1
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Baille G, Geoffre N, Wissocq A, Planté-Bordeneuve P, Mutez E, Huin V. Early-onset phenotype in a patient with an intermediate allele and a large SCA1 expansion: a case report. BMC Neurol 2024; 24:348. [PMID: 39289638 PMCID: PMC11406724 DOI: 10.1186/s12883-024-03846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 1, is a rare neurodegenerative disorder with autosomal dominant inheritance belonging to the polyglutamine diseases. The diagnosis of this disease requires genetic testing that may also include the search for CAT interruption of the CAG repeat tract. CASE PRESENTATION One 23-years-old patient suffers from a severe ataxia, with early-onset and rapid progression of the disease. His father might have been affected, but no molecular confirmation has been performed. The genetic results were negative for the Friedreich's ataxia, spinocerebellar ataxia type 2, 3, 6, 7 and 17. The numbers of CAG repeats in the ATXN1 gene was assessed by fluorescent PCR, tripled-primed PCR and enzymatic digestion for the search of sequence interruption in the CAG repeats. The patient carried one pathogenic allele of 61 CAG and one intermediate allele of 37 CAG in the ATXN1 gene. Both alleles were uninterrupted. CONCLUSIONS We report a rare case of spinocerebellar ataxia type 1 with an intermediate allele and a large SCA1 expansion. The determination of the absence of CAT interruption brought crucial information concerning this molecular diagnosis, the prediction of the disease and had practical consequences for genetic counseling.
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Affiliation(s)
- Guillaume Baille
- Delafontaine Hospital Center, Department of Neurology, Saint-Denis, F93200, France
| | - Nicolas Geoffre
- Department of Toxicology and Genopathies, UF Neurobiology, CHU Lille, Lille, F-59000, France
| | - Anna Wissocq
- Department of Toxicology and Genopathies, UF Neurobiology, CHU Lille, Lille, F-59000, France
| | | | - Eugénie Mutez
- Department of Neurology and Movement disorders, CHU Lille, Lille, F-59000, France
- Univ. Lille, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Inserm, Lille, F-59000, France
| | - Vincent Huin
- Department of Toxicology and Genopathies, UF Neurobiology, CHU Lille, Lille, F-59000, France.
- Univ. Lille, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Inserm, Lille, F-59000, France.
- Inserm UMRS1172, 'Alzheimer & Tauopathies', Bâtiment Biserte, Place de Verdun, Lille Cedex, 59045, France.
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2
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Sharafi S, Rezvani Z. Investigation of Spinocerebellar Ataxia (SCA) Disease in Iranian Patients and Accurate Trinucleotide Repeat Detection in the SCA3 by TP-PCR Method. Mol Neurobiol 2024:10.1007/s12035-024-04434-8. [PMID: 39155322 DOI: 10.1007/s12035-024-04434-8] [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: 12/20/2023] [Accepted: 08/09/2024] [Indexed: 08/20/2024]
Abstract
SCA (spinocerebellar ataxia) which is autosomal dominantly transferred is a subset of inherited cerebellar ataxia. These progressive neurological diseases have clinical features of ataxia and are derived from the destruction of the cerebellum. These diseases can also affect other areas, including the brainstem. Frequent proliferation of CAG nucleotides can encode polyglutamine and, as a result, produce the toxic polyglutamine (poly Q) protein that leads to many types of SCAs. They are categorized based on specific genetic mutations. The main symptoms of SCA, gait ataxia and incoordination, nystagmus, vision problems, and dysarthria, can be mentioned. In this study, 31 Iranians who were suspected of SCA disease were clinically diagnosed from November 2019 to September 2021. For these 31 patients suspected of spinocerebellar ataxia, PCR was performed, and the analysis was based on vertical electrophoresis. For SCA3 patients, the TP-PCR technique was carried out and evaluated by capillary electrophoresis. For all 31 patients, PCR function was successful according to the results attained by conventional PCR. The number of three nucleotide replications was within the normal range for 22 people, and nine patients were reported. Studies showed that three people suspected of SCA were infected with SCA3 according to the TP-PCR technique, and this was while seven people were diagnosed with SCA3 using the PCR method. As the purpose of this test is to provide a more accurate diagnostic method and prenatal diagnosis of this disease, the TP-PCR method proved to be more suitable when applied for the diagnosis of abnormal trinucleotides CAG in spinocerebellar ataxia type 3.
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Affiliation(s)
- Shafagh Sharafi
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Qutb Rawandi Blvd, Kashan City, Isfahan Province, Iran
| | - Zahra Rezvani
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Qutb Rawandi Blvd, Kashan City, Isfahan Province, Iran.
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3
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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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4
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Zhou X, He R, Zeng S, Li M, Pan H, Zhao Y, Liu Z, Xu Q, Guo J, Yan X, Li J, Tang B, Sun Q. Tremor-associated short tandem repeat intermediate and pathogenic expansions in familial essential tremor. Brain Commun 2024; 6:fcae217. [PMID: 38961870 PMCID: PMC11220504 DOI: 10.1093/braincomms/fcae217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/07/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024] Open
Abstract
There is an obvious clinical-pathological overlap between essential tremor and some known tremor-associated short tandem repeat expansion disorders. The aim is to analyse whether these short tandem repeat genes, including ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATXN8OS, ATXN10, PPP2R2B, TBP, BEAN1, NOP56, DAB1, ATN1, SADM12 and FMR1, are associated with familial essential tremor patients. Genetic analysis of repeat sizes in tremor-associated short tandem repeat expansions was performed in a large cohort of 515 familial essential tremor probands and 300 controls. The demographic and clinical features among carriers of pathogenic expansions, intermediate repeats and non-carriers were compared. A total of 18 out of 515 (18/515, 3.7%) patients were found to have repeats expansions, including 12 cases (12/515, 2.5%) with intermediate repeat expansions (one ATXN1, eight TBP, two FMR1, one ATN1), and six cases (6/515, 1.2%) with pathogenic expansions (one ATXN1, one ATXN2, one ATXN8OS, one PPP2R2B, one FMR1, one SAMD12). There were no statistically significant differences in intermediate repeats compared to healthy controls. Furthermore, there were no significant differences in demographics and clinical features among individuals with pathogenic expansions, intermediate repeat expansions carriers and non-carriers. Our study indicates that the intermediate repeat expansion in tremor-associated short tandem repeat expansions does not pose an increased risk for essential tremor, and rare pathogenic expansion carriers have been found in the familial essential tremor cohort. The diagnosis of essential tremor based solely on clinical symptoms remains a challenge in distinguishing it from known short tandem repeat expansions diseases with overlapping clinical-pathological features.
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Affiliation(s)
- Xun Zhou
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Sheng Zeng
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Mingqiang Li
- Department of Neurology, Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421000, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421000, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Qiying Sun
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
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5
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Shao YR, Yu JY, Ma Y, Dong Y, Wu ZY. CAT Interruption as a Protective Factor in Chinese Patients with Spinocerebellar Ataxia Type 1. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1211-1214. [PMID: 37491649 DOI: 10.1007/s12311-023-01586-6] [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: 07/06/2023] [Indexed: 07/27/2023]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is the third most common type of spinocerebellar ataxias in China. CAT interruptions in the pathogenic alleles of SCA1 patients had only been reported by limited documents and there was a lack of data based on the Chinese population. In this study, we detected CAT interrupted pathogenic alleles in SCA1 patients from 4 out of 79 (5.1%) Chinese families. Their total CAG repeats were larger (median 58 vs. 47, p < 0.001) but ages at onset were later (median 46 vs. 38, p = 0.020). The longest uninterrupted CAG repeats could explain 65.4% of the AAO variance, making an increase of 28.0% compared to the total CAG repeats. The interruption pattern was greatly different between Chinese cohort and Caucasian cohort, indicating the effect of race.
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Affiliation(s)
- Ya-Ru Shao
- Department of Neurology and Department of Medical Genetics in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Jin-Yang Yu
- Department of Neurology and Department of Medical Genetics in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Yin Ma
- Department of Neurology and Department of Medical Genetics in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Yi Dong
- Department of Neurology and Department of Medical Genetics in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhi-Ying Wu
- Department of Neurology and Department of Medical Genetics in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
- MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China.
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6
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Kacher R, Lejeune FX, David I, Boluda S, Coarelli G, Leclere-Turbant S, Heinzmann A, Marelli C, Charles P, Goizet C, Kabir N, Hilab R, Jornea L, Six J, Dommergues M, Fauret AL, Brice A, Humbert S, Durr A. CAG repeat mosaicism is gene specific in spinocerebellar ataxias. Am J Hum Genet 2024; 111:913-926. [PMID: 38626762 PMCID: PMC11080609 DOI: 10.1016/j.ajhg.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024] Open
Abstract
Expanded CAG repeats in coding regions of different genes are the most common cause of dominantly inherited spinocerebellar ataxias (SCAs). These repeats are unstable through the germline, and larger repeats lead to earlier onset. We measured somatic expansion in blood samples collected from 30 SCA1, 50 SCA2, 74 SCA3, and 30 SCA7 individuals over a mean interval of 8.5 years, along with postmortem tissues and fetal tissues from SCA1, SCA3, and SCA7 individuals to examine somatic expansion at different stages of life. We showed that somatic mosaicism in the blood increases over time. Expansion levels are significantly different among SCAs and correlate with CAG repeat lengths. The level of expansion is greater in individuals with SCA7 who manifest disease compared to that of those who do not yet display symptoms. Brain tissues from SCA individuals have larger expansions compared to the blood. The cerebellum has the lowest mosaicism among the studied brain regions, along with a high expression of ATXNs and DNA repair genes. This was the opposite in cortices, with the highest mosaicism and lower expression of ATXNs and DNA repair genes. Fetal cortices did not show repeat instability. This study shows that CAG repeats are increasingly unstable during life in the blood and the brain of SCA individuals, with gene- and tissue-specific patterns.
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Affiliation(s)
- Radhia Kacher
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - François-Xavier Lejeune
- Sorbonne Université, Paris Brain Institute's Data Analysis Core Facility, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Isabelle David
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Susana Boluda
- Sorbonne Université, Department of Neuropathology Raymond Escourolle, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Giulia Coarelli
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Sabrina Leclere-Turbant
- Sorbonne Université, Biobank Neuro-CEB Biological Resource Platform, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Anna Heinzmann
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Cecilia Marelli
- MMDN, Université Montpellier, EPHE, INSERM, Montpellier, France; Expert Center for Neurogenetic Diseases, CHU, Montpellier, France
| | - Perrine Charles
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Cyril Goizet
- Université Bordeaux, Equipe « Neurogénétique Translationnelle - NRGEN », INCIA CNRS UMR5287 Université Bordeaux and Centre de Reference Maladies Rares « Neurogénétique », Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), Bordeaux, France
| | - Nisha Kabir
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Rania Hilab
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Ludmila Jornea
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Julie Six
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Marc Dommergues
- Sorbonne Université, Service de Gynécologie Obstetrique, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Anne-Laure Fauret
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Sandrine Humbert
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France.
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7
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Yoon JG, Lee S, Cho J, Kim N, Kim S, Kim MJ, Kim SY, Moon J, Chae JH. Diagnostic uplift through the implementation of short tandem repeat analysis using exome sequencing. Eur J Hum Genet 2024; 32:584-587. [PMID: 38308084 PMCID: PMC11061289 DOI: 10.1038/s41431-024-01542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024] Open
Abstract
To date, approximately 50 short tandem repeat (STR) disorders have been identified; yet, clinical laboratories rarely conduct STR analysis on exomes. To assess its diagnostic value, we analyzed STRs in 6099 exomes from 2510 families with mostly suspected neurogenetic disorders. We employed ExpansionHunter and REViewer to detect pathogenic repeat expansions, confirming them using orthogonal methods. Genotype-phenotype correlations led to the diagnosis of thirteen individuals in seven previously undiagnosed families, identifying three autosomal dominant disorders: dentatorubral-pallidoluysian atrophy (n = 3), spinocerebellar ataxia type 7 (n = 2), and myotonic dystrophy type 1 (n = 2), resulting in a diagnostic gain of 0.28% (7/2510). Additionally, we found expanded ATXN1 alleles (≥39 repeats) with varying patterns of CAT interruptions in twelve individuals, accounting for approximately 0.19% in the Korean population. Our study underscores the importance of integrating STR analysis into exome sequencing pipeline, broadening the application of exome sequencing for STR assessments.
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Affiliation(s)
- Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea.
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8
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Novy C, Busk ØL, Tysnes OB, Landa SS, Aanjesen TN, Alstadhaug KB, Bjerknes TL, Bjørnå IK, Bråthen G, Dahl E, Demic N, Fahlström M, Flemmen HØ, Hallerstig E, HogenEsch I, Kampman MT, Kleveland G, Kvernmo HB, Ljøstad U, Maniaol A, Morsund AH, Nakken O, Olsen CG, Schlüter K, Utvik MS, Yaseen R, Holla ØL, Holmøy T, Høyer H. Repeat expansions in AR, ATXN1, ATXN2 and HTT in Norwegian patients diagnosed with amyotrophic lateral sclerosis. Brain Commun 2024; 6:fcae087. [PMID: 38585669 PMCID: PMC10998343 DOI: 10.1093/braincomms/fcae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/23/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Genetic repeat expansions cause neuronal degeneration in amyotrophic lateral sclerosis as well as other neurodegenerative disorders such as spinocerebellar ataxia, Huntington's disease and Kennedy's disease. Repeat expansions in the same gene can cause multiple clinical phenotypes. We aimed to characterize repeat expansions in a Norwegian amyotrophic lateral sclerosis cohort. Norwegian amyotrophic lateral sclerosis patients (n = 414) and neurologically healthy controls adjusted for age and gender (n = 713) were investigated for repeat expansions in AR, ATXN1, ATXN2 and HTT using short read exome sequencing and the ExpansionHunter software. Five amyotrophic lateral sclerosis patients (1.2%) and two controls (0.3%) carried ≥36 repeats in HTT (P = 0.032), and seven amyotrophic lateral sclerosis patients (1.7%) and three controls (0.4%) carried ≥29 repeats in ATXN2 (P = 0.038). One male diagnosed with amyotrophic lateral sclerosis carried a pathogenic repeat expansion in AR, and his diagnosis was revised to Kennedy's disease. In ATXN1, 50 amyotrophic lateral sclerosis patients (12.1%) and 96 controls (13.5%) carried ≥33 repeats (P = 0.753). None of the patients with repeat expansions in ATXN2 or HTT had signs of Huntington's disease or spinocerebellar ataxia type 2, based on a re-evaluation of medical records. The diagnosis of amyotrophic lateral sclerosis was confirmed in all patients, with the exception of one patient who had primary lateral sclerosis. Our findings indicate that repeat expansions in HTT and ATXN2 are associated with increased likelihood of developing amyotrophic lateral sclerosis. Further studies are required to investigate the potential relationship between HTT repeat expansions and amyotrophic lateral sclerosis.
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Affiliation(s)
- Camilla Novy
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Øyvind L Busk
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Ole-Bjørn Tysnes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5009 Bergen, Norway
| | - Sigve S Landa
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Tori N Aanjesen
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | | | - Tale L Bjerknes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5009 Bergen, Norway
- Institute of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
| | - Ingrid K Bjørnå
- Department of Neurology, Vestre Viken Hospital Trust, 3004 Drammen, Norway
| | - Geir Bråthen
- Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Elin Dahl
- Department of Neurology, Telemark Hospital Trust, 3710 Skien, Norway
| | - Natasha Demic
- Department of Neurology, Vestfold Hospital Trust, 3103 Tønsberg, Norway
| | - Maria Fahlström
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Heidi Ø Flemmen
- Department of Neurology, Telemark Hospital Trust, 3710 Skien, Norway
| | - Erika Hallerstig
- Department of Neurology, Østfold Hospital Trust, 1714 Grålum, Norway
| | - Ineke HogenEsch
- Department of Neurology, Fonna Hospital Trust, 5528 Haugesund, Norway
| | - Margitta T Kampman
- Department of Neurology, University Hospital of North Norway, 9019 Tromsø, Norway
| | - Grethe Kleveland
- Department of Neurology, Innlandet Hospital Trust, 2609 Lillehammer, Norway
| | - Helene B Kvernmo
- Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Unn Ljøstad
- Institute of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
- Department of Neurology, Sørlandet Hospital Trust, 4615 Kristiansand, Norway
| | - Angelina Maniaol
- Department of Neurology, Oslo University Hospital, 0450 Oslo, Norway
| | | | - Ola Nakken
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Cathrine G Olsen
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
| | - Katrin Schlüter
- Department of Neurology, Stavanger University Hospital, 4019 Stavanger, Norway
| | - May-Sissel Utvik
- Department of Neurology, Namsos Hospital Trust, 7803 Namsos, Norway
| | - Ryaz Yaseen
- Department of Neurology, Oslo University Hospital, 0450 Oslo, Norway
| | - Øystein L Holla
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trygve Holmøy
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Helle Høyer
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
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9
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Rajagopal S, Donaldson J, Flower M, Hensman Moss DJ, Tabrizi SJ. Genetic modifiers of repeat expansion disorders. Emerg Top Life Sci 2023; 7:325-337. [PMID: 37861103 PMCID: PMC10754329 DOI: 10.1042/etls20230015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Repeat expansion disorders (REDs) are monogenic diseases caused by a sequence of repetitive DNA expanding above a pathogenic threshold. A common feature of the REDs is a strong genotype-phenotype correlation in which a major determinant of age at onset (AAO) and disease progression is the length of the inherited repeat tract. Over a disease-gene carrier's life, the length of the repeat can expand in somatic cells, through the process of somatic expansion which is hypothesised to drive disease progression. Despite being monogenic, individual REDs are phenotypically variable, and exploring what genetic modifying factors drive this phenotypic variability has illuminated key pathogenic mechanisms that are common to this group of diseases. Disease phenotypes are affected by the cognate gene in which the expansion is found, the location of the repeat sequence in coding or non-coding regions and by the presence of repeat sequence interruptions. Human genetic data, mouse models and in vitro models have implicated the disease-modifying effect of DNA repair pathways via the mechanisms of somatic mutation of the repeat tract. As such, developing an understanding of these pathways in the context of expanded repeats could lead to future disease-modifying therapies for REDs.
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Affiliation(s)
- Sangeerthana Rajagopal
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Jasmine Donaldson
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Michael Flower
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Davina J Hensman Moss
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
- St George's University of London, London SW17 0RE, U.K
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
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10
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Thompson LM, Orr HT. HD and SCA1: Tales from two 30-year journeys since gene discovery. Neuron 2023; 111:3517-3530. [PMID: 37863037 PMCID: PMC10842341 DOI: 10.1016/j.neuron.2023.09.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Abstract
One of the more transformative findings in human genetics was the discovery that the expansion of unstable nucleotide repeats underlies a group of inherited neurological diseases. A subset of these unstable repeat neurodegenerative diseases is due to the expansion of a CAG trinucleotide repeat encoding a stretch of glutamines, i.e., the polyglutamine (polyQ) repeat neurodegenerative diseases. Among the CAG/polyQ repeat diseases are Huntington's disease (HD) and spinocerebellar ataxia type 1 (SCA1), in which the expansions are within widely expressed proteins. Although both HD and SCA1 are autosomal dominantly inherited, and both typically cause mid- to late-life-onset movement disorders with cognitive decline, they each are characterized by distinct clinical characteristics and predominant sites of neuropathology. Importantly, the respective affected proteins, Huntingtin (HTT, HD) and Ataxin 1 (ATXN1, SCA1), have unique functions and biological properties. Here, we review HD and SCA1 with a focus on how their disease-specific and shared features may provide informative insights.
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Affiliation(s)
- Leslie M Thompson
- Department of Psychiatry and Human Behavior, Department of Neurobiology and Behavior, Department of Biological Chemistry, Institute of Memory Impairments and Neurological Disorders, Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA 92697, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis and Saint Paul, MN 55455, USA.
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11
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Kandola T, Venkatesan S, Zhang J, Lerbakken BT, Von Schulze A, Blanck JF, Wu J, Unruh JR, Berry P, Lange JJ, Box AC, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. eLife 2023; 12:RP86939. [PMID: 37921648 PMCID: PMC10624427 DOI: 10.7554/elife.86939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- The Open UniversityMilton KeynesUnited Kingdom
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | | | | | | | - Jianzheng Wu
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Paula Berry
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Andrew C Box
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Malcolm Cook
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Celeste Sagui
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
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12
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Witzenberger M, Burczyk S, Settele D, Mayer W, Welp L, Heiss M, Wagner M, Monecke T, Janowski R, Carell T, Urlaub H, Hauck S, Voigt A, Niessing D. Human TRMT2A methylates tRNA and contributes to translation fidelity. Nucleic Acids Res 2023; 51:8691-8710. [PMID: 37395448 PMCID: PMC10484741 DOI: 10.1093/nar/gkad565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
5-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian enzyme for m5U formation at tRNA position 54. However, its RNA binding specificity and functional role in the cell are not well understood. Here we dissected structural and sequence requirements for binding and methylation of its RNA targets. Specificity of tRNA modification by hTRMT2A is achieved by a combination of modest binding preference and presence of a uridine in position 54 of tRNAs. Mutational analysis together with cross-linking experiments identified a large hTRMT2A-tRNA binding surface. Furthermore, complementing hTRMT2A interactome studies revealed that hTRMT2A interacts with proteins involved in RNA biogenesis. Finally, we addressed the question of the importance of hTRMT2A function by showing that its knockdown reduces translation fidelity. These findings extend the role of hTRMT2A beyond tRNA modification towards a role in translation.
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Affiliation(s)
- Monika Witzenberger
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - David Settele
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Wieland Mayer
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Matthias Heiss
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Mirko Wagner
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Carell
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Research Unit Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Aaron Voigt
- Department of Neurology, Faculty of Medicine, RWTH Aachen, Aachen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
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13
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Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533418. [PMID: 36993401 PMCID: PMC10055281 DOI: 10.1101/2023.03.20.533418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The Open University, Milton Keyes, MK7 6AA, UK
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Alex Von Schulze
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jillian F Blanck
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paula Berry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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14
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Kerkhof LMC, van de Warrenburg BPC, van Roon-Mom WMC, Buijsen RAM. Therapeutic Strategies for Spinocerebellar Ataxia Type 1. Biomolecules 2023; 13:biom13050788. [PMID: 37238658 DOI: 10.3390/biom13050788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder that affects one or two individuals per 100,000. The disease is caused by an extended CAG repeat in exon 8 of the ATXN1 gene and is characterized mostly by a profound loss of cerebellar Purkinje cells, leading to disturbances in coordination, balance, and gait. At present, no curative treatment is available for SCA1. However, increasing knowledge on the cellular and molecular mechanisms of SCA1 has led the way towards several therapeutic strategies that can potentially slow disease progression. SCA1 therapeutics can be classified as genetic, pharmacological, and cell replacement therapies. These different therapeutic strategies target either the (mutant) ATXN1 RNA or the ataxin-1 protein, pathways that play an important role in downstream SCA1 disease mechanisms or which help restore cells that are lost due to SCA1 pathology. In this review, we will provide a summary of the different therapeutic strategies that are currently being investigated for SCA1.
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Affiliation(s)
- Laurie M C Kerkhof
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Dutch Center for RNA Therapeutics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Bart P C van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Willeke M C van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Dutch Center for RNA Therapeutics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Ronald A M Buijsen
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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15
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KHC, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA50/ATX-FGF14. Am J Hum Genet 2023; 110:105-119. [PMID: 36493768 PMCID: PMC9892775 DOI: 10.1016/j.ajhg.2022.11.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
Adult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified an intronic (GAA) repeat expansion in fibroblast growth factor 14 (FGF14). Genetic analysis of 95 Australian individuals with adult-onset ataxia identified four (4.2%) with (GAA)>300 and a further nine individuals with (GAA)>250. PCR and long-read sequence analysis revealed these were pure (GAA) repeats. In comparison, no control subjects had (GAA)>300 and only 2/311 control individuals (0.6%) had a pure (GAA)>250. In a German validation cohort, 9/104 (8.7%) of affected individuals had (GAA)>335 and a further six had (GAA)>250, whereas 10/190 (5.3%) control subjects had (GAA)>250 but none were (GAA)>335. The combined data suggest (GAA)>335 are disease causing and fully penetrant (p = 6.0 × 10-8, OR = 72 [95% CI = 4.3-1,227]), while (GAA)>250 is likely pathogenic with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with variable features including vestibular impairment, hyper-reflexia, and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2 = 0.44, p = 0.00045, slope = -0.12) and identification of a shared haplotype in a minority of individuals suggests that the expansion can be inherited or generated de novo during meiotic division. This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansions via model-free, genome-wide analysis and identifies SCA50/ATX-FGF14 as a frequent cause of adult-onset ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Read
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - David J. Szmulewicz
- Cerebellar Ataxia Clinic, Eye and Ear Hospital, Melbourne, VIC, Australia,The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kayli C. Davies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam G. Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam Scott
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Mark F. Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathie J. Ngo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Luke Chen
- Alfred Hospital, Department of Neurology, Melbourne, VIC, Australia
| | - Mathew J. Wallis
- Clinical Genetics Service, Austin Health, Melbourne, VIC, Australia,Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Kishore R. Kumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord, NSW, Australia,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kathy HC. Wu
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Clinical Genomics, St Vincent’s Hospital, Darlinghurst, NSW, Australia,Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,School of Medicine, University of Notre Dame, Sydney, NSW, Australia
| | - Susan E. Tomlinson
- School of Medicine, University of Notre Dame, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Stephen Tisch
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Abhishek Malhotra
- Department of Neuroscience, University Hospital Geelong, Geelong, VIC, Australia
| | - Matthew Lee-Archer
- Launceston General Hospital, Tasmanian Health Service, Launceston, TAS, Australia
| | | | | | - Leslie J. Roberts
- Department of Neurology and Neurological Research, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Brent L. Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA,Departments of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Martin B. Delatycki
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Corresponding author
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16
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Dawson J, Baine-Savanhu FK, Ciosi M, Maxwell A, Monckton DG, Krause A. A probable cis-acting genetic modifier of Huntington disease frequent in individuals with African ancestry. HGG ADVANCES 2022; 3:100130. [PMID: 35935919 PMCID: PMC9352962 DOI: 10.1016/j.xhgg.2022.100130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Huntington disease (HD)is a dominantly inherited neurodegenerative disorder caused by the expansion of a polyglutamine encoding CAG repeat in the huntingtin gene. Recently, it has been established that disease severity in HD is best predicted by the number of pure CAG repeats rather than total glutamines encoded. Along with uncovering DNA repair gene variants as trans-acting modifiers of HD severity, these data reveal somatic expansion of the CAG repeat as a key driver of HD onset. Using high-throughput DNA sequencing, we have determined the precise sequence and somatic expansion profiles of the HTT repeat tract of 68 HD-affected and 158 HD-unaffected African ancestry individuals. A high level of HTT repeat sequence diversity was observed, with three likely African-specific alleles identified. In the most common disease allele (30 out of 68), the typical proline-encoding CCGCCA sequence was absent. This CCGCCA-loss disease allele was associated with an earlier age of diagnosis of approximately 7.1 years and occurred exclusively on haplotype B2. Although somatic expansion was associated with an earlier age of diagnosis in the study overall, the CCGCCA-loss disease allele displayed reduced somatic expansion relative to the typical HTT expansions in blood DNA. We propose that the CCGCCA loss occurring on haplotype B2 is an African cis-acting modifier that appears to alter disease diagnosis of HD through a mechanism that is not driven by somatic expansion. The assessment of a group of individuals from an understudied population has highlighted population-specific differences that emphasize the importance of studying genetically diverse populations in the context of disease.
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Affiliation(s)
- Jessica Dawson
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Fiona K. Baine-Savanhu
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Marc Ciosi
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alastair Maxwell
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Darren G. Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- Corresponding author
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17
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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18
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Sharma P, Sonakar AK, Goel V, Garg A, Srivastava AK, Faruq M. A Novel co‐existence of
SCA1
and
SCA2
mutations in Indian patients. Mov Disord Clin Pract 2022; 9:688-692. [PMID: 35844270 PMCID: PMC9274345 DOI: 10.1002/mdc3.13464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/19/2022] [Accepted: 04/10/2022] [Indexed: 11/08/2022] Open
Abstract
Background Spinocerebellar ataxia 1 (SCA1) and SCA2 are dominantly inherited ataxias caused due to CAG expansion mutation in ATXN1 (CAG≥39) and ATXN2 (CAG≥32) genes located at 6p22.3 and 12q24.12 loci, respectively, with key manifestations of progressive limb and gait ataxia and with or without brain stem and pyramidal tract involvement. Both SCA1 and SCA2 are quite prevalent subtypes among the SCAs. There are very few reports that describe a combinatorial SCA subtype mutation in a single patient. Cases Here, we report a novel co-occurrence of SCA1 and SCA2 mutations in two unrelated patients. Case-1 was observed to carry ATXN1-CAG (30/40) and ATXN2-CAG (23/45), while case-2 harbored ATXN1-CAG (29/42) and ATXN2-CAG (23/41). Overall, the clinical outcome was complex with probable early onset than expected in Case-1 and in Case-2, we observed a significant delayed onset of the disease than expected. Conclusion These cases highlight the probabilistic interactive outcome of two unrelated genetic events towards a converging phenotype.
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Affiliation(s)
- Pooja Sharma
- Genomics and Molecular Medicine, CSIR‐Institute of Genomics and Integrative Biology (CSIR ‐IGIB), Mall Road Delhi 110007 India
- Academy for Scientific and Innovative Research Ghaziabad 201002 India
| | - Akhilesh K. Sonakar
- Neurology Department, Neuroscience Centre All India Institute of Medical Sciences New Delhi 110029 India
| | - Vinay Goel
- Neuroradiology Department, Neuroscience Centre All India Institute of Medical Sciences New Delhi 110029 India
| | - Ajay Garg
- Neuroradiology Department, Neuroscience Centre All India Institute of Medical Sciences New Delhi 110029 India
| | - Achal K. Srivastava
- Neurology Department, Neuroscience Centre All India Institute of Medical Sciences New Delhi 110029 India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR‐Institute of Genomics and Integrative Biology (CSIR ‐IGIB), Mall Road Delhi 110007 India
- Academy for Scientific and Innovative Research Ghaziabad 201002 India
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19
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Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ferguson JM, Pineda SS, Scriba CK, Tchan M, Fung V, Ng K, Cortese A, Houlden H, Dobson-Stone C, Fitzpatrick L, Halliday G, Ravenscroft G, Davis MR, Laing NG, Fellner A, Kennerson M, Kumar KR, Deveson IW. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. SCIENCE ADVANCES 2022; 8:eabm5386. [PMID: 35245110 PMCID: PMC8896783 DOI: 10.1126/sciadv.abm5386] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care.
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Affiliation(s)
- Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sanjog R. Chintalaphani
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M. Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Carolin K. Scriba
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Michel Tchan
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Victor Fung
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital and The University of Sydney, Sydney, NSW, Australia
| | - Andrea Cortese
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Lauren Fitzpatrick
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Glenda Halliday
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Mark R. Davis
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Nigel G. Laing
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Avi Fellner
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- The Neurology Department, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Faculty of Health and Medicine, University of Sydney, Camperdown, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
- Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW, Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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20
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Jang JH, Yoon SJ, Kim SK, Cho JW, Kim JW. Detection Methods and Status of CAT Interruption of ATXN1 in Korean Patients With Spinocerebellar Ataxia Type 1. Ann Lab Med 2022; 42:274-277. [PMID: 34635619 PMCID: PMC8548249 DOI: 10.3343/alm.2022.42.2.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/09/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant disease caused by abnormal CAG repeat expansion in the ataxin 1 gene (ATXN1). The presence of CAT interruption(s) is important for diagnosing SCA1 in patients with 39–44 repeat alleles, as only uninterrupted alleles are considered abnormal. Determining the CAT interruption status might also be important for patients with >44 repeats, as the length of the longest uninterrupted CAG repeat stretch has been correlated with age at SCA1 onset. We detected CAT interruption(s) in the archived samples of Korean SCA1 patients using a traditional restriction enzyme method and validated the usefulness of a fluorescence-based tethering PCR procedure. Among the 2,312 alleles analyzed from 1,156 patients, we found 17 expanded alleles with ≥39 repeats, 71% of which harbored 39–44 repeats. Restriction enzyme method of six samples (four with 39–44 repeats and two with >44 repeats) revealed that none of the expanded alleles had CAT interruption(s). Tethering PCR showed the characteristic electropherogram pattern expected without CAT interruption(s). Along with the enzyme restriction method, tethering PCR can be applied to determine the number of allele repeats and provide information on CAT interruption(s) in clinical laboratories.
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Affiliation(s)
- Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Joo Yoon
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun-Kyung Kim
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jin Whan Cho
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Neuroscience Center, Samsung Medical Center, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
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21
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Haas E, Incebacak RD, Hentrich T, Huridou C, Schmidt T, Casadei N, Maringer Y, Bahl C, Zimmermann F, Mills JD, Aronica E, Riess O, Schulze-Hentrich JM, Hübener-Schmid J. A Novel SCA3 Knock-in Mouse Model Mimics the Human SCA3 Disease Phenotype Including Neuropathological, Behavioral, and Transcriptional Abnormalities Especially in Oligodendrocytes. Mol Neurobiol 2022; 59:495-522. [PMID: 34716557 PMCID: PMC8786755 DOI: 10.1007/s12035-021-02610-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022]
Abstract
Spinocerebellar ataxia type 3 is the most common autosomal dominant inherited ataxia worldwide, caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyglutamine (polyQ)-expansion in the corresponding protein. The disease is characterized by neuropathological, phenotypical, and specific transcriptional changes in affected brain regions. So far, there is no mouse model available representing all the different aspects of the disease, yet highly needed for a better understanding of the disease pathomechanisms. Here, we characterized a novel Ataxin-3 knock-in mouse model, expressing a heterozygous or homozygous expansion of 304 CAACAGs in the murine Ataxin-3 locus using biochemical, behavioral, and transcriptomic approaches. We compared neuropathological, and behavioral features of the new knock-in model with the in SCA3 research mostly used YAC84Q mouse model. Further, we compared transcriptional changes found in cerebellar samples of the SCA3 knock-in mice and post-mortem human SCA3 patients. The novel knock-in mouse is characterized by the expression of a polyQ-expansion in the murine Ataxin-3 protein, leading to aggregate formation, especially in brain regions known to be vulnerable in SCA3 patients, and impairment of Purkinje cells. Along these neuropathological changes, the mice showed a reduction in body weight accompanied by gait and balance instability. Transcriptomic analysis of cerebellar tissue revealed age-dependent differential expression, enriched for genes attributed to myelinating oligodendrocytes. Comparing these changes with those found in cerebellar tissue of SCA3 patients, we discovered an overlap of differentially expressed genes pointing towards similar gene expression perturbances in several genes linked to myelin sheaths and myelinating oligodendrocytes.
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Affiliation(s)
- Eva Haas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Rana D Incebacak
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Chrisovalantou Huridou
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Thorsten Schmidt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
- DFG NGS Competence Center Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Carola Bahl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Frank Zimmermann
- Interfaculty Biomedical Facility (IBF) Biotechnology lab, University of Heidelberg, Heidelberg, Germany
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
- DFG NGS Competence Center Tübingen, Tübingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Jeannette Hübener-Schmid
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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22
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Nethisinghe S, Kesavan M, Ging H, Labrum R, Polke JM, Islam S, Garcia-Moreno H, Callaghan MF, Cavalcanti F, Pook MA, Giunti P. Interruptions of the FXN GAA Repeat Tract Delay the Age at Onset of Friedreich's Ataxia in a Location Dependent Manner. Int J Mol Sci 2021; 22:7507. [PMID: 34299126 PMCID: PMC8307455 DOI: 10.3390/ijms22147507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/03/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a comparatively rare autosomal recessive neurological disorder primarily caused by the homozygous expansion of a GAA trinucleotide repeat in intron 1 of the FXN gene. The repeat expansion causes gene silencing that results in deficiency of the frataxin protein leading to mitochondrial dysfunction, oxidative stress and cell death. The GAA repeat tract in some cases may be impure with sequence variations called interruptions. It has previously been observed that large interruptions of the GAA repeat tract, determined by abnormal MboII digestion, are very rare. Here we have used triplet repeat primed PCR (TP PCR) assays to identify small interruptions at the 5' and 3' ends of the GAA repeat tract through alterations in the electropherogram trace signal. We found that contrary to large interruptions, small interruptions are more common, with 3' interruptions being most frequent. Based on detection of interruptions by TP PCR assay, the patient cohort (n = 101) was stratified into four groups: 5' interruption, 3' interruption, both 5' and 3' interruptions or lacking interruption. Those patients with 3' interruptions were associated with shorter GAA1 repeat tracts and later ages at disease onset. The age at disease onset was modelled by a group-specific exponential decay model. Based on this modelling, a 3' interruption is predicted to delay disease onset by approximately 9 years relative to those lacking 5' and 3' interruptions. This highlights the key role of interruptions at the 3' end of the GAA repeat tract in modulating the disease phenotype and its impact on prognosis for the patient.
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Affiliation(s)
- Suran Nethisinghe
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Maheswaran Kesavan
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Heather Ging
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Robyn Labrum
- Neurogenetics Service, Rare and Inherited Disease Laboratory, London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK; (R.L.); (J.M.P.)
| | - James M. Polke
- Neurogenetics Service, Rare and Inherited Disease Laboratory, London North Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK; (R.L.); (J.M.P.)
| | - Saiful Islam
- UCL Queen Square Institute of Neurology, London WC1N 3BG, UK;
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
| | - Martina F. Callaghan
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London WC1N 3AR, UK;
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy;
| | - Mark A. Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge UB8 3PH, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; (S.N.); (M.K.); (H.G.); (H.G.-M.)
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23
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Clinical and genetic profile in index patients with spinocerebellar ataxia type 3 in Indonesia: case report. Heliyon 2021; 7:e07519. [PMID: 34345727 PMCID: PMC8319015 DOI: 10.1016/j.heliyon.2021.e07519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/28/2021] [Accepted: 07/05/2021] [Indexed: 12/03/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is an autosomal dominant hereditary disease with progressive course, and no causal therapy. Diagnostics are still challenging, due to facility and protocols, and so as in Indonesia. As a national referral center, Dr. Hasan Sadikin Central General Hospital has received a lot of patients from all over Indonesia, particularly from Western Java. Study related to SCA (including clinical and genetic profile) is still limited in Indonesia. We identified index patients from three families with ataxia, hence intend to determine their clinical and genetic pattern. The hereditary pattern is autosomal dominant. Scale for the assessment and rating of ataxia (SARA) shows mild and moderate ataxia. Inventory of non-ataxia signs (INAS) scores of the patients were 3, 5 and 6. Montreal cognitive assessment-Indonesian version (MOCA-INA) shows only one patient has mild cognitive impairment, despite young age. Barthel index shows 1 subject has moderate dependency. Mutation in Ataxin3 polyQ repeats shows pathologically long CAG repeats, 72,10; 72,10; and 72,23 respectively in mutant and wild type allele. We diagnosed the index patients with spinocerebellar ataxia type 3. This study is the first case series study in Indonesia. The hereditary pattern is clearly shown as an autosomal dominant ataxia. The clinical and genetic profile was varied, and the symptom is progressive and deteriorates overtime, including wide based gait, speech problem, motor and sensor complaint, and cognitive decline complaint. Despite the same polyQ stretch length, the onset and clinical characteristics of patients are diverse.
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24
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Li J, Yu J, Xue W, Huang H, Yan L, Sang F, An S, Zhang J, Wang M, Zhang J, Li H, Cui X, He J, Hu Y. The engineered expression of secreted HSPB5-Fc in CHO cells exhibits cytoprotection in vitro. BMC Biotechnol 2021; 21:39. [PMID: 34126963 PMCID: PMC8204567 DOI: 10.1186/s12896-021-00700-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background HSPB5 is an ATP-independent molecular chaperone that is induced by heat shock or other proteotoxic stresses. HSPB5 is cytoprotective against stress both intracellularly and extracellularly. It acts as a potential therapeutic candidate in ischemia-reperfusion and neurodegenerative diseases. Results In this paper, we constructed a recombinant plasmid that expresses and extracellularly secrets a HSPB5-Fc fusion protein (sHSPB5-Fc) at 0.42 μg/ml in CHO-K1 cells. This sHSPB5-Fc protein contains a Fc-tag at the C-terminal extension of HSPB5, facilitating protein-affinity purification. Our study shows that sHSPB5-Fc inhibits heat-induced aggregation of citrate synthase in a time and dose dependent manner in vitro. Administration of sHSPB5-Fc protects lens epithelial cells against cisplatin- or UVB-induced cell apoptosis. It also decreases GFP-Httex1-Q74 insolubility, and reduces the size and cytotoxicity of GFP-Httex1-Q74 aggregates in PC-12 cells. Conclusion This recombinant sHSPB5-Fc exhibits chaperone activity to protect cells against proteotoxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00700-y.
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Affiliation(s)
- Jing Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China.,Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China
| | - Jingjing Yu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Wenxian Xue
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Huili Huang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Longjun Yan
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Fan Sang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Shuangshuang An
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jing Zhang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Mingli Wang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jun Zhang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Hui Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Xiukun Cui
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China
| | - Jiang He
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yanzhong Hu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital of Henan University, School of Basic Medical Sciences, Henan University, Jin-Ming Road, Kaifeng, 475004, China. .,Kaifeng Key Lab for Cataract and Myopia, Institute of Eye Disease, Kaifeng Central Hospital, Kaifeng, China. .,Department of Ophthalmology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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25
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Hong EP, MacDonald ME, Wheeler VC, Jones L, Holmans P, Orth M, Monckton DG, Long JD, Kwak S, Gusella JF, Lee JM. Huntington's Disease Pathogenesis: Two Sequential Components. J Huntingtons Dis 2021; 10:35-51. [PMID: 33579862 PMCID: PMC7990433 DOI: 10.3233/jhd-200427] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Historically, Huntington's disease (HD; OMIM #143100) has played an important role in the enormous advances in human genetics seen over the past four decades. This familial neurodegenerative disorder involves variable onset followed by consistent worsening of characteristic abnormal movements along with cognitive decline and psychiatric disturbances. HD was the first autosomal disease for which the genetic defect was assigned to a position on the human chromosomes using only genetic linkage analysis with common DNA polymorphisms. This discovery set off a multitude of similar studies in other diseases, while the HD gene, later renamed HTT, and its vicinity in chromosome 4p16.3 then acted as a proving ground for development of technologies to clone and sequence genes based upon their genomic location, with the growing momentum of such advances fueling the Human Genome Project. The identification of the HD gene has not yet led to an effective treatment, but continued human genetic analysis of genotype-phenotype relationships in large HD subject populations, first at the HTT locus and subsequently genome-wide, has provided insights into pathogenesis that divide the course of the disease into two sequential, mechanistically distinct components.
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Affiliation(s)
- Eun Pyo Hong
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, USA
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Lesley Jones
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Peter Holmans
- Medical Research Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurology, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael Orth
- Department of Neurology, University of Ulm, Germany
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jeffrey D Long
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Seung Kwak
- CHDI Management/CHDI Foundation, Princeton, NJ, USA
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, USA
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26
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Donaldson J, Powell S, Rickards N, Holmans P, Jones L. What is the Pathogenic CAG Expansion Length in Huntington's Disease? J Huntingtons Dis 2021; 10:175-202. [PMID: 33579866 PMCID: PMC7990448 DOI: 10.3233/jhd-200445] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Huntington's disease (HD) (OMIM 143100) is caused by an expanded CAG repeat tract in the HTT gene. The inherited CAG length is known to expand further in somatic and germline cells in HD subjects. Age at onset of the disease is inversely correlated with the inherited CAG length, but is further modulated by a series of genetic modifiers which are most likely to act on the CAG repeat in HTT that permit it to further expand. Longer repeats are more prone to expansions, and this expansion is age dependent and tissue-specific. Given that the inherited tract expands through life and most subjects develop disease in mid-life, this implies that in cells that degenerate, the CAG length is likely to be longer than the inherited length. These findings suggest two thresholds- the inherited CAG length which permits further expansion, and the intracellular pathogenic threshold, above which cells become dysfunctional and die. This two-step mechanism has been previously proposed and modelled mathematically to give an intracellular pathogenic threshold at a tract length of 115 CAG (95% confidence intervals 70- 165 CAG). Empirically, the intracellular pathogenic threshold is difficult to determine. Clues from studies of people and models of HD, and from other diseases caused by expanded repeat tracts, place this threshold between 60- 100 CAG, most likely towards the upper part of that range. We assess this evidence and discuss how the intracellular pathogenic threshold in manifest disease might be better determined. Knowing the cellular pathogenic threshold would be informative for both understanding the mechanism in HD and deploying treatments.
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Affiliation(s)
- Jasmine Donaldson
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Powell
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Nadia Rickards
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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27
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Tejwani L, Lim J. Pathogenic mechanisms underlying spinocerebellar ataxia type 1. Cell Mol Life Sci 2020; 77:4015-4029. [PMID: 32306062 PMCID: PMC7541529 DOI: 10.1007/s00018-020-03520-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/06/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
The family of hereditary cerebellar ataxias is a large group of disorders with heterogenous clinical manifestations and genetic etiologies. Among these, over 30 autosomal dominantly inherited subtypes have been identified, collectively referred to as the spinocerebellar ataxias (SCAs). Generally, the SCAs are characterized by a progressive gait impairment with classical cerebellar features, and in a subset of SCAs, accompanied by extra-cerebellar features. Beyond the common gait impairment and cerebellar atrophy, the wide range of additional clinical features observed across the SCAs is likely explained by the diverse set of mutated genes that encode proteins with seemingly disparate functional roles in nervous system biology. By synthesizing knowledge obtained from studies of the various SCAs over the past several decades, convergence onto a few key cellular changes, namely ion channel dysfunction and transcriptional dysregulation, has become apparent and may represent central mechanisms of cerebellar disease pathogenesis. This review will detail our current understanding of the molecular pathogenesis of the SCAs, focusing primarily on the first described autosomal dominant spinocerebellar ataxia, SCA1, as well as the emerging common core mechanisms across the various SCAs.
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Affiliation(s)
- Leon Tejwani
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Janghoo Lim
- Interdepartmental Neuroscience Program, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06510, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, 06510, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06510, USA.
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28
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Frequency and distribution of polyQ disease intermediate-length repeat alleles in healthy Italian population. Neurol Sci 2020; 41:1475-1482. [PMID: 31940111 DOI: 10.1007/s10072-019-04233-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Huntington disease (HD) and spinocerebellar ataxia type 1-2-17 (SCA1-2-17) are adult-onset autosomal dominant diseases, caused by triplet repeat expansions in the HTT, ATXN1, ATXN2, and TBP genes. Alleles with a repeat number just below the pathological threshold are associated with reduced penetrance and meiotic instability and are defined as intermediate alleles (IAs). OBJECTIVES We aimed to determine the frequencies of IAs in healthy Italian subjects and to compare the proportion of the IAs with the prevalence of the respective diseases. METHODS We analyzed the triplet repeat size in HTT, ATXN1, ATXN2, and TBP genes in the DNA samples from 729 consecutive adult healthy Italian subjects. RESULTS IAs associated with reduced penetrance were found in ATXN2 gene (1 subject, 0.1%) and TBP gene (0.82%). IAs at risk for meiotic instability were found in HTT (5.3%) and ATXN2 genes (2.7%). In ATXN1, we found a low percentage of IAs (0.4%). Alleles lacking the common CAT interruption within the CAG sequence were also rare (0.3%). CONCLUSIONS The high frequencies of IAs in HTT and ATXN2 genes suggest a correlation with the prevalence of the diseases in our population and support the hypothesis that IAs could represent a reservoir of new pathological expansions. On the opposite, ATXN1-IA were very rare in respect to the prevalence of SCA1 in our country, and TBP- IA were more frequent than expected, suggesting that other mechanisms could influence the occurrence of novel pathological expansions.
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29
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Tazelaar GHP, Boeynaems S, De Decker M, van Vugt JJFA, Kool L, Goedee HS, McLaughlin RL, Sproviero W, Iacoangeli A, Moisse M, Jacquemyn M, Daelemans D, Dekker AM, van der Spek RA, Westeneng HJ, Kenna KP, Assialioui A, Da Silva N, Povedano M, Pardina JSM, Hardiman O, Salachas F, Millecamps S, Vourc'h P, Corcia P, Couratier P, Morrison KE, Shaw PJ, Shaw CE, Pasterkamp RJ, Landers JE, Van Den Bosch L, Robberecht W, Al-Chalabi A, van den Berg LH, Van Damme P, Veldink JH, van Es MA. ATXN1 repeat expansions confer risk for amyotrophic lateral sclerosis and contribute to TDP-43 mislocalization. Brain Commun 2020; 2:fcaa064. [PMID: 32954321 PMCID: PMC7425293 DOI: 10.1093/braincomms/fcaa064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 02/01/2023] Open
Abstract
Increasingly, repeat expansions are being identified as part of the complex genetic architecture of amyotrophic lateral sclerosis. To date, several repeat expansions have been genetically associated with the disease: intronic repeat expansions in C9orf72, polyglutamine expansions in ATXN2 and polyalanine expansions in NIPA1. Together with previously published data, the identification of an amyotrophic lateral sclerosis patient with a family history of spinocerebellar ataxia type 1, caused by polyglutamine expansions in ATXN1, suggested a similar disease association for the repeat expansion in ATXN1. We, therefore, performed a large-scale international study in 11 700 individuals, in which we showed a significant association between intermediate ATXN1 repeat expansions and amyotrophic lateral sclerosis (P = 3.33 × 10-7). Subsequent functional experiments have shown that ATXN1 reduces the nucleocytoplasmic ratio of TDP-43 and enhances amyotrophic lateral sclerosis phenotypes in Drosophila, further emphasizing the role of polyglutamine repeat expansions in the pathophysiology of amyotrophic lateral sclerosis.
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Affiliation(s)
- Gijs H P Tazelaar
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Steven Boeynaems
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium,Department of Genetics, Stanford University School of Medicine,
Stanford, CA 94305-5120, USA
| | - Mathias De Decker
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium
| | - Joke J F A van Vugt
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Lindy Kool
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - H Stephan Goedee
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College
Dublin, Dublin D02 PN40, Republic of Ireland
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical
Neuroscience Institute and United Kingdom Dementia Research Institute, King’s College
London, London SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics & Health Informatics, Institute of Psychiatry,
Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Matthieu Moisse
- Division of Experimental Neurology, Department of Neurosciences, KU
Leuven—University of Leuven, Leuven 3000, Belgium,Laboratory of Neurobiology, VIB, Center for Brain & Disease
Research, Leuven 3000, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and
Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and
Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Annelot M Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Rick A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center,
Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Abdelilah Assialioui
- Servei de Neurologia, IDIBELL-Hospital de Bellvitge, Hospitalet de
Llobregat, Barcelona 08908, Spain
| | - Nica Da Silva
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical
Neuroscience Institute and United Kingdom Dementia Research Institute, King’s College
London, London SE5 9NU, UK
| | | | - Mónica Povedano
- Servei de Neurologia, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona 08908, Spain
| | | | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin D02 PN40, Republic of Ireland.,Department of Neurology, Beaumont Hospital, Dublin D02 PN40, Republic of Ireland
| | - François Salachas
- Centre de compétence SLA-Département de Neurologie, Hôpital Pitié-Salpêtrière, Paris 75651, France.,Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, Paris 75651, France
| | - Stéphanie Millecamps
- Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR7225, Sorbonne Universités, Paris 75651, France
| | - Patrick Vourc'h
- INSERM U930, Université François Rabelais, Tours 92120, France
| | - Philippe Corcia
- Centre de compétence SLA-fédération Tours-Limoges, Tours 92120, France
| | - Philippe Couratier
- Centre de compétence SLA-fédération Tours-Limoges, Limoges 87100, France
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute, King's College London, London SE5 9NU, UK.,Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Utrecht University, 3508 GA, Utrecht, The Netherlands
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ludo Van Den Bosch
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium
| | - Wim Robberecht
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute, King's College London, London SE5 9NU, UK.,Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Philip Van Damme
- Division of Experimental Neurology, Department of Neurosciences, KU Leuven-University of Leuven, Leuven 3000, Belgium.,Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Michael A van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center, Utrecht, University of Utrecht, 3508 GA, Utrecht, The Netherlands
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30
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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31
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Gardiner SL, Boogaard MW, Trompet S, de Mutsert R, Rosendaal FR, Gussekloo J, Jukema JW, Roos RAC, Aziz NA. Prevalence of Carriers of Intermediate and Pathological Polyglutamine Disease-Associated Alleles Among Large Population-Based Cohorts. JAMA Neurol 2020; 76:650-656. [PMID: 30933216 DOI: 10.1001/jamaneurol.2019.0423] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance Nine hereditary neurodegenerative diseases are known as polyglutamine diseases, including Huntington disease, 6 spinocerebellar ataxias (SCAs) (SCA1, SCA2, SCA3, SCA6, SCA7, and SCA17), dentatorubral-pallidoluysion atrophy, and spinal bulbar muscular atrophy. Objective To determine the prevalence of carriers of intermediate and pathological polyglutamine disease-associated alleles among the general population. Design, Setting, and Participants This observational cross-sectional study included data from 5 large European population-based cohorts that were compiled between 1997 and 2012, and the analyses were conducted in 2018. In total, 16 547 DNA samples were obtained from participants of the 5 cohorts. Individuals with a lifetime diagnosis of major depression were excluded (n = 2351). In the remaining 14 196 participants without an established polyglutamine disease diagnosis, the CAG repeat size in both alleles of all 9 polyglutamine disease-associated genes (PDAGs) (ie, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, HTT, ATN1, and AR) was determined. Exposure The number of CAG repeats in the alleles of the 9 PDAGs. Main Outcomes and Measures The number of individuals with alleles within the intermediate or pathological range per PDAG, as well as differences in sex, age, and body mass index between individuals carrying alleles within the normal or intermediate range and individuals carrying alleles within the pathological range of PDAGs. Results In the 14 196 analyzed participants (age range, 18-99 years; 56.3% female), 10.7% had a CAG repeat number within the intermediate range of at least 1 PDAG. Moreover, up to 1.3% of the participants had a CAG repeat number within the disease-causing range, predominantly in the lower pathological range associated with elderly onset. No differences in sex, age, or body mass index were found between individuals with CAG repeat numbers within the pathological range and individuals with CAG repeat numbers within the normal or intermediate range. Conclusions and Relevance These results indicate a high prevalence of individuals carrying intermediate and pathological ranges of polyglutamine disease-associated alleles among the general population. Therefore, a substantially larger proportion of individuals than previously estimated may be at risk of developing a polyglutamine disease later in life or bearing children with a de novo mutation.
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Affiliation(s)
- Sarah L Gardiner
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Merel W Boogaard
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jacobijn Gussekloo
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Public Health and Primary Care, Leiden University Medical Centre, Leiden, the Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - N Ahmad Aziz
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
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32
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Srinivasan SR, Shakkottai VG. Moving Towards Therapy in SCA1: Insights from Molecular Mechanisms, Identification of Novel Targets, and Planning for Human Trials. Neurotherapeutics 2019; 16:999-1008. [PMID: 31338702 PMCID: PMC6985354 DOI: 10.1007/s13311-019-00763-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The spinocerebellar ataxias (SCAs) are a group of neurodegenerative disorders inherited in an autosomal dominant fashion. The SCAs result in progressive gait imbalance, incoordination of the limbs, speech changes, and oculomotor dysfunction, among other symptoms. Over the past few decades, significant strides have been made in understanding the pathogenic mechanisms underlying these diseases. Although multiple efforts using a combination of genetics and pharmacology with small molecules have been made towards developing new therapeutics, no FDA approved treatment currently exists. In this review, we focus on SCA1, a common SCA subtype, in which some of the greatest advances have been made in understanding disease biology, and consequently potential therapeutic targets. Understanding of the underlying basic biology and targets of therapy in SCA1 is likely to give insight into treatment strategies in other SCAs. The diversity of the biology in the SCAs, and insight from SCA1 suggests, however, that both shared treatment strategies and specific approaches tailored to treat distinct genetic causes of SCA are likely needed for this group of devastating neurological disorders.
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Affiliation(s)
| | - Vikram G Shakkottai
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA.
- Department of Molecular and Integrative Physiology, University of Michigan, 4009 BSRB, 109 Zina Pitcher Place, Ann Arbor, Michigan, 48109, USA.
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33
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Abstract
The spinocerebellar ataxias (SCAs) comprise more than 40 autosomal dominant neurodegenerative disorders that present principally with progressive ataxia. Within the past few years, studies of pathogenic mechanisms in the SCAs have led to the development of promising therapeutic strategies, especially for SCAs caused by polyglutamine-coding CAG repeats. Nucleotide-based gene-silencing approaches that target the first steps in the pathogenic cascade are one promising approach not only for polyglutamine SCAs but also for the many other SCAs caused by toxic mutant proteins or RNA. For these and other emerging therapeutic strategies, well-coordinated preparation is needed for fruitful clinical trials. To accomplish this goal, investigators from the United States and Europe are now collaborating to share data from their respective SCA cohorts. Increased knowledge of the natural history of SCAs, including of the premanifest and early symptomatic stages of disease, will improve the prospects for success in clinical trials of disease-modifying drugs. In addition, investigators are seeking validated clinical outcome measures that demonstrate responsiveness to changes in SCA populations. Findings suggest that MRI and magnetic resonance spectroscopy biomarkers will provide objective biological readouts of disease activity and progression, but more work is needed to establish disease-specific biomarkers that track target engagement in therapeutic trials. Together, these efforts suggest that the development of successful therapies for one or more SCAs is not far away.
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34
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Lee JM, Correia K, Loupe J, Kim KH, Barker D, Hong EP, Chao MJ, Long JD, Lucente D, Vonsattel JPG, Pinto RM, Abu Elneel K, Ramos EM, Mysore JS, Gillis T, Wheeler VC, MacDonald ME, Gusella JF, McAllister B, Massey T, Medway C, Stone TC, Hall L, Jones L, Holmans P, Kwak S, Ehrhardt AG, Sampaio C, Ciosi M, Maxwell A, Chatzi A, Monckton DG, Orth M, Landwehrmeyer GB, Paulsen JS, Dorsey ER, Shoulson I, Myers RH. CAG Repeat Not Polyglutamine Length Determines Timing of Huntington's Disease Onset. Cell 2019; 178:887-900.e14. [PMID: 31398342 PMCID: PMC6700281 DOI: 10.1016/j.cell.2019.06.036] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/08/2019] [Accepted: 06/27/2019] [Indexed: 01/27/2023]
Abstract
Variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from the length of huntingtin's polyglutamine segment, dictates the rate at which Huntington's disease (HD) develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific manner, by polymorphic variation at multiple DNA maintenance genes, suggesting that the special onset-determining property of the uninterrupted CAG repeat is a propensity for length instability that leads to its somatic expansion. Additional naturally occurring genetic modifier loci, defined by GWAS, may influence HD pathogenesis through other mechanisms. These findings have profound implications for the pathogenesis of HD and other repeat diseases and question the fundamental premise that polyglutamine length determines the rate of pathogenesis in the "polyglutamine disorders."
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35
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Kevadiya BD, Ottemann BM, Thomas MB, Mukadam I, Nigam S, McMillan J, Gorantla S, Bronich TK, Edagwa B, Gendelman HE. Neurotheranostics as personalized medicines. Adv Drug Deliv Rev 2019; 148:252-289. [PMID: 30421721 PMCID: PMC6486471 DOI: 10.1016/j.addr.2018.10.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 12/16/2022]
Abstract
The discipline of neurotheranostics was forged to improve diagnostic and therapeutic clinical outcomes for neurological disorders. Research was facilitated, in largest measure, by the creation of pharmacologically effective multimodal pharmaceutical formulations. Deployment of neurotheranostic agents could revolutionize staging and improve nervous system disease therapeutic outcomes. However, obstacles in formulation design, drug loading and payload delivery still remain. These will certainly be aided by multidisciplinary basic research and clinical teams with pharmacology, nanotechnology, neuroscience and pharmaceutic expertise. When successful the end results will provide "optimal" therapeutic delivery platforms. The current report reviews an extensive body of knowledge of the natural history, epidemiology, pathogenesis and therapeutics of neurologic disease with an eye on how, when and under what circumstances neurotheranostics will soon be used as personalized medicines for a broad range of neurodegenerative, neuroinflammatory and neuroinfectious diseases.
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Affiliation(s)
- Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Brendan M Ottemann
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Midhun Ben Thomas
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Insiya Mukadam
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Saumya Nigam
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - JoEllyn McMillan
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Tatiana K Bronich
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benson Edagwa
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA; Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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36
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Kourkouta E, Weij R, González-Barriga A, Mulder M, Verheul R, Bosgra S, Groenendaal B, Puoliväli J, Toivanen J, van Deutekom JCT, Datson NA. Suppression of Mutant Protein Expression in SCA3 and SCA1 Mice Using a CAG Repeat-Targeting Antisense Oligonucleotide. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:601-614. [PMID: 31394429 PMCID: PMC6695277 DOI: 10.1016/j.omtn.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
Spinocerebellar ataxia type 3 (SCA3) and type 1 (SCA1) are dominantly inherited neurodegenerative disorders that are currently incurable. Both diseases are caused by a CAG-repeat expansion in exon 10 of the Ataxin-3 and exon 8 of the Ataxin-1 gene, respectively, encoding an elongated polyglutamine tract that confers toxic properties to the resulting proteins. We have previously shown lowering of the pathogenic polyglutamine protein in Huntington's disease mouse models using (CUG)7, a CAG repeat-targeting antisense oligonucleotide. Here we evaluated the therapeutic capacity of (CUG)7 for SCA3 and SCA1, in vitro in patient-derived cell lines and in vivo in representative mouse models. Repeated intracerebroventricular (CUG)7 administration resulted in a significant reduction of mutant Ataxin-3 and Ataxin-1 proteins throughout the brain of SCA3 and SCA1 mouse models, respectively. Furthermore, in both a SCA3 patient cell line and the MJD84.2 mouse model, (CUG)7 induced formation of a truncated Ataxin-3 protein species lacking the polyglutamine stretch, likely arising from (CUG)7-mediated exon 10 skipping. In contrast, skipping of exon 8 of Ataxin-1 did not significantly contribute to the Ataxin-1 protein reduction observed in (CUG)7-treated SCA1154Q/2Q mice. These findings support the therapeutic potential of a single CAG repeat-targeting AON for the treatment of multiple polyglutamine disorders.
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Affiliation(s)
| | - Rudie Weij
- BioMarin Nederland BV, Leiden, the Netherlands
| | | | | | | | | | | | | | - Jussi Toivanen
- Charles River Discovery Research Services, Kuopio, Finland
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37
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Loureiro JR, Oliveira CL, Mota C, Castro AF, Costa C, Loureiro JL, Coutinho P, Martins S, Sequeiros J, Silveira I. Mutational mechanism for DAB1 (ATTTC) n insertion in SCA37: ATTTT repeat lengthening and nucleotide substitution. Hum Mutat 2019; 40:404-412. [PMID: 30588707 DOI: 10.1002/humu.23704] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/28/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022]
Abstract
Dynamic mutations by microsatellite instability are the molecular basis of a growing number of neuromuscular and neurodegenerative diseases. Repetitive stretches in the human genome may drive pathogenicity, either by expansion above a given threshold, or by insertion of abnormal tracts in nonpathogenic polymorphic repetitive regions, as is the case in spinocerebellar ataxia type 37 (SCA37). We have recently established that this neurodegenerative disease is caused by an (ATTTC)n insertion within an (ATTTT)n in a noncoding region of DAB1. We now investigated the mutational mechanism that originated the (ATTTC)n insertion within an ancestral (ATTTT)n . Approximately 3% of nonpathogenic (ATTTT)n alleles are interspersed by AT-rich motifs, contrarily to mutant alleles that are composed of pure (ATTTT)n and (ATTTC)n stretches. Haplotype studies in unaffected chromosomes suggested that the primary mutational mechanism, leading to the (ATTTC)n insertion, was likely one or more T>C substitutions in an (ATTTT)n pure allele of approximately 200 repeats. Then, the (ATTTC)n expanded in size, originating a deleterious allele in DAB1 that leads to SCA37. This is likely the mutational mechanism in three similar (TTTCA)n insertions responsible for familial myoclonic epilepsy. Because (ATTTT)n tracts are frequent in the human genome, many loci could be at risk for this mutational process.
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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, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal
| | - Cláudia L Oliveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Carolina Mota
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Ana F Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
| | - Cristina Costa
- Department of Neurology, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - José L Loureiro
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Department of Neurology, Hospital São Sebastião, Feira, Portugal
| | - Paula Coutinho
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sandra Martins
- Population Genetics & Evolution, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Jorge Sequeiros
- IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal.,ICBAS, Universidade do Porto, Porto, Portugal.,UnIGENe, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC- Institute for Molecular and Cell Biology, Universidade do Porto, Porto, Portugal
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38
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Nethisinghe S, Lim WN, Ging H, Zeitlberger A, Abeti R, Pemble S, Sweeney MG, Labrum R, Cervera C, Houlden H, Rosser E, Limousin P, Kennedy A, Lunn MP, Bhatia KP, Wood NW, Hardy J, Polke JM, Veneziano L, Brusco A, Davis MB, Giunti P. Complexity of the Genetics and Clinical Presentation of Spinocerebellar Ataxia 17. Front Cell Neurosci 2018; 12:429. [PMID: 30532692 PMCID: PMC6265347 DOI: 10.3389/fncel.2018.00429] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Spinocerebellar ataxia type 17 (SCA17) is a rare autosomal dominant neurodegenerative disease caused by a CAG repeat expansion in the TATA-box binding protein gene (TBP). The disease has a varied age at onset and clinical presentation. It is distinct from other SCAs for its association with dementia, psychiatric symptoms, and some patients presenting with chorea. For this reason, it is also called Huntington’s disease-like 4 (HDL-4). Here we examine the distribution of SCA17 allele repeat sizes in a United Kingdom-based cohort with ataxia and find that fully penetrant pathogenic alleles are very rare (5 in 1,316 chromosomes; 0.38%). Phenotype-genotype correlation was performed on 30 individuals and the repeat structure of their TBP genes was examined. We found a negative linear correlation between total CAG repeat length and age at disease onset and, unlike SCA1, there was no correlation between the longest contiguous CAG tract and age at disease onset. We were unable to identify any particular phenotypic trait that segregated with particular CAG/CAA repeat tract structures or repeat lengths. One individual within the cohort was homozygous for variable penetrance range SCA17 alleles. This patient had a similar age at onset to heterozygotes with the same repeat sizes, but also presented with a rapidly progressive dementia. A pair of monozygotic twins within the cohort presented 3 years apart with the sibling with the earlier onset having a more severe phenotype with dementia and chorea in addition to the ataxia observed in their twin. This appears to be a case of variable expressivity, possibly influenced by other environmental or epigenetic factors. Finally, there was an asymptomatic father with a severely affected child with an age at onset in their twenties. Despite this, they share the same expanded allele repeat sizes and sequences, which would suggest that there is marked difference in the penetrance of this 51-repeat allele. We therefore propose that the variable penetrance range extend from 48 repeats to incorporate this allele. This study shows that there is variability in the presentation and penetrance of the SCA17 phenotype and highlights the complexity of this disorder.
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Affiliation(s)
- Suran Nethisinghe
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Wei N Lim
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Heather Ging
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Anna Zeitlberger
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Rosella Abeti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sally Pemble
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Mary G Sweeney
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Robyn Labrum
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Charisse Cervera
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom.,MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Patricia Limousin
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Angus Kennedy
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Michael P Lunn
- Department of Neuroimmunology, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Kailash P Bhatia
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Nicholas W Wood
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, United Kingdom.,The Reta Lila Weston Institute of Neurological Studies, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - James M Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Liana Veneziano
- Istituto di Farmacologia Traslazionale - National Research Council, Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Mary B Davis
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
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39
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Al-Mahdawi S, Ging H, Bayot A, Cavalcanti F, La Cognata V, Cavallaro S, Giunti P, Pook MA. Large Interruptions of GAA Repeat Expansion Mutations in Friedreich Ataxia Are Very Rare. Front Cell Neurosci 2018; 12:443. [PMID: 30519163 PMCID: PMC6258883 DOI: 10.3389/fncel.2018.00443] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/05/2018] [Indexed: 12/19/2022] Open
Abstract
Friedreich ataxia is a multi-system autosomal recessive inherited disorder primarily caused by homozygous GAA repeat expansion mutations within intron 1 of the frataxin gene. The resulting deficiency of frataxin protein leads to progressive mitochondrial dysfunction, oxidative stress, and cell death, with the main affected sites being the large sensory neurons of the dorsal root ganglia and the dentate nucleus of the cerebellum. The GAA repeat expansions may be pure (GAA)n in sequence or may be interrupted with regions of non-GAA sequence. To our knowledge, there has been no large-scale study of FRDA patient DNA samples to determine the frequency of large interruptions in GAA repeat expansions. Therefore, we have investigated a panel of 245 Friedreich ataxia patient and carrier DNA samples using GAA repeat PCR amplification and MboII restriction enzyme digestion. We demonstrate that the vast majority (97.8%) of Friedreich ataxia GAA repeat expansion samples do not contain significant sequence changes that would result in abnormal MboII digestion profiles, indicating that they are primarily pure GAA repeats. These results show for the first time that large interruptions in the GAA repeats are very rare.
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Affiliation(s)
- Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Heather Ging
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | - Aurelien Bayot
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | | | | | | | - Paola Giunti
- Ataxia Centre, Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | - Mark A Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom.,Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, United Kingdom
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40
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Wiethoff S, O'Connor E, Haridy NA, Nethisinghe S, Wood N, Giunti P, Bettencourt C, Houlden H. Sequencing analysis of the SCA6 CAG expansion excludes an influence of repeat interruptions on disease onset. J Neurol Neurosurg Psychiatry 2018; 89:1226-1227. [PMID: 29367260 PMCID: PMC6227801 DOI: 10.1136/jnnp-2017-317253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/30/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Sarah Wiethoff
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard Karls-University, Tübingen, Germany
| | - Emer O'Connor
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Nourelhoda A Haridy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,Department of Neurology and Psychiatry, Faculty of Medicine, Assiut University Hospital, Assiut, Egypt
| | - Suran Nethisinghe
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Nicholas Wood
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Paola Giunti
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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41
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Nethisinghe S, Pigazzini ML, Pemble S, Sweeney MG, Labrum R, Manso K, Moore D, Warner J, Davis MB, Giunti P. PolyQ Tract Toxicity in SCA1 is Length Dependent in the Absence of CAG Repeat Interruption. Front Cell Neurosci 2018; 12:200. [PMID: 30108484 PMCID: PMC6080413 DOI: 10.3389/fncel.2018.00200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/19/2018] [Indexed: 11/20/2022] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder caused by an expansion of a polyglutamine tract within the ATXN1 gene. Normal alleles have been reported to range from 6 to 35 repeats, intermediate alleles from 36 to 38 repeats and fully penetrant pathogenic alleles have at least 39 repeats. This distribution was based on relatively few samples and the narrow intermediate range makes the accuracy of the repeat sizing crucial for interpreting and reporting diagnostic tests, which can vary between laboratories. Here, we examine the distribution of 6378 SCA1 chromosomes and identify a very late onset SCA1 family with a fully penetrant uninterrupted pathogenic allele containing 38 repeats. This finding supports the theory that polyQ toxicity is related to the increase of the length of the inherited tracts and not as previously hypothesized to the structural transition occurring above a specific threshold. In addition, the threshold of toxicity shifts to a shorter polyQ length with the increase of the lifespan in SCA1. Furthermore, we show that SCA1 intermediate alleles have a different behavior compared to the other polyglutamine disorders as they do not show reduced penetrance when uninterrupted. Therefore, the pathogenic mechanism in SCA1 is distinct from other cytosine-adenine-guanine (CAG) repeat disorders. Accurately sizing repeats is paramount in precision medicine and can be challenging particularly with borderline alleles. We examined plasmids containing cloned CAG repeat tracts alongside a triplet repeat primed polymerase chain reaction (TP PCR) CAG repeat ladder to improve accuracy in repeat sizing by fragment analysis. This method accurately sizes the repeats irrespective of repeat composition or length. We also improved the model for calculating repeat length from fragment analysis sizing by fragment analyzing 100 cloned repeats of known size. Therefore, we recommend these methods for accurately sizing repeat lengths and restriction enzyme digestion to identify interruptions for interpretation of a given allele’s pathogenicity.
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Affiliation(s)
- Suran Nethisinghe
- Ataxia Centre, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Maria Lucia Pigazzini
- Ataxia Centre, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - Sally Pemble
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery (NHNN), London, United Kingdom
| | - Mary G Sweeney
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery (NHNN), London, United Kingdom
| | - Robyn Labrum
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery (NHNN), London, United Kingdom
| | - Katarina Manso
- Ataxia Centre, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | - David Moore
- Molecular Genetics Laboratory, South East Scotland Genetics Service, Western General Hospital, Edinburgh, United Kingdom
| | - Jon Warner
- Molecular Genetics Laboratory, South East Scotland Genetics Service, Western General Hospital, Edinburgh, United Kingdom
| | - Mary B Davis
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery (NHNN), London, United Kingdom
| | - Paola Giunti
- Ataxia Centre, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
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42
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McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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43
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Vishwakarma P, Muthuswamy S, Agarwal S. Current molecular insight to reveal the dynamics of CAG repeating units in spinocerebellar ataxia. Intractable Rare Dis Res 2018; 7:79-86. [PMID: 29862148 PMCID: PMC5982628 DOI: 10.5582/irdr.2018.01039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is a heterogeneous genetic disorder with overlapping clinical phenotypes arising from the degeneration of purkinje cells and other regions of the brain. There are approximately 36 different subtypes of SCA, but SCA 1, 2, 3, 6 and 7 are most prevalent in the Indian population. Many findings suggested that cerebellar Purkinje cells region may be a uniquely vulnerable neuronal cell type, and more susceptible to a wider variety of genetic or cellular problems than other neuron types. In this review we emphasized mainly five common subtypes of SCA (1, 2, 3, 6 and 7) their pathophysiology, therapeutics, drugs studies and the technical challenges in the field of molecular genetic diagnosis.
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Affiliation(s)
- Priyanka Vishwakarma
- Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Srinivasan Muthuswamy
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Sarita Agarwal
- Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
- Address correspondence to:Dr. Sarita Agarwal, Department of Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India. E-mail:
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44
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Zeitlberger A, Ging H, Nethisinghe S, Giunti P. Advances in the understanding of hereditary ataxia – implications for future patients. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1444477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Anna Zeitlberger
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Heather Ging
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Suran Nethisinghe
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Paola Giunti
- Department of Molecular Neuroscience, UCL, Institute of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
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45
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Mier P, Andrade-Navarro MA. Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length. Genome Biol Evol 2018; 10:816-825. [PMID: 29608721 PMCID: PMC5841385 DOI: 10.1093/gbe/evy046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 12/16/2022] Open
Abstract
Amino acid usage in a proteome depends mostly on its taxonomy, as it does the codon usage in transcriptomes. Here, we explore the level of variation in the codon usage of a specific amino acid, glutamine, in relation to the number of consecutive glutamine residues. We show that CAG triplets are consistently more abundant in short glutamine homorepeats (polyQ, four to eight residues) than in shorter glutamine stretches (one to three residues), leading to the evolutionary growth of the repeat region in a CAG-dependent manner. The length of orthologous polyQ regions is mostly stable in primates, particularly the short ones. Interestingly, given a short polyQ the CAG usage is higher in unstable-in-length orthologous polyQ regions. This indicates that CAG triplets produce the necessary instability for a glutamine stretch to grow. Proteins related to polyQ-associated diseases behave in a more extreme way, with longer glutamine stretches in human and evolutionarily closer nonhuman primates, and an overall higher CAG usage. In the light of our results, we suggest an evolutionary model to explain the glutamine codon usage in polyQ regions.
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Affiliation(s)
- Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
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46
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Abstract
Diseases such as Huntington's disease and certain spinocerebellar ataxias are caused by the expansion of genomic cytosine-adenine-guanine (CAG) trinucleotide repeats beyond a specific threshold. These diseases are all characterised by neurological symptoms and central neurodegeneration, but our understanding of how expanded repeats drive neuronal loss is incomplete. Recent human genetic evidence implicates DNA repair pathways, especially mismatch repair, in modifying the onset and progression of CAG repeat diseases. Repair pathways might operate directly on repeat sequences by licensing or inhibiting repeat expansion in neurons. Alternatively, or in addition, because many of the genes containing pathogenic CAG repeats encode proteins that themselves have roles in the DNA damage response, it is possible that repeat expansions impair specific DNA repair pathways. DNA damage could then accrue in neurons, leading to further expansion at repeat loci, thus setting up a vicious cycle of pathology. In this review, we consider DNA damage and repair pathways in postmitotic neurons in the context of disease-causing CAG repeats. Investigating and understanding these pathways, which are clearly relevant in promoting and ameliorating disease in humans, is a research priority, as they are known to modify disease and therefore constitute prevalidated drug targets.
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Affiliation(s)
- Thomas H Massey
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Lesley Jones
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, CF24 4HQ, UK
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47
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Schüle B, McFarland KN, Lee K, Tsai YC, Nguyen KD, Sun C, Liu M, Byrne C, Gopi R, Huang N, Langston JW, Clark T, Gil FJJ, Ashizawa T. Parkinson's disease associated with pure ATXN10 repeat expansion. NPJ PARKINSONS DISEASE 2017; 3:27. [PMID: 28890930 PMCID: PMC5585403 DOI: 10.1038/s41531-017-0029-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022]
Abstract
Large, non-coding pentanucleotide repeat expansions of ATTCT in intron 9 of the ATXN10 gene typically cause progressive spinocerebellar ataxia with or without seizures and present neuropathologically with Purkinje cell loss resulting in symmetrical cerebellar atrophy. These ATXN10 repeat expansions can be interrupted by sequence motifs which have been attributed to seizures and are likely to act as genetic modifiers. We identified a Mexican kindred with multiple affected family members with ATXN10 expansions. Four affected family members showed clinical features of spinocerebellar ataxia type 10 (SCA10). However, one affected individual presented with early-onset levodopa-responsive parkinsonism, and one family member carried a large repeat ATXN10 expansion, but was clinically unaffected. To characterize the ATXN10 repeat, we used a novel technology of single-molecule real-time (SMRT) sequencing and CRISPR/Cas9-based capture. We sequenced the entire span of ~5.3-7.0 kb repeat expansions. The Parkinson's patient carried an ATXN10 expansion with no repeat interruption motifs as well as an unaffected sister. In the siblings with typical SCA10, we found a repeat pattern of ATTCC repeat motifs that have not been associated with seizures previously. Our data suggest that the absence of repeat interruptions is likely a genetic modifier for the clinical presentation of l-Dopa responsive parkinsonism, whereas repeat interruption motifs contribute clinically to epilepsy. Repeat interruptions are important genetic modifiers of the clinical phenotype in SCA10. Advanced sequencing techniques now allow to better characterize the underlying genetic architecture for determining accurate phenotype-genotype correlations.
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Affiliation(s)
- Birgitt Schüle
- Parkinson's Institute and Clinical Center, Sunnyvale, CA 94028 USA
| | - Karen N McFarland
- Center for Translational Research in Neurodegenerative Disease and The McKnight Brain Institute, University of Florida, College of Medicine, Department of Neurology, Gainesville, FL 32610 USA
| | - Kelsey Lee
- Parkinson's Institute and Clinical Center, Sunnyvale, CA 94028 USA
| | | | | | - Chao Sun
- Biogen Idec, Cambridge, MA 02142 USA
| | - Mei Liu
- Biogen Idec, Cambridge, MA 02142 USA
| | - Christie Byrne
- Parkinson's Institute and Clinical Center, Sunnyvale, CA 94028 USA
| | - Ramesh Gopi
- Silicon Valley Diagnostic Imaging, El Camino Hospital, Mountain View, CA 94040 USA
| | - Neng Huang
- Valley Parkinson Clinic, Los Gatos, CA 95032 USA
| | | | - Tyson Clark
- Pacific Biosciences, Menlo Park, CA 94025 USA
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48
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Herranz-Martin S, Chandran J, Lewis K, Mulcahy P, Higginbottom A, Walker C, Valenzuela IMPY, Jones RA, Coldicott I, Iannitti T, Akaaboune M, El-Khamisy SF, Gillingwater TH, Shaw PJ, Azzouz M. Viral delivery of C9orf72 hexanucleotide repeat expansions in mice leads to repeat-length-dependent neuropathology and behavioural deficits. Dis Model Mech 2017; 10:859-868. [PMID: 28550099 PMCID: PMC5536911 DOI: 10.1242/dmm.029892] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023] Open
Abstract
Intronic GGGGCC repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two major pathologies stemming from the hexanucleotide RNA expansions (HREs) have been identified in postmortem tissue: intracellular RNA foci and repeat-associated non-ATG dependent (RAN) dipeptides, although it is unclear how these and other hallmarks of disease contribute to the pathophysiology of neuronal injury. Here, we describe two novel lines of mice that overexpress either 10 pure or 102 interrupted GGGGCC repeats mediated by adeno-associated virus (AAV) and recapitulate the relevant human pathology and disease-related behavioural phenotypes. Similar levels of intracellular RNA foci developed in both lines of mice, but only mice expressing 102 repeats generated C9orf72 RAN pathology, neuromuscular junction (NMJ) abnormalities, dispersal of the hippocampal CA1, enhanced apoptosis, and deficits in gait and cognition. Neither line of mice, however, showed extensive TAR DNA-binding protein 43 (TDP-43) pathology or neurodegeneration. Our data suggest that RNA foci pathology is not a good predictor of C9orf72 RAN dipeptide formation, and that RAN dipeptides and NMJ dysfunction are drivers of C9orf72 disease pathogenesis. These AAV-mediated models of C9orf72-associated ALS/FTD will be useful tools for studying disease pathophysiology and developing new therapeutic approaches. Summary:C9orf72-linked motor neuron disease models with viral-mediated expression of GGGGCC repeat expansion in mice show neuropathology and behavioural deficits.
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Affiliation(s)
- Saul Herranz-Martin
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Jayanth Chandran
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Katherine Lewis
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Padraig Mulcahy
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Callum Walker
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK.,Department of Molecular Biology and Biotechnology, Krebs and Sheffield Institute for Nucleic Acids, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | | | - Ross A Jones
- Centre for Integrative Physiology & Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, The University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
| | - Ian Coldicott
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Tommaso Iannitti
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Mohammed Akaaboune
- Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Krebs and Sheffield Institute for Nucleic Acids, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas H Gillingwater
- Centre for Integrative Physiology & Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, The University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
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49
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Kuiper EFE, de Mattos EP, Jardim LB, Kampinga HH, Bergink S. Chaperones in Polyglutamine Aggregation: Beyond the Q-Stretch. Front Neurosci 2017; 11:145. [PMID: 28386214 PMCID: PMC5362620 DOI: 10.3389/fnins.2017.00145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/08/2017] [Indexed: 01/12/2023] Open
Abstract
Expanded polyglutamine (polyQ) stretches in at least nine unrelated proteins lead to inherited neuronal dysfunction and degeneration. The expansion size in all diseases correlates with age at onset (AO) of disease and with polyQ protein aggregation, indicating that the expanded polyQ stretch is the main driving force for the disease onset. Interestingly, there is marked interpatient variability in expansion thresholds for a given disease. Between different polyQ diseases the repeat length vs. AO also indicates the existence of modulatory effects on aggregation of the upstream and downstream amino acid sequences flanking the Q expansion. This can be either due to intrinsic modulation of aggregation by the flanking regions, or due to differential interaction with other proteins, such as the components of the cellular protein quality control network. Indeed, several lines of evidence suggest that molecular chaperones have impact on the handling of different polyQ proteins. Here, we review factors differentially influencing polyQ aggregation: the Q-stretch itself, modulatory flanking sequences, interaction partners, cleavage of polyQ-containing proteins, and post-translational modifications, with a special focus on the role of molecular chaperones. By discussing typical examples of how these factors influence aggregation, we provide more insight on the variability of AO between different diseases as well as within the same polyQ disorder, on the molecular level.
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Affiliation(s)
- E F E Kuiper
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Eduardo P de Mattos
- Department of Cell Biology, University Medical Center Groningen, University of GroningenGroningen, Netherlands; Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil
| | - Laura B Jardim
- Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil; Departamento de Medicina Interna, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Harm H Kampinga
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Steven Bergink
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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50
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Ardui S, Race V, Zablotskaya A, Hestand MS, Van Esch H, Devriendt K, Matthijs G, Vermeesch JR. Detecting AGG Interruptions in Male and Female FMR1 Premutation Carriers by Single-Molecule Sequencing. Hum Mutat 2017; 38:324-331. [DOI: 10.1002/humu.23150] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/02/2016] [Accepted: 11/17/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Simon Ardui
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | - Valerie Race
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | | | | | | | | | - Gert Matthijs
- Department of Human Genetics; KU Leuven; Leuven Belgium
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