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Rudaks LI, Stevanovski I, Yeow D, Reis ALM, Chintalaphani SR, Cheong PL, Gamaarachchi H, Worgan L, Ahmad K, Hayes M, Hannaford A, Kim S, Fung VSC, Halmagyi GM, Martin A, Manser D, Tchan M, Ng K, Kennerson ML, Deveson IW, Kumar KR. Targeted Long-Read Sequencing as a Single Assay Improves the Diagnosis of Spastic-Ataxia Disorders. Ann Clin Transl Neurol 2025; 12:832-841. [PMID: 40007153 PMCID: PMC12040508 DOI: 10.1002/acn3.70008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Accepted: 01/19/2025] [Indexed: 02/27/2025] Open
Abstract
OBJECTIVE The hereditary spastic-ataxia spectrum disorders are a group of disabling neurological diseases. The traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline and improve this process using long-read sequencing. METHODS We developed a targeted long-read sequencing strategy with the capacity to characterise the genetic variation of all types and sizes within 469 disease-associated genes, in a single assay. We applied this to a cohort of 34 individuals with unsolved spastic-ataxia. An additional five individuals with a known genetic diagnosis were included as positive controls. RESULTS We identified causative pathogenic variants that would be sufficient for genetic diagnosis in 14/34 (41%) unsolved participants. The success rate was 5/11 (45%) in those who were naïve to genetic testing and 9/23 (39%) in those who were undiagnosed after prior genetic testing, completed on a clinical basis. Short tandem repeat expansions in FGF14 were the most common (7/34, 21%). Two individuals (2/34, 6%) had biallelic pathogenic expansions in RFC1 and one individual had a monoallelic pathogenic expansion in ATXN8OS/ATXN8. Causative pathogenic sequence variants other than short tandem repeat expansions were found in four individuals, including in VCP, STUB1, ANO10 and SPG7. Furthermore, all five positive controls were identified. INTERPRETATION Our results demonstrate the utility of targeted long-read sequencing in the genetic evaluation of patients with spastic-ataxia spectrum disorders, highlighting both the capacity to increase overall diagnostic yield and to streamline the testing pathway by capturing all known genetic causes in a single assay.
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Liu P, Zhang F, Chen X, Zheng X, Chen M, Lin Z, Chen S, Wang L, Wang X, Jin N, Ying C, Xie F, Wang B, Wu S, Cen Z, Luo W. Long-read sequencing revealed complex biallelic pentanucleotide repeat expansions in RFC1-related Parkinson's disease. NPJ Parkinsons Dis 2025; 11:21. [PMID: 39833204 PMCID: PMC11747075 DOI: 10.1038/s41531-025-00868-6] [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: 03/08/2024] [Accepted: 12/31/2024] [Indexed: 01/22/2025] Open
Abstract
Biallelic intronic pentanucleotide repeat expansions, mainly (AAGGG)exp and/or (ACAGG)exp in RFC1, are detected in cerebellar ataxia, neuropathy and vestibular areflexia syndrome, late-onset ataxia, and in a wide disease spectrum including Charcot-Marie-Tooth disease, multiple system atrophy, and Parkinson's disease (PD). However, the genotype-phenotype correlation and underlying mechanism are mostly unknown. We screened RFC1-repeat expansions in 1445 patients with parkinsonism. Comprehensive genetic and clinical, and pathological assessments were performed. We report two early-onset patients with PD carrying complex biallelic pentanucleotide repeat expansions in RFC1. Long-read sequencing revealed a novel repeat configuration of (AGGGG)exp(AAGGG)14 and a possible somatic variant of (AAGGG)exp(AATGG)exp(AAGGG)exp in the (AAGGG)exp alleles in two RFC1-related PD patients. RNA foci were detected in the (AGGGG)exp-expressed HEK293T cell line as well as (AAGGG)exp and (ACAGG)exp, supporting (AGGGG)exp as a novel pathogenic repeat motif. This work revealed complex genotypes with novel repeat configuration of (AGGGG)exp and possible somatic (AATGG)exp insertion in RFC1-related PD.
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Affiliation(s)
- Peng Liu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fan Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinhui Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaosheng Zheng
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Miao Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiru Lin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuqi Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lebo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinchen Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Nan Jin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chenxin Ying
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sheng Wu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhidong Cen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Shukla S, Gupta K, Singh K, Mishra A, Kumar A. An Updated Canvas of the RFC1-mediated CANVAS (Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome). Mol Neurobiol 2025; 62:693-707. [PMID: 38898197 DOI: 10.1007/s12035-024-04307-0] [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: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Proliferation of specific nucleotide sequences within the coding and non-coding regions of numerous genes has been implicated in approximately 40 neurodegenerative disorders. Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), a neurodegenerative disorder, is distinguished by a pathological triad of sensory neuropathy, bilateral vestibular areflexia and cerebellar impairments. It manifests in adults gradually and is autosomal recessive and multi-system ataxia. Predominantly, CANVAS is associated with biallelic AAGGG repeat expansions in intron 2 of the RFC1 gene. Although various motifs have been identified, only a subset induces pathological consequences, by forming stable secondary structures that disrupt gene functions both in vitro and in vivo. The pathogenesis of CANVAS remains a subject of intensive research, yet its precise mechanisms remain elusive. Herein, we aim to comprehensively review the epidemiology, clinical ramifications, molecular mechanisms, genetics, and potential therapeutics in light of the current findings, extending an overview of the most significant research on CANVAS.
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Affiliation(s)
- Sakshi Shukla
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Kanav Gupta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Krishna Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
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Davies KC, Fearnley LG, Snell P, Bourke D, Mossman S, Kyne K, McKeown C, Delatycki MB, Bahlo M, Lockhart PJ. A multi-exon RFC1 deletion in a case of CANVAS: expanding the genetic mechanism of disease. J Neurol 2024; 271:7622-7627. [PMID: 39249106 DOI: 10.1007/s00415-024-12675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/10/2024]
Affiliation(s)
- Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
| | - Liam G Fearnley
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3052, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - David Bourke
- Department of Neurology, Wellington Hospital, Wellington, 6242, New Zealand
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington, 6242, New Zealand
| | - Karen Kyne
- Capital and Coast District Health Board, Wellington Regional Hospital, Wellington, 6021, New Zealand
| | - Colina McKeown
- Genetic Health Service New Zealand, Wellington Hospital, Wellington, 6242, New Zealand
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.
- Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia.
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Falcone GMI, Tessa A, Arena IG, Barghigiani M, Migliorato A, Incensi A, Rodolico C, Donadio V, Santorelli FM, Musumeci O. Pseudodominance in RFC1-Spectrum Disorder. CEREBELLUM (LONDON, ENGLAND) 2024; 23:2622-2628. [PMID: 39230846 DOI: 10.1007/s12311-024-01735-5] [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: 08/14/2024] [Indexed: 09/05/2024]
Abstract
Cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and disease spectrum is an autosomal recessive disorder associated with biallelic repeat expansion (RE) in the RFC1 gene. A high carrier frequency in the healthy population determines the possibility of having affected members in two consecutive generations. We describe pseudodominance in two families affected with RFC1 disorder (10 affected, 5 oligo/asymptomatic individuals). In Family A, after the 75-year-old index case was diagnosed with CANVAS, the 73-year-old wife decided to undergo screening for carrier testing. Although she did not report any symptoms, she resulted positive for the biallelic AAGGG RE thus leading to a diagnosis in the asymptomatic offspring as well and revealing a pseudodominant pattern of inheritance. In Family B pseudodominance was suspected after the identification of the RFC1 RE in the proband affected by sensitive neuropathy because of a positive family history for undetermined polyneuropathy in the mother. The post-mortem identification of the RFC1 RE in a sample specimen from the deceased mother, who had been under our care, allowed the solution of a "cold case". Our report suggests that pseudodominance is a confounding phenomenon to consider in RFC1-spectrum disorder and genetic counselling is instrumental in families with affected individuals.
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Affiliation(s)
- Grazia Maria Igea Falcone
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, 98125, Italy
| | | | - Ignazio Giuseppe Arena
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, 98125, Italy
| | | | - Alba Migliorato
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, Messina, Italy
| | - Alex Incensi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Carmelo Rodolico
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, 98125, Italy
| | - Vincenzo Donadio
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | | | - Olimpia Musumeci
- Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, 98125, Italy.
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Abstract
PURPOSE OF REVIEW Inherited peripheral neuropathies can be divided into those diseases in which peripheral neuropathy is the sole or main feature of the disease (Charcot-Marie-Tooth disease) and those in which peripheral neuropathy is just one feature of a more complex syndrome. In recent years there has been a substantial expansion in the number of genes associated with complex neuropathy syndromes. RECENT FINDINGS This review will focus on emerging themes in this group of diseases, namely the increasing number of diseases due to repeat expansions; the emergence of both recessive and dominant negative alleles in the same gene producing a common phenotype and diseases in which there is selective loss of the allele from haematopoietic stem cells making genetic diagnosis on blood derived DNA problematic. SUMMARY In this review we provide a practical approach to investigating and diagnosing patients with peripheral neuropathy as part of a complex syndrome and provide an updated table of the genes associated with this group of diseases.
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Affiliation(s)
- Alexander M Rossor
- Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square institute of Neurology and National Hospital for Neurology and Neurosurgery
- Department of Neurology, Guys and St Thomas' Hospitals NHS Foundation Trust, UK
| | - Saif Haddad
- Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square institute of Neurology and National Hospital for Neurology and Neurosurgery
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, Department of Neuromuscular Diseases, UCL Queen Square institute of Neurology and National Hospital for Neurology and Neurosurgery
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Rudaks LI, Yeow D, Ng K, Deveson IW, Kennerson ML, Kumar KR. An Update on the Adult-Onset Hereditary Cerebellar Ataxias: Novel Genetic Causes and New Diagnostic Approaches. CEREBELLUM (LONDON, ENGLAND) 2024; 23:2152-2168. [PMID: 38760634 PMCID: PMC11489183 DOI: 10.1007/s12311-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
The hereditary cerebellar ataxias (HCAs) are rare, progressive neurologic disorders caused by variants in many different genes. Inheritance may follow autosomal dominant, autosomal recessive, X-linked or mitochondrial patterns. The list of genes associated with adult-onset cerebellar ataxia is continuously growing, with several new genes discovered in the last few years. This includes short-tandem repeat (STR) expansions in RFC1, causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS), FGF14-GAA causing spinocerebellar ataxia type 27B (SCA27B), and THAP11. In addition, the genetic basis for SCA4, has recently been identified as a STR expansion in ZFHX3. Given the large and growing number of genes, and different gene variant types, the approach to diagnostic testing for adult-onset HCA can be complex. Testing methods include targeted evaluation of STR expansions (e.g. SCAs, Friedreich ataxia, fragile X-associated tremor/ataxia syndrome, dentatorubral-pallidoluysian atrophy), next generation sequencing for conventional variants, which may include targeted gene panels, whole exome, or whole genome sequencing, followed by various potential additional tests. This review proposes a diagnostic approach for clinical testing, highlights the challenges with current testing technologies, and discusses future advances which may overcome these limitations. Implementing long-read sequencing has the potential to transform the diagnostic approach in HCA, with the overall aim to improve the diagnostic yield.
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Affiliation(s)
- Laura Ivete Rudaks
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia.
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia.
- Clinical Genetics Unit, Royal North Shore Hospital, Sydney, Australia.
| | - Dennis Yeow
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Neurodegenerative Service, Prince of Wales Hospital, Sydney, Australia
- Neuroscience Research Australia, Sydney, Australia
| | - Karl Ng
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Neurology Department, Royal North Shore Hospital, Sydney, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Marina L Kennerson
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- The Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney Local Health District, Sydney, Australia
| | - Kishore Raj Kumar
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Sydney, Australia
- Faculty of Medicine, St Vincent's Healthcare Campus, UNSW Sydney, Sydney, Australia
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8
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Morimoto M, Ryu E, Steger BJ, Dixit A, Saito Y, Yoo J, van der Ven AT, Hauser N, Steinbach PJ, Oura K, Huang AY, Kortüm F, Ninomiya S, Rosenthal EA, Robinson HK, Guegan K, Denecke J, Subramony SH, Diamonstein CJ, Ping J, Fenner M, Balton EV, Strohbehn S, Allworth A, Bamshad MJ, Gandhi M, Dipple KM, Blue EE, Jarvik GP, Lau CC, Holm IA, Weisz-Hubshman M, Solomon BD, Nelson SF, Nishino I, Adams DR, Kang S, Gahl WA, Toro C, Myung K, Malicdan MCV. Expanding the genetic and phenotypic landscape of replication factor C complex-related disorders: RFC4 deficiency is linked to a multisystemic disorder. Am J Hum Genet 2024; 111:1970-1993. [PMID: 39106866 PMCID: PMC11393705 DOI: 10.1016/j.ajhg.2024.07.008] [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: 11/20/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/09/2024] Open
Abstract
The precise regulation of DNA replication is vital for cellular division and genomic integrity. Central to this process is the replication factor C (RFC) complex, encompassing five subunits, which loads proliferating cell nuclear antigen onto DNA to facilitate the recruitment of replication and repair proteins and enhance DNA polymerase processivity. While RFC1's role in cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is known, the contributions of RFC2-5 subunits on human Mendelian disorders is largely unexplored. Our research links bi-allelic variants in RFC4, encoding a core RFC complex subunit, to an undiagnosed disorder characterized by incoordination and muscle weakness, hearing impairment, and decreased body weight. We discovered across nine affected individuals rare, conserved, predicted pathogenic variants in RFC4, all likely to disrupt the C-terminal domain indispensable for RFC complex formation. Analysis of a previously determined cryo-EM structure of RFC bound to proliferating cell nuclear antigen suggested that the variants disrupt interactions within RFC4 and/or destabilize the RFC complex. Cellular studies using RFC4-deficient HeLa cells and primary fibroblasts demonstrated decreased RFC4 protein, compromised stability of the other RFC complex subunits, and perturbed RFC complex formation. Additionally, functional studies of the RFC4 variants affirmed diminished RFC complex formation, and cell cycle studies suggested perturbation of DNA replication and cell cycle progression. Our integrated approach of combining in silico, structural, cellular, and functional analyses establishes compelling evidence that bi-allelic loss-of-function RFC4 variants contribute to the pathogenesis of this multisystemic disorder. These insights broaden our understanding of the RFC complex and its role in human health and disease.
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Affiliation(s)
- Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Benjamin J Steger
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yoshihiko Saito
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Amelie T van der Ven
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Natalie Hauser
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Peter J Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kazumasa Oura
- Division of Neurology and Gerontology, Department of Internal Medicine, School of Medicine Iwate Medical University, Morioka, Japan
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Okayama, Japan
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah K Robinson
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Katie Guegan
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Callie J Diamonstein
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark Fenner
- Nottingham University Hospital, Nottingham, UK
| | - Elsa V Balton
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sam Strohbehn
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mahi Gandhi
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Katrina M Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; University of Washington School of Public Health, Institute for Public Health Genetics, Seattle, WA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - C Christopher Lau
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Stanley F Nelson
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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9
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Palones E, Plaza V, Gonzalez-Quereda L, Segarra-Casas A, Querol L, Bertoletti F, Rodriguez MJ, Gallano P, Crespo-Lessmann A. Chronic Cough and Cerebellar Ataxia With Neuropathy and Bilateral Vestibular Areflexia Syndrome (CANVAS): Screening for Mutations in Replication Factor C Subunit 1 (RFC1). Arch Bronconeumol 2024; 60:468-474. [PMID: 38755058 DOI: 10.1016/j.arbres.2024.04.028] [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: 02/21/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION A common complaint in patients is chronic cough (CC), which may be refractory (RCC) or unexplained (UCC). Recent studies point, as a possible cause of CC, to the hereditary cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS), with an estimated carrier prevalence of 1 in 20000. AIM In patients with CC, determine the prevalence of the biallelic (AAGGG)exp mutation in replication factor C subunit 1 (RFC1) responsible for CANVAS, test the usefulness of the Rydel-Seiffer fork test, and evaluate patient quality of life (QoL). METHODS Clinical and functional data were collected for the 33 included patients undergoing CC studies in our specialized unit. Performed were an etiological study of CC following European Respiratory Society recommendations, a genetic study of RFC1 mutations, and Rydel-Seiffer fork testing to detect possible peripheral vibratory sensitivity impairment. Administered to evaluate QoL were 4 questionnaires. RESULTS Prevalence of biallelic (AAGGG)exp in RFC1 was 6.1% (n=2) overall, increasing to 7.1% in the RCC subgroup, and to 33.3% in the Rydel-Seiffer fork altered results subgroup. Prevalence of monoallelic (AAGGG)exp in RFC1 was 18.2% (n=6) overall, rising to 50.0% (n=2) in the UCC subgroup. CONCLUSION Genetic screening for (AAGGG)exp in RFC1, and also use of the Rydel-Seiffer fork test, should be considered in specialized CC consultations for patients with RCC and UCC. Detecting possible CANVAS symptoms in CC studies would identify candidates for early genetic screening, of interest in reducing the disease burden for patients and health systems alike.
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Affiliation(s)
- Esther Palones
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Respiratory Medicine, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
| | - Vicente Plaza
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Respiratory Medicine, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Lidia Gonzalez-Quereda
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain; Genetics Department, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alba Segarra-Casas
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain; Genetics Department, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Luis Querol
- Neuromuscular Disease Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Federico Bertoletti
- Department of Digestive Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - María José Rodriguez
- Genetics Department, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Pía Gallano
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain; Genetics Department, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain; Networked Biomedical Research Centre for Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Astrid Crespo-Lessmann
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain; Department of Respiratory Medicine, Institut de Recerca Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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10
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Frachet S, Chazelas P, Magy L, Cintas P, Brouquières D, Girardie P, Espagno L, Melloni B, Guilleminault L, Lia AS. Early Peripheral Nerve Involvement at the Time of Coughing in Patients With RFC1 Intronic Expansion. Neurol Genet 2024; 10:e200166. [PMID: 39507594 PMCID: PMC11271393 DOI: 10.1212/nxg.0000000000200166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/07/2024] [Indexed: 11/08/2024]
Abstract
Objectives Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome results from variations in RFC1 and is mostly caused by intronic biallelic pathogenic expansions (RE-RFC1). Refractory chronic cough (RCC) is frequently observed for years to decades preceding ataxia onset. Whether peripheral nerves are involved in the presymptomatic phase characterized by RCC is uncertain. Methods Here, patients previously screened for RCC and identified as having at least one RE-RFC1 intronic expansion underwent a comprehensive clinical and neurophysiologic assessment and were screened for additional exonic variations. Results Fourteen patients with RCC and RE-RFC1 were investigated. Seven patients presented with biallelic RE-RFC1 (Bi-RE-RFC1) while 7 presented with monoallelic RE-RFC1 (Mono-RE-RFC1). In patients with Mono-RE-RFC1, no additional exonic variation was identified, and clinical examinations were normal. Most of the patients with Bi-RE-RFC1 presented with subtle neurologic impairment, mainly exhibiting decreased lower limb vibration sense (85.7%). Nerve conduction studies revealed that all patients with Bi-RE-RFC1 exhibited lower sensory sum scores than patients with Mono-RE-RFC1 (median 20.2 µV vs 84.9 µV, p = 0.0012). In addition, the radial-to-sural sensory ratios were null or inverted (>0.5) in all patients but one with Bi-RE-RFC1, which is consistent with sensory neuronopathy. Discussion Patients with Bi-RE-RFC1 already exhibit widespread sensory neuron involvement at the time of apparently isolated RCC.
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Affiliation(s)
- Simon Frachet
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Pauline Chazelas
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Laurent Magy
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Pascal Cintas
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Danielle Brouquières
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Pierre Girardie
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Louise Espagno
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Boris Melloni
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Laurent Guilleminault
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
| | - Anne-Sophie Lia
- From the Neurology Department (S.F., L.M.), University Hospital of Limoges; UR20218-NEURIT (S.F., P. Chazelas, L.M., A.-S.L.), University of Limoges; Biochemistry and Molecular Genetic Department (P. Chazelas, A.-S.L.), University Hospital of Limoges; Neurology Department (P. Cintas, P.G.); Department of Respiratory Medicine (D.B., L.G.), University Hospital of Toulouse; Neurology Department (L.E.), Cahors Hospital; and Department of Respiratory Medicine (B.M.), University Hospital of Limoges, France
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11
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Vegezzi E, Ishiura H, Bragg DC, Pellerin D, Magrinelli F, Currò R, Facchini S, Tucci A, Hardy J, Sharma N, Danzi MC, Zuchner S, Brais B, Reilly MM, Tsuji S, Houlden H, Cortese A. Neurological disorders caused by novel non-coding repeat expansions: clinical features and differential diagnosis. Lancet Neurol 2024; 23:725-739. [PMID: 38876750 DOI: 10.1016/s1474-4422(24)00167-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 06/16/2024]
Abstract
Nucleotide repeat expansions in the human genome are a well-known cause of neurological disease. In the past decade, advances in DNA sequencing technologies have led to a better understanding of the role of non-coding DNA, that is, the DNA that is not transcribed into proteins. These techniques have also enabled the identification of pathogenic non-coding repeat expansions that cause neurological disorders. Mounting evidence shows that adult patients with familial or sporadic presentations of epilepsy, cognitive dysfunction, myopathy, neuropathy, ataxia, or movement disorders can be carriers of non-coding repeat expansions. The description of the clinical, epidemiological, and molecular features of these recently identified non-coding repeat expansion disorders should guide clinicians in the diagnosis and management of these patients, and help in the genetic counselling for patients and their families.
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Affiliation(s)
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Pellerin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Stefano Facchini
- IRCCS Mondino Foundation, Pavia, Italy; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Arianna Tucci
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - John Hardy
- Department of Neurogedengerative Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Matt C Danzi
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
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12
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Guilleminault L, Mazzone SB, Chazelas P, Frachet S, Lia AS, Magy L. Cerebellar ataxia, neuropathy and vestibular areflexia syndrome: a neurogenic cough prototype. ERJ Open Res 2024; 10:00024-2024. [PMID: 39076534 PMCID: PMC11284589 DOI: 10.1183/23120541.00024-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 07/31/2024] Open
Abstract
Chronic cough is a frequent disorder that is defined by cough of more than 8 weeks duration. Despite extensive investigation, some patients exhibit no aetiology and others do not respond to specific treatments directed against apparent causes of cough. Such patients are identified as having unexplained or refractory chronic cough. Recently, a high proportion of patients with chronic cough in the context of cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) was highlighted. CANVAS is a rare neurological disorder with a biallelic variation in the replication factor C subunit 1 (RFC1) gene corresponding mostly to an intronic AAGGG repeat expansion. Chronic cough in patients with CANVAS shares similar characteristics with cough hypersensitivity syndrome. The high prevalence of chronic cough in CANVAS gives the opportunity to better understand the neurogenic mechanism of chronic cough. In this review, we will describe the characteristics and mechanisms of CANVAS. We will also address the potential mechanisms responsible for chronic cough in CANVAS. Finally, we will address chronic cough management in the context of CANVAS.
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Affiliation(s)
- Laurent Guilleminault
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, Toulouse, France
- Department of Respiratory Medicine, Faculty of Medicine, Toulouse University Hospital, Toulouse, France
- These authors contributed equally to this work
| | - Stuart B. Mazzone
- Department of Anatomy and Physiology, University of Melbourne, Victoria, Australia
- These authors contributed equally to this work
| | - Pauline Chazelas
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France
- NeurIT-UR20218, Université de Limoges, Limoges, France
| | - Simon Frachet
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service et Laboratoire de Neurologie, Centre de Référence “Neuropathies Périphériques Rares (NNerf)”, CHU Limoges, Limoges, France
| | - Anne-Sophie Lia
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service de Bioinformatique, CHU Limoges, Limoges, France
| | - Laurent Magy
- NeurIT-UR20218, Université de Limoges, Limoges, France
- Service et Laboratoire de Neurologie, Centre de Référence “Neuropathies Périphériques Rares (NNerf)”, CHU Limoges, Limoges, France
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13
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Votsi C, Tomazou M, Nicolaou P, Pantzaris MC, Pitsas G, Adamou A, Kleopa KA, Zamba-Papanicolaou E, Christodoulou K. RFC1 Repeat Distribution in the Cypriot Population: Study of a Large Cohort of Patients With Undiagnosed Ataxia and Non-Disease Controls. Neurol Genet 2024; 10:e200149. [PMID: 38685975 PMCID: PMC11057437 DOI: 10.1212/nxg.0000000000200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/20/2024] [Indexed: 05/02/2024]
Abstract
Background and Objectives The intronic biallelic AAGGG expansion in the replication factor C subunit 1 (RFC1) gene was recently associated with a phenotype combining cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, as well as with late-onset ataxia. Following this discovery, studies in multiple populations extended the phenotypic and genotypic spectrum of this locus. Multiple benign and additional pathogenic configurations are currently known. Our main objectives were to study the prevalence of the pathogenic AAGGG expansion in the Cypriot population, to further characterize the RFC1 repeat locus allele distribution, and to search for possible novel repeat configurations. Methods Cypriot undiagnosed patients, in the majority presenting at least with cerebellar ataxia and non-neurologic disease controls, were included in this study. A combination of conventional methods was used, including standard PCR flanking the repeat region, repeat-primed PCR, long-range PCR, and Sanger sequencing. Bioinformatics analysis of already available in-house short-read whole-genome sequencing data was also performed. Results A large group of undiagnosed patients (n = 194), mainly presenting with pure ataxia or with ataxia accompanied by neuropathy or additional symptoms, as well as a group of non-disease controls (n = 100), were investigated in the current study. Our findings include the diagnosis of 10 patients homozygous for the pathogenic AAGGG expansion and a high percentage of heterozygous AAGGG carriers in both groups. The benign AAAAGn, AAAGGn, and AAGAGn configurations were also identified in our cohorts. We also report and discuss the identification of 2 recently reported novel and possibly benign repeat configurations, AAAGGGn and AAGACn, thus confirming their existence in another distinct population, and we highlight an increased frequency of the AAAGGGn in the patient group, including a single case of homozygosity. Discussion Our findings indicate the existence of genetic heterogeneity regarding the RFC1 repeat configurations and that the AAGGG pathogenic expansion is a frequent cause of ataxia in the Cypriot population.
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Affiliation(s)
- Christina Votsi
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paschalis Nicolaou
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios C Pantzaris
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Giorgos Pitsas
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Archontia Adamou
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kleopas A Kleopa
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Eleni Zamba-Papanicolaou
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyproula Christodoulou
- From the Neurogenetics Department (C.V., P.N., K.C.); Bioinformatics Department (M.T.); Neuroimmunology Department (M.C.P., G.P.); Neuroepidemiology Department (A.A.); Neuroscience Department and Center for Neuromascular Disorders (K.A.K.); and Neuroepidemiology Department and Center for Neuromascular Disorders (E.Z.-P.), The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Hisey JA, Radchenko EA, Mandel NH, McGinty R, Matos-Rodrigues G, Rastokina A, Masnovo C, Ceschi S, Hernandez A, Nussenzweig A, Mirkin S. Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures. Nucleic Acids Res 2024; 52:4361-4374. [PMID: 38381906 PMCID: PMC11077069 DOI: 10.1093/nar/gkae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | | | - Ryan J McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115, USA
| | | | | | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD20892, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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Currò R, Dominik N, Facchini S, Vegezzi E, Sullivan R, Galassi Deforie V, Fernández-Eulate G, Traschütz A, Rossi S, Garibaldi M, Kwarciany M, Taroni F, Brusco A, Good JM, Cavalcanti F, Hammans S, Ravenscroft G, Roxburgh RH, Parolin Schnekenberg R, Rugginini B, Abati E, Manini A, Quartesan I, Ghia A, Lòpez de Munaìn A, Manganelli F, Kennerson M, Santorelli FM, Infante J, Marques W, Jokela M, Murphy SM, Mandich P, Fabrizi GM, Briani C, Gosal D, Pareyson D, Ferrari A, Prados F, Yousry T, Khurana V, Kuo SH, Miller J, Troakes C, Jaunmuktane Z, Giunti P, Hartmann A, Basak N, Synofzik M, Stojkovic T, Hadjivassiliou M, Reilly MM, Houlden H, Cortese A. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 2024; 147:1887-1898. [PMID: 38193360 PMCID: PMC11068103 DOI: 10.1093/brain/awad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson's coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P < 0.001; larger allele HR = 1.53, P < 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P < 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P < 0.001; larger allele HR = 1.60; P < 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P < 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I-V β = -1.06, P < 0.001; lobules VI-VII β = -0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
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Affiliation(s)
- Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stefano Facchini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Gorka Fernández-Eulate
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Andreas Traschütz
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Salvatore Rossi
- Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Facoltà di Medicina e Chirurgia, Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Center, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sant'Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdańsk, 80-952 Gdańsk, Poland
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy
| | - Simon Hammans
- Wessex Neurological Centre, Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedland, WA 6009, Australia
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, New Zealand and the Centre for Brain Research, University of Auckland, Auckland 1142, New Zealand
| | | | - Bianca Rugginini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Arianna Manini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Arianna Ghia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Adolfo Lòpez de Munaìn
- Neurology Department, Donostia University Hospital, University of the Basque Country-Osakidetza-CIBERNED-Biodonostia, 20014 Donostia-San Sebastián, Spain
| | - Fiore Manganelli
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Marina Kennerson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, 56128 Pisa, Italy
| | - Jon Infante
- University Hospital Marquès de Valdecilla-IDIVAL, University of Cantabria, 39008 Santander, Spain
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University of São Paulo, 2650 Ribeirão Preto, Brazil
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland
- Neurocenter, Department of Neurology, Clinical Neurosciences, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino-UOC Genetica Medica, 16132 Genova, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Chiara Briani
- Department of Neurosciences, ERN Neuromuscular Unit, University of Padova, 35100 Padova, Italy
| | - David Gosal
- Manchester Centre for Clinical Neurosciences, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Greater Manchester, M6 8HD, UK
| | - Davide Pareyson
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Ferran Prados
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, WC1V 6LJ, UK
- NMR Research Unit, Institute of Neurology, University College London (UCL), London, WC1N 3BG, UK
- e-Health Centre, Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Tarek Yousry
- Neuroradiological Academic Unit, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James Miller
- Department of Neurology, Royal Victoria Hospitals, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE21 8EA, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paola Giunti
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Annette Hartmann
- Division of General Psychiatry, Medical University of Vienna, 1090 Vienna, Austria
| | - Nazli Basak
- Koç University, School of Medicine, Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine, 34010 Istanbul, Turkey
| | - Matthis Synofzik
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Tanya Stojkovic
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, S10 2JF, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
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16
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Delforge V, Tard C, Davion JB, Dujardin K, Wissocq A, Dhaenens CM, Mutez E, Huin V. RFC1: Motifs and phenotypes. Rev Neurol (Paris) 2024; 180:393-409. [PMID: 38627134 DOI: 10.1016/j.neurol.2024.03.006] [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: 01/30/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 05/28/2024]
Abstract
Biallelic intronic expansions (AAGGG)exp in intron 2 of the RFC1 gene have been shown to be a common cause of late-onset ataxia. Since their first description, the phenotypes, neurological damage, and pathogenic variants associated with the RFC1 gene have been frequently updated. Here, we review the various motifs, genetic variants, and phenotypes associated with the RFC1 gene. We searched PubMed for scientific articles published between March 1st, 2019, and January 15th, 2024. The motifs and phenotypes associated with the RFC1 gene are highly heterogeneous, making molecular diagnosis and clinical screening and investigation challenging. In this review we will provide clues to give a better understanding of RFC1 disease. We briefly discuss new methods for molecular diagnosis, the origin of cough in RFC1 disease, and research perspectives.
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Affiliation(s)
- V Delforge
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France
| | - C Tard
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Neurology and Movement disorders, CHU de Lille, 59000 Lille, France
| | - J-B Davion
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Neurology and Movement disorders, CHU de Lille, 59000 Lille, France
| | - K Dujardin
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Neurology and Movement disorders, CHU de Lille, 59000 Lille, France
| | - A Wissocq
- Department of Toxicology and Genopathies, UF Neurobiology, CHU de Lille, 59000 Lille, France
| | - C-M Dhaenens
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Toxicology and Genopathies, UF Neurobiology, CHU de Lille, 59000 Lille, France
| | - E Mutez
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Neurology and Movement disorders, CHU de Lille, 59000 Lille, France
| | - V Huin
- Inserm, U1172 - LilNCog - Lille Neuroscience & Cognition, CHU de Lille, University Lille, 59000 Lille, France; Department of Toxicology and Genopathies, UF Neurobiology, CHU de Lille, 59000 Lille, France.
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17
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Wang Y, Wang J, Yan Z, Hou J, Wan L, Yang Y, Liu Y, Yi J, Guo P, Han D. Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS. Nucleic Acids Res 2024; 52:2698-2710. [PMID: 38266156 PMCID: PMC10954463 DOI: 10.1093/nar/gkae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.
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Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, Tianjin University, Tianjin 300350, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jie Yi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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18
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Wada T, Doi H, Okubo M, Tada M, Ueda N, Suzuki H, Tominaga W, Koike H, Komiya H, Kubota S, Hashiguchi S, Nakamura H, Takahashi K, Kunii M, Tanaka K, Miyaji Y, Higashiyama Y, Koshimizu E, Miyatake S, Katsuno M, Fujii S, Takahashi H, Matsumoto N, Takeuchi H, Tanaka F. RNA Foci in Two bi-Allelic RFC1 Expansion Carriers. Ann Neurol 2024; 95:607-613. [PMID: 38062616 DOI: 10.1002/ana.26848] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
Cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) is a late-onset, autosomal recessive neurodegenerative disorder caused by biallelic AAGGG/ACAGG repeat expansion (AAGGG-exp/ACAGG-exp) in RFC1. The recent identification of patients with CANVAS exhibiting compound heterozygosity for AAGGG-exp and truncating variants supports the loss-of-function of RFC1 in CANVAS patients. We investigated the pathological changes in 2 autopsied patients with CANVAS harboring biallelic ACAGG-exp and AAGGG-exp. RNA fluorescence in situ hybridization of the 2 patients revealed CCTGT- and CCCTT-containing RNA foci, respectively, in neuronal nuclei of tissues with neuronal loss. Our findings suggest that RNA toxicity may be involved in the pathogenesis of CANVAS. ANN NEUROL 2024;95:607-613.
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Affiliation(s)
- Taishi Wada
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaki Okubo
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mikiko Tada
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naohisa Ueda
- Department of Neurology, Yokohama City University Medical Center, Yokohama, Japan
| | - Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Wakana Tominaga
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Haruki Koike
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyasu Komiya
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shun Kubota
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shunta Hashiguchi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Haruko Nakamura
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keita Takahashi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Misako Kunii
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kenichi Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yosuke Miyaji
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuichi Higashiyama
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Fujii
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Yokohama, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideyuki Takeuchi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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19
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Palones E, Curto E, Plaza V, Gonzalez-Quereda L, Segarra-Casas A, Querol L, Bertoletti F, Rodriguez MJ, Gallano P, Crespo-Lessmann A. Clinical and functional characteristics, possible causes, and impact of chronic cough in patients with cerebellar ataxia, neuropathy, and bilateral vestibular areflexia syndrome (CANVAS). J Neurol 2024; 271:1204-1212. [PMID: 37917234 PMCID: PMC10896788 DOI: 10.1007/s00415-023-12001-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 11/04/2023]
Abstract
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is an hereditary autosomal recessive disease. Recent studies propose including chronic cough (CC) as a symptom of CANVAS. For 10 patients with CANVAS as genetically confirmed by biallelic expansion of the AAGG repeat motif (AAGGGexp) in intron 2 of replication factor C subunit 1 (RFC1), our aim was, as a multidisciplinary team, to describe clinical and functional characteristics and possible causes of CC following European Respiratory Society (ERS) recommendations, and to evaluate CC impact on quality of life (QoL) using self-administered questionnaires (Cough Severity Diary, Leicester Cough Questionnaire, Discrete Emotions Questionnaire, and EQ-5D-5L). In all 10 patients, the CC was a dry cough that developed several years prior to the neurological symptoms (mean 14.2 years); 7 patients had symptoms compatible with gastroesophageal reflux (GER), 5 with pathological GER diagnosed by 24-h esophageal pH testing, and 6 patients had impaired esophageal motility diagnosed by high-resolution esophageal manometry, most frequently ineffective peristalsis. Although further studies are required for confirmation, we conclude that CC may be a characteristic prodrome of CANVAS and may be related to GER and esophageal disorders. Furthermore, CC affects patients' QoL, especially in the psychosocial sphere.
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Affiliation(s)
- Esther Palones
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Respiratory Medicine, Sant Pau Biomedical Research Institute (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
| | - Elena Curto
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Respiratory Medicine, Sant Pau Biomedical Research Institute (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Vicente Plaza
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Respiratory Medicine, Sant Pau Biomedical Research Institute (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Lidia Gonzalez-Quereda
- Genetics Department, Institute of Biomedical Research Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alba Segarra-Casas
- Genetics Department, Institute of Biomedical Research Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Querol
- Neuromuscular Disease Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Federico Bertoletti
- Department of Digestive Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - María José Rodriguez
- Genetics Department, Institute of Biomedical Research Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Pía Gallano
- Genetics Department, Institute of Biomedical Research Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Networked Biomedical Research Centre for Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Astrid Crespo-Lessmann
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Respiratory Medicine, Sant Pau Biomedical Research Institute (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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20
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Turner RD, Hirons B, Cortese A, Birring SS. Chronic Cough as a Genetic Neurological Disorder? Insights from Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome (CANVAS). Lung 2023; 201:511-519. [PMID: 37979058 PMCID: PMC10673766 DOI: 10.1007/s00408-023-00660-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Chronic cough is common, and in many cases unexplained or refractory to otherwise effective treatment of associated medical conditions. Cough hypersensitivity has developed as a paradigm that helps to explain clinical and research observations that frequently point towards chronic cough as a neuropathic disorder. Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recently described neurological condition whose clinical features include gait ataxia, unsteadiness, peripheral neuropathy, and autonomic dysfunction. Chronic cough is also a common feature of the syndrome, with features of hypersensitivity, often preceding core neurological symptoms by up to 30 years or more. The genetic basis in a majority of cases of CANVAS appears to be biallelic variable repeat intron expansion sequences within RFC1, a gene normally involved in the regulation of DNA replication and repair. The same polymorphism has now been identified at an increased frequency in patients with unexplained or refractory chronic cough in the absence of defining clinical features of CANVAS. This review expands on these points, aiming to increase the awareness of CANVAS amongst clinicians and researchers working with chronic cough. We discuss the implications of a link between RFC1 disease and cough. Improved understanding of CANVAS may lead to an enhanced grasp of the pathophysiology of chronic cough, and new approaches to antitussive treatments.
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Affiliation(s)
- Richard D Turner
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, QLD, Australia.
- School of Medicine and Dentistry, Griffith University, Southport, QLD, Australia.
| | - Barnaby Hirons
- Department of Respiratory Medicine, King's College Hospital, London, UK
- Centre for Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
- Department of Brain and Behaviour Sciences, University of Pavia, Pavia, Italy
| | - Surinder S Birring
- Department of Respiratory Medicine, King's College Hospital, London, UK
- Centre for Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, King's College London, London, UK
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21
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Dominik N, Magri S, Currò R, Abati E, Facchini S, Corbetta M, Macpherson H, Di Bella D, Sarto E, Stevanovski I, Chintalaphani SR, Akcimen F, Manini A, Vegezzi E, Quartesan I, Montgomery KA, Pirota V, Crespan E, Perini C, Grupelli GP, Tomaselli PJ, Marques W, Shaw J, Polke J, Salsano E, Fenu S, Pareyson D, Pisciotta C, Tofaris GK, Nemeth AH, Ealing J, Radunovic A, Kearney S, Kumar KR, Vucic S, Kennerson M, Reilly MM, Houlden H, Deveson I, Tucci A, Taroni F, Cortese A. Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis. Brain 2023; 146:5060-5069. [PMID: 37450567 PMCID: PMC10689911 DOI: 10.1093/brain/awad240] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing data from nearly 10 000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n = 6 from five families), AAGGC (n = 2 from one family) and AGAGG (n = 1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, we revealed a pathogenic role for large AAAGG repeat configuration expansions (n = 5). Long-read sequencing was used to characterize the entire repeat sequence, and six patients exhibited a pure AGGGC expansion, while the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs appeared to have arisen from a common haplotype and were predicted to form highly stable G quadruplexes, which have previously been demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions when the AAAGG motif is very large (>500 repeats) or the AAGGG motif is interrupted. Accurate sizing and full sequencing of the satellite repeat with long-read sequencing is recommended in clinically selected cases to enable accurate molecular diagnosis and counsel patients and their families.
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Affiliation(s)
- Natalia Dominik
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Riccardo Currò
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
| | - Stefano Facchini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- IRCCS Mondino Foundation, Pavia 27100,
Italy
| | - Marinella Corbetta
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Hannah Macpherson
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Elisa Sarto
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Sanjog R Chintalaphani
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Fulya Akcimen
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, MD 2292, USA
| | - Arianna Manini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto
Auxologico Italiano, Milan 20145, Italy
| | | | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Kylie-Ann Montgomery
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Valentina Pirota
- Department of Chemistry, University of Pavia,
Pavia 27100, Italy
- G4-INTERACT, USERN, 27100 Pavia,
Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Glenda Paola Grupelli
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Pedro J Tomaselli
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Joseph Shaw
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - James Polke
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ettore Salsano
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Silvia Fenu
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Davide Pareyson
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Chiara Pisciotta
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - George K Tofaris
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS
Foundation Trust, Oxford OX3 7HE, UK
| | - John Ealing
- Salford Royal NHS Foundation Trust Greater Manchester Neuroscience Centre,
Manchester Centre for Clinical Neurosciences Salford, Greater
Manchester M6 8HD, UK
| | | | - Seamus Kearney
- Department of Neurology, Royal Victoria Hospital,
Belfast BT12 6BA, UK
| | - Kishore R Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical
Research, Darlinghurst, NSW 2010, Australia
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
| | - Steve Vucic
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
- Brain and Nerve Research Centre, Concord Hospital,
Sydney, NSW 2139, Australia
| | - Marina Kennerson
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute
SLHD, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2050, Australia
| | - Mary M Reilly
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ira Deveson
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
| | - Arianna Tucci
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Andrea Cortese
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
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22
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Facchini S, Dominik N, Manini A, Efthymiou S, Currò R, Rugginini B, Vegezzi E, Quartesan I, Perrone B, Kutty SK, Galassi Deforie V, Schnekenberg RP, Abati E, Pichiecchio A, Valente EM, Tassorelli C, Reilly MM, Houlden H, Bugiardini E, Cortese A. Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions. Biomolecules 2023; 13:1546. [PMID: 37892228 PMCID: PMC10605474 DOI: 10.3390/biom13101546] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/13/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions is based on Southern Blotting (SB), a time-consuming and a relatively imprecise technique. In this paper, we compare SB with Optical Genome Mapping (OGM), a method for detecting Structural Variants (SVs) based on the measurement of distances between fluorescently labelled probes, for the diagnosis of RFC1 CANVAS and disease spectrum. The two methods are applied to 17 CANVAS patients' blood samples and resulting sizes compared, showing a good agreement. Further, long-read sequencing is used for two patients to investigate the agreement of sizes with either SB or OGM. Our study concludes that OGM represents a viable alternative to SB, allowing for a simpler technique, a more precise sizing of the expansion and ability to expand analysis of SV in the entire genome as opposed to SB which is a locus specific method.
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Affiliation(s)
- Stefano Facchini
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Natalia Dominik
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Arianna Manini
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, 20149 Milan, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Riccardo Currò
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Bianca Rugginini
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elisa Vegezzi
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
| | - Ilaria Quartesan
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Benedetta Perrone
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Shahedah Koya Kutty
- Department of Internal Medicine, Kulliyah of Medicine, International Islamic University Malaysia (IIUM), Pahang 53100, Malaysia;
| | - Valentina Galassi Deforie
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Ricardo P. Schnekenberg
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Anna Pichiecchio
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Enza Maria Valente
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Cristina Tassorelli
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (I.Q.); (A.P.); (E.M.V.); (C.T.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Mary M. Reilly
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
| | - Andrea Cortese
- Department of Neuromuscular Diseases, University College London, London WC1N 3BG, UK; (N.D.); (A.M.); (S.E.); (R.C.); (B.R.); (B.P.); (V.G.D.); (R.P.S.); (E.A.); (M.M.R.); (H.H.); (E.B.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
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23
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Traschütz A, Heindl F, Bilal M, Hartmann AM, Dufke C, Riess O, Zwergal A, Rujescu D, Haack T, Synofzik M, Strupp M. Frequency and Phenotype of RFC1 Repeat Expansions in Bilateral Vestibulopathy. Neurology 2023; 101:e1001-e1013. [PMID: 37460231 PMCID: PMC10491447 DOI: 10.1212/wnl.0000000000207553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Bilateral vestibulopathy (BVP) is a chronic debilitating neurologic disorder with no monogenic cause established so far despite familiar presentations. We hypothesized that replication factor complex subunit 1 (RFC1) repeat expansions might present a recurrent monogenic cause of BVP. METHODS The study involved RFC1 screening and in-depth neurologic, vestibulo-oculomotor, and disease evolution phenotyping of 168 consecutive patients with idiopathic at least "probable BVP" from a tertiary referral center for balance disorders, with127 of them meeting current diagnostic criteria of BVP (Bárány Society Classification). RESULTS Biallelic AAGGG repeat expansions in RFC1 were identified in 10/127 patients (8%) with BVP and 1/41 with probable BVP. Heterozygous expansions in 10/127 patients were enriched compared with those in reference populations. RFC1-related BVP manifested at a median age of 60 years (range 34-72 years) and co-occurred predominantly with mild polyneuropathy (10/11). Additional cerebellar involvement (7/11) was subtle and limited to oculomotor signs in early stages, below recognition of classic cerebellar ataxia, neuropathy, and vestibular areflexia syndrome. Clear dysarthria, appendicular ataxia, or cerebellar atrophy developed 6-8 years after onset. Dysarthria, absent patellar reflexes, and downbeat nystagmus best discriminated RFC1-positive BVP from RFC1-negative BVP, but neither sensory symptoms nor fine motor problems. Video head impulse gains of patients with RFC1-positive BVP were lower relative to those of patients with RFC1-negative BVP and decreased until 10 years disease duration, indicating a potential progression and outcome marker for RFC1-disease. DISCUSSION This study identifies RFC1 as the first-and frequent-monogenic cause of BVP. It characterizes RFC1-related BVP as part of the multisystemic evolution of RFC1 spectrum disease, with implications for designing natural history studies and future treatment trials. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that RFC1 repeat expansions cause BVP.
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Affiliation(s)
- Andreas Traschütz
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Felix Heindl
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Muhammad Bilal
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Annette M Hartmann
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Claudia Dufke
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Olaf Riess
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Andreas Zwergal
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Dan Rujescu
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Tobias Haack
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Matthis Synofzik
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany
| | - Michael Strupp
- From the Research Division Translational Genomics of Neurodegenerative Diseases (A.T., M. Synofzik), Hertie-Institute for Clinical Brain Research and Center of Neurology, and German Center for Neurodegenerative Diseases (DZNE) (A.T., M. Synofzik), University of Tübingen; Department of Neurology and German Center for Vertigo and Balance Disorders (F.H., A.Z., M. Strupp), University Hospital, Ludwig-Maximilians University, Munich, Germany; Department of Biochemistry (M.B.), Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan; Institute of Medical Genetics and Applied Genomics (A.M.H., D.R.), University of Tübingen, Germany; Department of Psychiatry and Psychotherapy (M.B., C.D., O.R., T.H.), Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria; and Center for Rare Diseases (C.D., O.R., T.H.), University of Tübingen, Germany.
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24
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Hisey JA, Radchenko EA, Ceschi S, Rastokina A, Mandel NH, McGinty RJ, Matos-Rodrigues G, Hernandez A, Nussenzweig A, Mirkin SM. Pathogenic CANVAS (AAGGG) n repeats stall DNA replication due to the formation of alternative DNA structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550509. [PMID: 37546920 PMCID: PMC10402041 DOI: 10.1101/2023.07.25.550509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the main pathogenic (A2G3)n and the main nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in supercoiled DNA reveals triplex H-DNA formation by the pathogenic repeat. Consistently, bioinformatic analysis of the S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs in vivo. Finally, the pathogenic, but not the non-pathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A. Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | | | - Ryan J. McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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25
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Scriba CK, Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ghaoui R, Ghia D, Henderson RD, Jordan N, Winkel A, Lamont PJ, Rodrigues MJ, Roxburgh RH, Weisburd B, Laing NG, Deveson IW, Davis MR, Ravenscroft G. RFC1 in an Australasian neurological disease cohort: extending the genetic heterogeneity and implications for diagnostics. Brain Commun 2023; 5:fcad208. [PMID: 37621409 PMCID: PMC10445415 DOI: 10.1093/braincomms/fcad208] [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: 02/01/2023] [Revised: 06/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome is a progressive, generally late-onset, neurological disorder associated with biallelic pentanucleotide expansions in Intron 2 of the RFC1 gene. The locus exhibits substantial genetic variability, with multiple pathogenic and benign pentanucleotide repeat alleles previously identified. To determine the contribution of pathogenic RFC1 expansions to neurological disease within an Australasian cohort and further investigate the heterogeneity exhibited at the locus, a combination of flanking and repeat-primed PCR was used to screen a cohort of 242 Australasian patients with neurological disease. Patients whose data indicated large gaps within expanded alleles following repeat-primed PCR, underwent targeted long-read sequencing to identify novel repeat motifs at the locus. To increase diagnostic yield, additional probes at the RFC1 repeat region were incorporated into the PathWest diagnostic laboratory targeted neurological disease gene panel to enable first-pass screening of the locus for all samples tested on the panel. Within the Australasian cohort, we detected known pathogenic biallelic expansions in 15.3% (n = 37) of patients. Thirty indicated biallelic AAGGG expansions, two had biallelic 'Māori alleles' [(AAAGG)exp(AAGGG)exp], two samples were compound heterozygous for the Māori allele and an AAGGG expansion, two samples had biallelic ACAGG expansions and one sample was compound heterozygous for the ACAGG and AAGGG expansions. Forty-five samples tested indicated the presence of biallelic expansions not known to be pathogenic. A large proportion (84%) showed complex interrupted patterns following repeat-primed PCR, suggesting that these expansions are likely to be comprised of more than one repeat motif, including previously unknown repeats. Using targeted long-read sequencing, we identified three novel repeat motifs in expanded alleles. Here, we also show that short-read sequencing can be used to reliably screen for the presence or absence of biallelic RFC1 expansions in all samples tested using the PathWest targeted neurological disease gene panel. Our results show that RFC1 pathogenic expansions make a substantial contribution to neurological disease in the Australasian population and further extend the heterogeneity of the locus. To accommodate the increased complexity, we outline a multi-step workflow utilizing both targeted short- and long-read sequencing to achieve a definitive genotype and provide accurate diagnoses for patients.
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Affiliation(s)
- Carolin K Scriba
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Sanjog R Chintalaphani
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Roula Ghaoui
- Department of Neurology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Darshan Ghia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
- Neurology and Stroke Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Robert D Henderson
- Centre for Clinical Research, University of Queensland, Herston, QLD 4006, Australia
| | - Nerissa Jordan
- Department of Neurology, Fiona Stanley Hospital, Perth, WA 6150, Australia
| | - Antony Winkel
- Department of Neurosciences, Griffith University, Sunshine Coast University Hospital, Mount Gravatt, QLD 4111, Australia
| | | | | | - Richard H Roxburgh
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nigel G Laing
- Preventive Genetics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Mark R Davis
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Gianina Ravenscroft
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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26
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Guilleminault L, Chazelas P, Melloni B, Magdelaine C, Villeneuve T, Brouquières D, Lia AS, Magy L. Repeat Expansions of RFC1 in Refractory Chronic Cough: A Missing Piece of the Puzzle? Chest 2022; 163:911-915. [PMID: 36403641 DOI: 10.1016/j.chest.2022.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Laurent Guilleminault
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, Toulouse, France; Department of Respiratory Medicine, Toulouse University Hospital, Faculty of Medicine, Toulouse, France.
| | - Pauline Chazelas
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France; NeurIT-UR20218, Université de Limoges, Limoges, France
| | - Boris Melloni
- Department of Respiratory Diseases, CHU Limoges, Dupuytren 2, Limoges, France
| | | | - Thomas Villeneuve
- Department of Respiratory Medicine, Toulouse University Hospital, Faculty of Medicine, Toulouse, France
| | - Danielle Brouquières
- Department of Respiratory Medicine, Toulouse University Hospital, Faculty of Medicine, Toulouse, France
| | - Anne-Sophie Lia
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France; NeurIT-UR20218, Université de Limoges, Limoges, France; Service de Bioinformatique-CHU Limoges, Limoges, France
| | - Laurent Magy
- Service de Biochimie et Génétique Moléculaire, CHU Limoges, Limoges, France; NeurIT-UR20218, Université de Limoges, Limoges, France; Service et Laboratoire de Neurologie, Centre de Référence Neuropathies Périphériques Rares, NNerf, CHU Limoges, Limoges, France
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