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Leitão E, Schröder C, Depienne C. Identification and characterization of repeat expansions in neurological disorders: Methodologies, tools, and strategies. Rev Neurol (Paris) 2024; 180:383-392. [PMID: 38594146 DOI: 10.1016/j.neurol.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Tandem repeats are a common, highly polymorphic class of variation in human genomes. Their expansion beyond a pathogenic threshold is a process that contributes to a wide range of neurological and neuromuscular genetic disorders, of which over 60 have been identified to date. The last few years have seen a resurgence in repeat expansion discovery propelled by technological advancements, enabling the identification of over 20 novel repeat expansion disorders. These expansions can occur in coding or non-coding regions of genes, resulting in a range of pathogenic mechanisms. In this article, we review strategies, tools and methods that can be used for efficient detection and characterization of known repeat expansions and identification of new expansion disorders. Features that can be used to prioritize repeat expansions include anticipation, which is characterized by increased severity or earlier onset of symptoms across generations, and founder effects, which contribute to higher prevalence rates in certain populations. Classical technologies such as Southern blotting, repeat-primed polymerase chain reaction (PCR) and long-range PCR can still be used to detect known repeat expansions, although they usually have significant limitations linked to the absence of sequence context. Targeted sequencing of known expansions using either long-range PCR or CRISPR-Cas9 enrichment combined with long-read sequencing or adaptive nanopore sampling are usually better but more expensive alternatives. The development of new bioinformatics tools applied to short-read genome data can now be used to detect repeat expansions either in a targeted manner or at the genome-wide level. In addition, technological advances, particularly long-read technologies such as optical genome mapping (Bionano Genomics), Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) HiFi sequencing, offer promising avenues for the detection of repeat expansions. Despite challenges in specific DNA extraction requirements, computation resources needed and data interpretation, these technologies have an immense potential to advance our understanding of repeat expansion disorders and improve diagnostic accuracy.
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Affiliation(s)
- E Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - C Schröder
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - C Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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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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Yeetong P, Dembélé ME, Pongpanich M, Cissé L, Srichomthong C, Maiga AB, Dembélé K, Assawapitaksakul A, Bamba S, Yalcouyé A, Diarra S, Mefoung SE, Rakwongkhachon S, Traoré O, Tongkobpetch S, Fischbeck KH, Gahl WA, Guinto CO, Shotelersuk V, Landouré G. Pentanucleotide Repeat Insertions in RAI1 Cause Benign Adult Familial Myoclonic Epilepsy Type 8. Mov Disord 2024; 39:164-172. [PMID: 37994247 PMCID: PMC10872918 DOI: 10.1002/mds.29654] [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: 07/11/2023] [Revised: 10/04/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Benign adult familial myoclonic epilepsy (BAFME) is an autosomal dominant disorder characterized by cortical tremors and seizures. Six types of BAFME, all caused by pentanucleotide repeat expansions in different genes, have been reported. However, several other BAFME cases remain with no molecular diagnosis. OBJECTIVES We aim to characterize clinical features and identify the mutation causing BAFME in a large Malian family with 10 affected members. METHODS Long-read whole genome sequencing, repeat-primed polymerase chain reaction and RNA studies were performed. RESULTS We identified TTTTA repeat expansions and TTTCA repeat insertions in intron 4 of the RAI1 gene that co-segregated with disease status in this family. TTTCA repeats were absent in 200 Malian controls. In the affected individuals, we found a read with only nine TTTCA repeat units and somatic instability. The RAI1 repeat expansions cause the only BAFME type in which the disease-causing repeats are in a gene associated with a monogenic disorder in the haploinsufficiency state (ie, Smith-Magenis syndrome [SMS]). Nevertheless, none of the Malian patients exhibited symptoms related to SMS. Moreover, leukocyte RNA levels of RAI1 in six Malian BAFME patients were no different from controls. CONCLUSIONS These findings establish a new type of BAFME, BAFME8, in an African family and suggest that haploinsufficiency is unlikely to be the main pathomechanism of BAFME. © 2023 International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Patra Yeetong
- Division of Human Genetics, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Lassana Cissé
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | | | | | - Adjima Assawapitaksakul
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Salia Bamba
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
| | | | - Salimata Diarra
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | - Supphakorn Rakwongkhachon
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Oumou Traoré
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
| | - Siraprapa Tongkobpetch
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | | | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cheick O Guinto
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok 10330, Thailand
| | - Guida Landouré
- Faculté de Médecine et d’Odontostomatologie, USTTB, Bamako, Mali
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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5
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Jagota P, Ugawa Y, Aldaajani Z, Ibrahim NM, Ishiura H, Nomura Y, Tsuji S, Diesta C, Hattori N, Onodera O, Bohlega S, Al-Din A, Lim SY, Lee JY, Jeon B, Pal PK, Shang H, Fujioka S, Kukkle PL, Phokaewvarangkul O, Lin CH, Shambetova C, Bhidayasiri R. Nine Hereditary Movement Disorders First Described in Asia: Their History and Evolution. J Mov Disord 2023; 16:231-247. [PMID: 37309109 PMCID: PMC10548072 DOI: 10.14802/jmd.23065] [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: 03/31/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
Clinical case studies and reporting are important to the discovery of new disorders and the advancement of medical sciences. Both clinicians and basic scientists play equally important roles leading to treatment discoveries for both cures and symptoms. In the field of movement disorders, exceptional observation of patients from clinicians is imperative, not just for phenomenology but also for the variable occurrences of these disorders, along with other signs and symptoms, throughout the day and the disease course. The Movement Disorders in Asia Task Force (TF) was formed to help enhance and promote collaboration and research on movement disorders within the region. As a start, the TF has reviewed the original studies of the movement disorders that were preliminarily described in the region. These include nine disorders that were first described in Asia: Segawa disease, PARK-Parkin, X-linked dystonia-parkinsonism, dentatorubral-pallidoluysian atrophy, Woodhouse-Sakati syndrome, benign adult familial myoclonic epilepsy, Kufor-Rakeb disease, tremulous dystonia associated with mutation of the calmodulin-binding transcription activator 2 gene, and paroxysmal kinesigenic dyskinesia. We hope that the information provided will honor the original researchers and help us learn and understand how earlier neurologists and basic scientists together discovered new disorders and made advances in the field, which impact us all to this day.
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Affiliation(s)
- Priya Jagota
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Yoshikazu Ugawa
- Department of Human Neurophysiology, Faculty of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Zakiyah Aldaajani
- Neurology Unit, King Fahad Military Medical Complex, Dhahran, Saudi Arabia
| | - Norlinah Mohamed Ibrahim
- Neurology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hiroyuki Ishiura
- Department of Neurology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshiko Nomura
- Yoshiko Nomura Neurological Clinic for Children, Tokyo, Japan
| | - Shoji Tsuji
- Institute of Medical Genomics, International University of Health and Welfare, Narita, Chiba, Japan
| | - Cid Diesta
- Section of Neurology, Department of Neuroscience, Makati Medical Center, NCR, Makati City, Philippines
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Saeed Bohlega
- Department of Neurosciences, King Faisal Specialist Hospital & Research Center, Riyad, Saudi Arabia
| | - Amir Al-Din
- Mid Yorkshire Hospitals National Health Services Trust, Wakefield, UK
| | - Shen-Yang Lim
- Division of Neurology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- The Mah Pooi Soo & Tan Chin Nam Centre for Parkinson’s & Related Disorders, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jee-Young Lee
- Department of Neurology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center & Seoul National University Medical College, Seoul, Korea
| | - Beomseok Jeon
- Department of Neurology, Seoul National University, Seoul, Korea
- Movement Disorder Center, Seoul National University Hospital, Seoul, Korea
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health & Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shinsuke Fujioka
- Department of Neurology, Fukuoka University, Faculty of Medicine, Fukuoka, Japan
| | - Prashanth Lingappa Kukkle
- Center for Parkinson’s Disease and Movement Disorders, Manipal Hospital, Bangalore, India
- Parkinson's Disease and Movement Disorders Clinic, Bangalore, India
| | - Onanong Phokaewvarangkul
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Roongroj Bhidayasiri
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- The Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
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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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7
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Berkovic SF, Striano P, Tsuji S. History of familial adult myoclonus epilepsy/benign adult familial myoclonic epilepsy around the world. Epilepsia 2023; 64 Suppl 1:S3-S8. [PMID: 36707971 PMCID: PMC10952646 DOI: 10.1111/epi.17519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/29/2023]
Abstract
Familial adult myoclonus epilepsy/benign adult familial myoclonic epilepsy (FAME/BAFME) has emerged as a specific and recognizable epilepsy syndrome with autosomal dominant inheritance found around the world. Here, we trace the history of this syndrome. Initially, it was likely conflated with other familial myoclonus epilepsies, especially the progressive myoclonus epilepsies. As the progressive myoclonus epilepsies became better understood clinically and genetically, this group began to stand out and was first recognized as such in Japan. Subsequently, families were recognized around the world and there was debate as to whether they represented one or multiple disorders. Clarification came with the identification of pentanucleotide repeats in Japanese families, and FAME/BAFME was quickly shown to be due to pentanucleotide expansions in at least six genes. These have geographic predilections and appear to have been caused by historically ancient initial mutations. Within and between families, there is some variation in the phenotype, explained in large part by expansion size, but whether there are features specific to individual genes remains uncertain.
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Affiliation(s)
- Samuel F. Berkovic
- Department of Medicine, Epilepsy Research CentreUniversity of MelbourneHeidelbergVictoriaAustralia
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases UnitGiannina Gaslini Institute, Scientific Institute for Research and Health CareGenoaItaly
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversity of GenoaGenoaItaly
| | - Shoji Tsuji
- Department of NeurologyUniversity of Tokyo HospitalTokyoJapan
- Institute of Medical GenomicsInternational University of Health and WelfareChibaJapan
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8
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Corbett MA, Depienne C, Veneziano L, Klein KM, Brancati F, Guerrini R, Zara F, Tsuji S, Gecz J. Genetics of familial adult myoclonus epilepsy: From linkage studies to noncoding repeat expansions. Epilepsia 2023; 64 Suppl 1:S14-S21. [PMID: 37021642 PMCID: PMC10952679 DOI: 10.1111/epi.17610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/07/2023]
Abstract
Familial adult myoclonus epilepsy (FAME) is a genetic epilepsy syndrome that for many years has resisted understanding of its underlying molecular cause. This review covers the history of FAME genetic studies worldwide, starting with linkage and culminating in the discovery of noncoding TTTTA and inserted TTTCA pentanucleotide repeat expansions within six different genes to date (SAMD12, STARD7, MARCHF6, YEATS2, TNRC6A, and RAPGEF2). FAME occurs worldwide; however, repeat expansions in particular genes have regional geographical distributions. FAME repeat expansions are dynamic in nature, changing in length and structure within germline and somatic tissues. This variation poses challenges for molecular diagnosis such that molecular methods used to identify FAME repeat expansions typically require a trade-off between cost and efficiency. A rigorous evaluation of the sensitivity and specificity of each molecular approach remains to be performed. The origin of FAME repeat expansions and the genetic and environmental factors that modulate repeat variability are not well defined. Longer repeats and particular arrangements of the TTTTA and TTTCA motifs within an expansion are correlated with earlier onset and increased severity of disease. Other factors such as maternal or paternal inheritance, parental age, and repeat length alone have been suggested to influence repeat variation; however, further research is required to confirm this. The history of FAME genetics to the present is a chronicle of perseverance and predominantly collaborative efforts that yielded a successful outcome. The discovery of FAME repeats will spark progress toward a deeper understanding of the molecular pathogenesis of FAME, discovery of new loci, and development of cell and animal models.
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Affiliation(s)
- Mark A. Corbett
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Christel Depienne
- Institute of Human GeneticsUniversity Hospital Essen, University Duisburg–EssenEssenGermany
| | - Liana Veneziano
- Institute of Translational PharmacologyNational Research CouncilRomeItaly
| | - Karl Martin Klein
- Departments of Clinical Neurosciences, Medical Genetics, and Community Health Sciences, Hotchkiss Brain Institute and Alberta Children's HospitalResearch Institute, Cumming School of Medicine, University of CalgaryCalgaryAlbertaCanada
- Epilepsy Center Frankfurt Rhine–Main, Department of Neurology, Center of Neurology and NeurosurgeryCenter for Personalized Translational Epilepsy Research, University Hospital, Goethe University FrankfurtFrankfurt am MainGermany
| | - Francesco Brancati
- Institute of Translational PharmacologyNational Research CouncilRomeItaly
- Medical Genetics, Department of Life, Health, and Environmental SciencesUniversity of L'AquilaL'AquilaItaly
- Laboratory of Human Functional GenomicsIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San RaffaeleRomeItaly
| | - Renzo Guerrini
- Neuroscience and Neurogenetics DepartmentMeyer Children's HospitalFlorenceItaly
| | - Federico Zara
- Laboratory of NeurogeneticsIRCCS Institute "G. Gaslini"GenoaItaly
| | - Shoji Tsuji
- Department of Neurology, Graduate School of MedicineUniversity of TokyoTokyoJapan
- Institute of Medical GenomicsInternational University of Health and WelfareChibaJapan
| | - Jozef Gecz
- Robinson Research Institute and Adelaide Medical SchoolUniversity of AdelaideAdelaideSouth AustraliaAustralia
- South Australian Health and Medical Research InstituteAdelaideSouth AustraliaAustralia
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Ruggiero SM, Xian J, Helbig I. The current landscape of epilepsy genetics: where are we, and where are we going? Curr Opin Neurol 2023; 36:86-94. [PMID: 36762645 PMCID: PMC10088099 DOI: 10.1097/wco.0000000000001141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
PURPOSE OF REVIEW In this review, we aim to analyse the progress in understanding the genetic basis of the epilepsies, as well as ongoing efforts to define the increasingly diverse and novel presentations, phenotypes and divergences from the expected that have continually characterized the field. RECENT FINDINGS A genetic workup is now considered to be standard of care for individuals with an unexplained epilepsy, due to mounting evidence that genetic diagnoses significantly influence treatment choices, prognostication, community support, and increasingly, access to clinical trials. As more individuals with epilepsy are tested, novel presentations of known epilepsy genes are being discovered, and more individuals with self-limited epilepsy are able to attain genetic diagnoses. In addition, new genes causative of epilepsy are being uncovered through both traditional and novel methods, including large international data-sharing collaborations and massive sequencing efforts as well as computational methods and analyses driven by the Human Phenotype Ontology (HPO). SUMMARY New approaches to gene discovery and characterization are advancing rapidly our understanding of the genetic and phenotypic architecture of the epilepsies. This review highlights relevant and groundbreaking studies published recently that have pushed forward the field of epilepsy genetics.
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Affiliation(s)
- Sarah M Ruggiero
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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10
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Maroilley T, Tsai MH, Mascarenhas R, Diao C, Khanbabaei M, Kaya S, Depienne C, Tarailo-Graovac M, Klein KM. A novel FAME1 repeat configuration in a European family identified using a combined genomics approach. Epilepsia Open 2023. [PMID: 36740228 DOI: 10.1002/epi4.12702] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
Familial adult myoclonic epilepsy (FAME) is an adult-onset neurological disease characterized by cortical tremor, myoclonus, and seizures due to a pentanucleotide repeat expansion: a combination of pathogenic TTTCA expansion associated with a TTTTA repeat in introns of six different genes. Repeat-primed PCR (RP-PCR) is an inexpensive test for expansions at known loci. The analysis of the SAMD12 locus revealed that the repeats have different size, configuration, and composition. The TTTCA repeats can be very long (>1000 repeats) but also very short (14 being the shortest identified). Here, we report siblings of European descent with the clinical diagnosis of FAME yet a negative RP-PCR test. Using short-read genome sequencing, we identified the pentanucleotide expansion in intron 4 of SAMD12, which was confirmed by CRIPSR-Cas9-mediated enrichment and long-read sequencing to be of (TTTTA)~879 (TTTCA)3 (TTTTA)7 (TTTCA)7 configuration. Our finding is the first to associate the SAMD12 locus in European patients with FAME and currently represents the shortest identified TTTCA expansion. Our results suggest that the SAMD12 locus should be tested in patients with suspected FAME independent of ethnicity. Furthermore, RP-PCR may miss the underlying mutation, and genome sequencing may be needed to confirm the pathogenic repeat.
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Affiliation(s)
- Tatiana Maroilley
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Meng-Han Tsai
- Department of Neurology and Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,School of Medicine, College of Medicine, Taoyuan, Chang Gung University, Taoyuan City, Taiwan
| | - Rumika Mascarenhas
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Catherine Diao
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Maryam Khanbabaei
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Maja Tarailo-Graovac
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Karl Martin Klein
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Center of Neurology and Neurosurgery, University Hospital, Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt, Germany
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11
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Li J, Wan L, Wang Y, Chen Y, Lee HK, Lam SL, Guo P. Solution Nuclear Magnetic Resonance Structures of ATTTT and ATTTC Pentanucleotide Repeats Associated with SCA37 and FAMEs. ACS Chem Neurosci 2023; 14:289-299. [PMID: 36580663 DOI: 10.1021/acschemneuro.2c00593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Expansions of ATTTT and ATTTC pentanucleotide repeats in the human genome are recently found to be associated with at least seven neurodegenerative diseases, including spinocerebellar ataxia type 37 (SCA37) and familial adult myoclonic epilepsy (FAME) types 1, 2, 3, 4, 6, and 7. The formation of non-B DNA structures during some biological processes is thought as a causative factor for repeat expansions. Yet, the structural basis for these pyrimidine-rich ATTTT and ATTTC repeat expansions remains elusive. In this study, we investigated the solution structures of ATTTT and ATTTC repeats using nuclear magnetic resonance spectroscopy. Here, we reveal that ATTTT and ATTTC repeats can form a highly compact minidumbbell structure at the 5'-end using their first two repeats. The high-resolution structure of two ATTTT repeats was determined, showing a regular TTTTA pentaloop and a quasi TTTT/A pentaloop. Furthermore, the minidumbbell structure could escape from proofreading by the Klenow fragment of DNA polymerase I when it was located at five or more base pairs away from the priming site, leading to a small-scale repeat expansion. Results of this work improve our understanding of ATTTT and ATTTC repeat expansions in SCA37 and FAMEs, and provide high-resolution structural information for rational drug design.
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Affiliation(s)
- Jinxia Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Liqi Wan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Yang Wang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yawen Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Pei Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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12
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Aberrant visual-related networks in familial cortical myoclonic tremor with epilepsy. Parkinsonism Relat Disord 2022; 101:105-110. [PMID: 35870251 DOI: 10.1016/j.parkreldis.2022.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022]
Abstract
INTRODUCTION In familial cortical myoclonic tremor with epilepsy, photic stimulation can trigger visual symptoms and induce a photoparoxysmal response, or photosensitivity, on electroencephalography. However, the mechanism is poorly understood. In this study, we aimed to explore the neuroimaging changes related to visual symptoms and photosensitivity in genetically confirmed familial cortical myoclonic tremor with epilepsy type 1. METHODS Resting-state functional magnetic resonance imaging and electroencephalography data were collected from 31 patients carrying the heterozygous pathogenic intronic pentanucleotide (TTTCA)n insertion in the sterile alpha motif domain-containing 12 gene and from 52 age- and sex-matched healthy controls. RESULTS (1) Both regional homogeneity and degree centrality values in the bilateral calcarine sulcus were significantly increased in patients compared with healthy controls. (2) When the calcarine sulcus area with increased regional homogeneity was taken as a seed, increased functional connectivity values were observed in the right precentral gyrus, while decreased functional connectivity values were observed in the right superior frontal gyrus and right inferior parietal lobule. (3) Independent component analysis showed increased connectivity in the left calcarine sulcus inside the medial visual network. (4) Correlation analysis revealed a significant positive correlation between regional homogeneity values and frequency of seizure, and photoparoxysmal response grades were positively correlated with the severity of cortical tremor and duration of epilepsy. CONCLUSION These findings provide strong evidence for the interpretation of visual symptoms and photosensitivity in familial cortical myoclonic tremor with epilepsy. We speculate that functional changes in the primary visual cortex may be an imaging biomarker for the disease.
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13
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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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14
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Peters L, Depienne C, Klebe S. Familial adult myoclonic epilepsy (FAME): clinical features, molecular characteristics, pathophysiological aspects and diagnostic work-up. MED GENET-BERLIN 2021; 33:311-318. [PMID: 38835431 PMCID: PMC11006339 DOI: 10.1515/medgen-2021-2100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/16/2021] [Indexed: 06/06/2024]
Abstract
Familial adult myoclonic epilepsy (FAME) is a rare autosomal dominant disorder characterized by myoclonus and seizures. The genetic variant underlying FAME is an intronic repeat expansion composed of two different pentamers: an expanded TTTTA, which is the motif originally present at the locus, and an insertion of TTTCA repeats, which is usually located at the 3' end and likely corresponds to the pathogenic part of the expansion. This repeat expansion has been identified so far in six genes located on different chromosomes, which remarkably encode proteins with distinct cellular localizations and functions. Although the exact pathophysiological mechanisms remain to be clarified, it is likely that FAME repeat expansions lead to disease independently of the gene where they occur. We herein review the clinical and molecular characteristics of this singular genetic disorder, which interestingly shares clinical features with other more common neurological disorders whose etiology remains mainly unsolved.
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Affiliation(s)
- Lorenz Peters
- Department of Neurology, University Hospital Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stephan Klebe
- Department of Neurology, University Hospital Essen, Essen, Germany
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15
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Qaiser F, Sadoway T, Yin Y, Zulfiqar Ali Q, Nguyen CM, Shum N, Backstrom I, Marques PT, Tabarestani S, Munhoz RP, Krings T, Pearson CE, Yuen RKC, Andrade DM. Genome sequencing identifies rare tandem repeat expansions and copy number variants in Lennox-Gastaut syndrome. Brain Commun 2021; 3:fcab207. [PMID: 34622207 PMCID: PMC8491034 DOI: 10.1093/braincomms/fcab207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022] Open
Abstract
Epilepsies are a group of common neurological disorders with a substantial
genetic basis. Despite this, the molecular diagnosis of epilepsies remains
challenging due to its heterogeneity. Studies utilizing whole-genome sequencing
may provide additional insights into genetic causes of epilepsies of unknown
aetiology. Whole-genome sequencing was used to evaluate a cohort of adults with
unexplained developmental and epileptic encephalopathies (n
= 30), for whom prior genetic tests, including whole-exome sequencing in
some cases, were negative or inconclusive. Rare single nucleotide variants,
insertions/deletions, copy number variants and tandem repeat expansions were
analysed. Seven pathogenic or likely pathogenic single nucleotide variants, and
two pathogenic deleterious copy number variants were identified in nine patients
(32.1% of the cohort). One of the copy number variants, identified in a
patient with Lennox–Gastaut syndrome, was too small to be detected by
chromosomal microarray techniques. We also identified two tandem repeat
expansions with clinical implications in two other patients with
Lennox–Gastaut syndrome: a CGG repeat expansion in the
5′untranslated region of DIP2B, and a CTG expansion in
ATXN8OS (previously implicated in spinocerebellar ataxia
type 8). Three patients had KCNA2 pathogenic variants. One of
them died of sudden unexpected death in epilepsy. The other two patients had, in
addition to a KCNA2 variant, a second de novo
variant impacting potential epilepsy-relevant genes (KCNIP4 and
UBR5). Overall, whole-genome sequencing provided a genetic
explanation in 32.1% of the total cohort. This is also the first report
of coding and non-coding tandem repeat expansions identified in patients with
Lennox–Gastaut syndrome. This study demonstrates that using whole-genome
sequencing, the examination of multiple types of rare genetic variation,
including those found in the non-coding region of the genome, can help resolve
unexplained epilepsies.
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Affiliation(s)
- Farah Qaiser
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada.,Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Tara Sadoway
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Yue Yin
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Quratulain Zulfiqar Ali
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Charlotte M Nguyen
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Natalie Shum
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ian Backstrom
- Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Paula T Marques
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Sepideh Tabarestani
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Renato P Munhoz
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, Canada.,Neuromodulation Unit and Ataxia Clinic, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Timo Krings
- Department of Medical Imaging, University of Toronto, Toronto, Canada.,Division of Neuroradiology, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Christopher E Pearson
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Ryan K C Yuen
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada.,Genetics & Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - Danielle M Andrade
- Adult Epilepsy Genetics Research Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Toronto, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, Canada.,Epilepsy Program, Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Canada
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16
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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 DOI: 10.1016/j.ajhg.2021.03.011] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [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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17
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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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The clinical utility of exome sequencing and extended bioinformatic analyses in adolescents and adults with a broad range of neurological phenotypes: an Australian perspective. J Neurol Sci 2020; 420:117260. [PMID: 33310205 DOI: 10.1016/j.jns.2020.117260] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/21/2022]
Abstract
Currently there is no secured ongoing funding in Australia for next generation sequencing (NGS) such as exome sequencing (ES) for adult neurological disorders. Studies have focused on paediatric populations in research or highly specialised settings, utilised standard NGS pipelines focusing only on small insertions, deletions and single nucleotide variants, and not explored impacts on management in detail. This prospective multi-site study performed ES and an extended bioinformatics repeat expansion analysis pipeline, on patients with broad phenotypes (ataxia, dementia, dystonia, spastic paraparesis, motor neuron disease, Parkinson's disease and complex/not-otherwise-specified), with symptom onset between 2 and 60 years. Genomic data analysis was phenotype-driven, using virtual gene panels, reported according to American College of Medical Genetics and Genomics guidelines. One-hundred-and-sixty patients (51% female) were included, median age 52 years (range 14-79) and median 9 years of symptoms. 34/160 (21%) patients received a genetic diagnosis. Highest diagnostic rates were in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified (10/38, 26%) and ataxia (7/28, 25%) groups. Findings were considered 'possible/uncertain' in 21/160 patients. Repeat expansion detection identified an unexpected diagnosis of Huntington disease in an ataxic patient with negative ES. Impacts on management, such as more precise and tailored care, were seen in most diagnosed patients (23/34, 68%). ES and a novel bioinformatics analysis pipepline had a substantial diagnostic yield (21%) and management impacts for most diagnosed patients, in heterogeneous, complex, mainly adult-onset neurological disorders in real-world settings in Australia, providing evidence for NGS and complementary multiple, new technologies as valuable diagnostic tools.
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Advances in repeat expansion diseases and a new concept of repeat motif-phenotype correlation. Curr Opin Genet Dev 2020; 65:176-185. [PMID: 32777681 DOI: 10.1016/j.gde.2020.05.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022]
Abstract
Recently repeat expansions have been found in more than 10 diseases in the past two years. Because the same repeat motifs are found in similar disease (as exemplified by benign adult familial myoclonic epilepsy) or in diseases with overlapping phenotype (as exemplified by fragile X tremor/ataxia syndrome, neuronal intranuclear inclusion disease, oculopharyngeal myopathy with leukoencephalopathy, and oculopharyngodistal myopathy), we propose a new concept of 'repeat motif-phenotype correlation', which argue for toxic gain-of-function mechanism caused by expanded repeats, rather than altered functions of genes harboring expanded repeats. The concept is expected to help identify repeat expansions taking the similar or overlapping clinical presentations as the clues. Although repeat expansions have been identified predominantly in autosomal dominant diseases, recent progresses have demonstrated that they are also observed in autosomal recessive diseases. Furthermore, repeat expansions are not infrequently observed in patients without family histories, which urges us to pay attention to sporadic diseases. We should expand our views toward repeat expansion diseases to accelerate discovery of diseases caused by repeat expansions, better understanding the disease mechanisms, and development of therapeutic measures.
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