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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 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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2
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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) 2024:10.1007/s12311-024-01735-5. [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] [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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3
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Record CJ, Pipis M, Skorupinska M, Blake J, Poh R, Polke JM, Eggleton K, Nanji T, Zuchner S, Cortese A, Houlden H, Rossor AM, Laura M, Reilly MM. Whole genome sequencing increases the diagnostic rate in Charcot-Marie-Tooth disease. Brain 2024; 147:3144-3156. [PMID: 38481354 PMCID: PMC11370804 DOI: 10.1093/brain/awae064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 09/04/2024] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most common and genetically heterogeneous inherited neurological diseases, with more than 130 disease-causing genes. Whole genome sequencing (WGS) has improved diagnosis across genetic diseases, but the diagnostic impact in CMT is yet to be fully reported. We present the diagnostic results from a single specialist inherited neuropathy centre, including the impact of WGS diagnostic testing. Patients were assessed at our specialist inherited neuropathy centre from 2009 to 2023. Genetic testing was performed using single gene testing, next-generation sequencing targeted panels, research whole exome sequencing and WGS and, latterly, WGS through the UK National Health Service. Variants were assessed using the American College of Medical Genetics and Genomics and Association for Clinical Genomic Science criteria. Excluding patients with hereditary ATTR amyloidosis, 1515 patients with a clinical diagnosis of CMT and related disorders were recruited. In summary, 621 patients had CMT1 (41.0%), 294 CMT2 (19.4%), 205 intermediate CMT (CMTi, 13.5%), 139 hereditary motor neuropathy (HMN, 9.2%), 93 hereditary sensory neuropathy (HSN, 6.1%), 38 sensory ataxic neuropathy (2.5%), 72 hereditary neuropathy with liability to pressure palsies (HNPP, 4.8%) and 53 'complex' neuropathy (3.5%). Overall, a genetic diagnosis was reached in 76.9% (1165/1515). A diagnosis was most likely in CMT1 (96.8%, 601/621), followed by CMTi (81.0%, 166/205) and then HSN (69.9%, 65/93). Diagnostic rates remained less than 50% in CMT2, HMN and complex neuropathies. The most common genetic diagnosis was PMP22 duplication (CMT1A; 505/1165, 43.3%), then GJB1 (CMTX1; 151/1165, 13.0%), PMP22 deletion (HNPP; 72/1165, 6.2%) and MFN2 (CMT2A; 46/1165, 3.9%). We recruited 233 cases to the UK 100 000 Genomes Project (100KGP), of which 74 (31.8%) achieved a diagnosis; 28 had been otherwise diagnosed since recruitment, leaving a true diagnostic rate of WGS through the 100KGP of 19.7% (46/233). However, almost half of the solved cases (35/74) received a negative report from the study, and the diagnosis was made through our research access to the WGS data. The overall diagnostic uplift of WGS for the entire cohort was 3.5%. Our diagnostic rate is the highest reported from a single centre and has benefitted from the use of WGS, particularly access to the raw data. However, almost one-quarter of all cases remain unsolved, and a new reference genome and novel technologies will be important to narrow the 'diagnostic gap'.
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Affiliation(s)
- Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Menelaos Pipis
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mariola Skorupinska
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Julian Blake
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK
| | - Roy Poh
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - James M Polke
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Kelly Eggleton
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Tina Nanji
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrea Cortese
- 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
| | - Alexander M Rossor
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Matilde Laura
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
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4
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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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5
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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) 2024:10.1007/s12311-024-01703-z. [PMID: 38760634 DOI: 10.1007/s12311-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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6
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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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7
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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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8
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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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9
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Park J, Sturm M, Seibel-Kelemen O, Ossowski S, Haack TB. Lessons Learned from Translating Genome Sequencing to Clinical Routine: Understanding the Accuracy of a Diagnostic Pipeline. Genes (Basel) 2024; 15:136. [PMID: 38275617 PMCID: PMC10815474 DOI: 10.3390/genes15010136] [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: 12/20/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The potential of genome sequencing (GS), which allows detection of almost all types of genetic variation across nearly the entire genome of an individual, greatly expands the possibility for diagnosing genetic disorders. The opportunities provided with this single test are enticing to researchers and clinicians worldwide for human genetic research as well as clinical application. Multiple studies have highlighted the advantages of GS for genetic variant discovery, emphasizing its added value for routine clinical use. We have implemented GS as first-line genetic testing for patients with rare diseases. Here, we report on our experiences in establishing GS as a reliable diagnostic method for almost all types of genetic disorders, from validating diagnostic accuracy of sequencing pipelines to clinical implementation in routine practice.
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Affiliation(s)
- Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; (J.P.); (O.S.-K.); (S.O.)
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; (J.P.); (O.S.-K.); (S.O.)
| | - Olga Seibel-Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; (J.P.); (O.S.-K.); (S.O.)
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; (J.P.); (O.S.-K.); (S.O.)
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; (J.P.); (O.S.-K.); (S.O.)
- Center for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
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10
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Tyagi N, Uppili B, Sharma P, Parveen S, Saifi S, Jain A, Sonakar A, Ahmed I, Sahni S, Shamim U, Anand A, Suroliya V, Asokachandran V, Srivastava A, Sivasubbu S, Scaria V, Faruq M. Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort. Neurogenetics 2024; 25:13-25. [PMID: 37917284 DOI: 10.1007/s10048-023-00736-6] [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: 06/02/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
An intronic bi-allelic pentanucleotide repeat expansion mutation, (AAGGG)400-2000, at AAAAG repeat locus in RFC1 gene, is known as underlying genetic cause in cases with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and late-onset sporadic ataxia. Biallelic positive cases carry a common recessive risk haplotype, "AAGA," spanning RFC1 gene. In this study, our aim is to find prevalence of bi-allelic (AAGGG)exp in Indian ataxia and other neurological disorders and investigate the complexity of RFC1 repeat locus and its potential association with neurodegenerative diseases in Indian population-based cohorts. We carried out repeat number and repeat type estimation using flanking PCR and repeat primed PCR (AAAAG/AAAGG/AAGGG) in four Indian disease cohorts and healthy controls. Haplotype assessment of suspected cases was done by genotyping and confirmed by Sanger sequencing. Blood samples and consent of all the cases and detailed clinical details of positive cases were collected in collaboration with A.I.I.M.S. Furthermore, comprehension of RFC1 repeat locus and risk haplotype analysis in Indian background was performed on the NGS data of Indian healthy controls by ExpansionHunter, ExpansionHunter Denovo, and PHASE analysis, respectively. Genetic screening of RFC1-TNR locus in 1998 uncharacterized cases (SCA12: 87; uncharacterized ataxia: 1818, CMT: 93) and 564 heterogenous controls showed that the frequency of subjects with bi-allelic (AAGGG)exp are 1.15%, < 0.05%, 2.15%, and 0% respectively. Two RFC1 positive sporadic late-onset ataxia cases, one bi-allelic (AAGGG)exp and another, (AAAGG)~700/(AAGGG)exp, had recessive risk haplotype and CANVAS symptoms. Long normal alleles, 15-27, are significantly rare in ataxia cohort. In IndiGen control population (IndiGen; N = 1029), long normal repeat range, 15-27, is significantly associated with A3G3 and some rare repeat motifs, AGAGG, AACGG, AAGAG, and AAGGC. Risk-associated "AAGA" haplotype of the original pathogenic expansion of A2G3 was found associated with the A3G3 representing alleles in background population. Apart from bi-allelic (AAGGG)exp, we report cases with a new pathogenic expansion of (AAAGG)exp/(AAGGG)exp in RFC1 and recessive risk haplotype. We found different repeat motifs at RFC1 TNR locus, like AAAAG, AAAGG, AAAGGG, AAAAGG, AAGAG, AACGG, AAGGC, AGAGG, and AAGGG, in Indian background population except ACAGG and (AAAGG)n/(AAGGG)n. Our findings will help in further understanding the role of long normal repeat size and different repeat motifs, specifically AAAGG, AAAGGG, and other rare repeat motifs, at the RFC1 locus.
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Affiliation(s)
- Nishu Tyagi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bharathram Uppili
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pooja Sharma
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shaista Parveen
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Sheeba Saifi
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Abhinav Jain
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akhilesh Sonakar
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Istaq Ahmed
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Shweta Sahni
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Uzma Shamim
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Avni Anand
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Varun Suroliya
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Vivekanand Asokachandran
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Achal Srivastava
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences (AIIMS), 110608, New Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Vinod Scaria
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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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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