes in repeat number). Repeat fragility and expansions are linked to several diseases, including many cancers and neurodegenerative diseases, hence the importance of understanding the mechanisms that cause genome instability and contribute to these diseases. This review focuses on recent findings of mechanisms causing repeat fragility and instability, new associations between repeat expansions and genetic diseases, and potential therapeutic options to target repeat expansions.
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Affiliation(s)
- Rebecca E Brown
- Program in Genetics, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA.
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16
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Akçimen F, Ross JP, Bourassa CV, Liao C, Rochefort D, Gama MTD, Dicaire MJ, Barsottini OG, Brais B, Pedroso JL, Dion PA, Rouleau GA. Investigation of the RFC1 Repeat Expansion in a Canadian and a Brazilian Ataxia Cohort: Identification of Novel Conformations. Front Genet 2019; 10:1219. [PMID: 31824583 PMCID: PMC6884024 DOI: 10.3389/fgene.2019.01219] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/04/2019] [Indexed: 12/30/2022] Open
Abstract
A biallelic pentanucleotide expansion in the RFC1 gene has been reported to be a common cause of late-onset ataxia. In the general population, four different repeat conformations are observed: wild type sequence AAAAG (11 repeats) and longer expansions of either AAAAG, AAAGG or AAGGG sequences. However only the biallelic AAGGG expansions were reported to cause late-onset ataxia. In this study, we aimed to assess the prevalence and nature of RFC1 repeat expansions in three cohorts of adult-onset ataxia cases: Brazilian (n = 23) and Canadian (n = 26) cases that are negative for the presence of variants in other known ataxia-associated genes, as well as a cohort of randomly selected Canadian cases (n = 128) without regard to a genetic diagnosis. We identified the biallelic AAGGG expansion in only one Brazilian family which presented two affected siblings, and in one Canadian case. We also observed two new repeat conformations, AAGAG and AGAGG, which suggests the pentanucleotide expansion sequence has a dynamic nature. To assess the frequency of these new repeat conformations in the general population, we screened 163 healthy individuals and observed the AAGAG expansion to be more frequent in cases than in control individuals. While additional studies will be necessary to asses the pathogenic impact of biallelic genotypes that include the novel expanded conformations, their occurrence should nonetheless be examined in future studies.
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Affiliation(s)
- Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Cynthia V. Bourassa
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Calwing Liao
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Daniel Rochefort
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Maria Thereza Drumond Gama
- Division of General Neurology and Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Marie-Josée Dicaire
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Orlando G. Barsottini
- Division of General Neurology and Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Bernard Brais
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - José Luiz Pedroso
- Division of General Neurology and Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Patrick A. Dion
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
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17
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Corbett MA, Kroes T, Veneziano L, Bennett MF, Florian R, Schneider AL, Coppola A, Licchetta L, Franceschetti S, Suppa A, Wenger A, Mei D, Pendziwiat M, Kaya S, Delledonne M, Straussberg R, Xumerle L, Regan B, Crompton D, van Rootselaar AF, Correll A, Catford R, Bisulli F, Chakraborty S, Baldassari S, Tinuper P, Barton K, Carswell S, Smith M, Berardelli A, Carroll R, Gardner A, Friend KL, Blatt I, Iacomino M, Di Bonaventura C, Striano S, Buratti J, Keren B, Nava C, Forlani S, Rudolf G, Hirsch E, Leguern E, Labauge P, Balestrini S, Sander JW, Afawi Z, Helbig I, Ishiura H, Tsuji S, Sisodiya SM, Casari G, Sadleir LG, van Coller R, Tijssen MAJ, Klein KM, van den Maagdenberg AMJM, Zara F, Guerrini R, Berkovic SF, Pippucci T, Canafoglia L, Bahlo M, Striano P, Scheffer IE, Brancati F, Depienne C, Gecz J. Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2. Nat Commun 2019; 10:4920. [PMID: 31664034 PMCID: PMC6820779 DOI: 10.1038/s41467-019-12671-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Familial Adult Myoclonic Epilepsy (FAME) is characterised by cortical myoclonic tremor usually from the second decade of life and overt myoclonic or generalised tonic-clonic seizures. Four independent loci have been implicated in FAME on chromosomes (chr) 2, 3, 5 and 8. Using whole genome sequencing and repeat primed PCR, we provide evidence that chr2-linked FAME (FAME2) is caused by an expansion of an ATTTC pentamer within the first intron of STARD7. The ATTTC expansions segregate in 158/158 individuals typically affected by FAME from 22 pedigrees including 16 previously reported families recruited worldwide. RNA sequencing from patient derived fibroblasts shows no accumulation of the AUUUU or AUUUC repeat sequences and STARD7 gene expression is not affected. These data, in combination with other genes bearing similar mutations that have been implicated in FAME, suggest ATTTC expansions may cause this disorder, irrespective of the genomic locus involved.
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Affiliation(s)
- Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, 5005, SA, Australia
| | - Thessa Kroes
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, 5005, SA, Australia
| | - Liana Veneziano
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Mark F Bennett
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Melbourne, 3010, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Rahel Florian
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Antonietta Coppola
- Department of Neuroscience, Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Laura Licchetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Silvana Franceschetti
- Neurophysiopathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Member of the European Reference Network on Rare and Complex epilepsies, ERN EpiCARE, London, UK
| | - Antonio Suppa
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
| | | | - Davide Mei
- Neuroscience and Neurogenetics Department, Meyer Children's Hospital, Florence, Italy
| | - Manuela Pendziwiat
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany
| | - Sabine Kaya
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Rachel Straussberg
- Institute of Pediatric Neurology, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Tel Aviv University Medical School, 69978, Tel Aviv, Israel
| | - Luciano Xumerle
- Personal Genomics, Strada le Grazie 15, 37134, Verona, Italy
| | - Brigid Regan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Douglas Crompton
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
- Department of Neurology, Northern Health, Melbourne, VIC, Australia
| | - Anne-Fleur van Rootselaar
- Amsterdam UMC, University of Amsterdam, Department of Neurology and Clinical Neurophysiology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Anthony Correll
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Rachael Catford
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Francesca Bisulli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | - Sara Baldassari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Paolo Tinuper
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Kirston Barton
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Shaun Carswell
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Martin Smith
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, 2010, Australia
- St-Vincent's Clinical School, Faulty of Medicine, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
| | - Alfredo Berardelli
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, 5005, SA, Australia
| | - Alison Gardner
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, 5005, SA, Australia
| | - Kathryn L Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Ilan Blatt
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Michele Iacomino
- Laboratory of Neurogenetics, IRCCS Istituto "G. Gaslini", Genova, Italy
| | - Carlo Di Bonaventura
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185, Rome, Italy
| | | | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Sylvie Forlani
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Gabrielle Rudolf
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Department of Neurology, Strasbourg University Hospital, Strasbourg, France
- Centre National de la Recherche Scientifique, U7104, Illkirch, France
| | - Edouard Hirsch
- Department of Neurology, Strasbourg University Hospital, Strasbourg, France
| | - Eric Leguern
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Pierre Labauge
- MS Unit, Montpellier University Hospital, Montpellier, France
| | - Simona Balestrini
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, SL9 0RJ, UK
| | - Josemir W Sander
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, SL9 0RJ, UK
| | - Zaid Afawi
- Tel Aviv University Medical School, 69978, Tel Aviv, Israel
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany
- Division of Neurology Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hiroyuki Ishiura
- Department of Neurology, the University of Tokyo Hospital, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, the University of Tokyo Hospital, Tokyo, Japan
- Medical Genome Center, the University of Tokyo Hospital, Tokyo, Japan
- International University of Health and Welfare, Chiba, Japan
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, SL9 0RJ, UK
| | - Giorgio Casari
- TIGEM - Telethon Institute of Genetics and Medicine, Naples, and San Raffaele University, Milan, Italy
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, Wellington, New Zealand
| | | | - Marina A J Tijssen
- Department of Neurology, University of Groningen, Groningen, The Netherlands
| | - Karl Martin Klein
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Goethe University, Frankfurt am Main, Frankfurt, Germany
- Department of Neurology, Epilepsy Center Hessen, Philipps University, Marburg, Marburg, Germany
- Departments of Clinical Neurosciences, Medical Genetics and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Federico Zara
- Laboratory of Neurogenetics, IRCCS Istituto "G. Gaslini", Genova, Italy
| | - Renzo Guerrini
- Neuroscience and Neurogenetics Department, Meyer Children's Hospital, Florence, Italy
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
| | - Tommaso Pippucci
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Laura Canafoglia
- Neurophysiopathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Member of the European Reference Network on Rare and Complex epilepsies, ERN EpiCARE, London, UK
| | - Melanie Bahlo
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "G. Gaslini", Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genova, Italy
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, 3084, VIC, Australia
- Royal Children's Hospital, Murdoch Children's Research Institute and Florey Institute, Melbourne, VIC, Australia
| | - Francesco Brancati
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
- Medical Genetics, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy
| | - Christel Depienne
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, U7104, Illkirch, France
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, 5005, SA, Australia.
- South Australian Health and Medical Research Institute, Adelaide, 5000, SA, Australia.
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