1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Mohren L, Erdlenbruch F, Leitão E, Kilpert F, Hönes GS, Kaya S, Schröder C, Thieme A, Sturm M, Park J, Schlüter A, Ruiz M, Morales de la Prida M, Casasnovas C, Becker K, Roggenbuck U, Pechlivanis S, Kaiser FJ, Synofzik M, Wirth T, Anheim M, Haack TB, Lockhart PJ, Jöckel KH, Pujol A, Klebe S, Timmann D, Depienne C. Identification and characterisation of pathogenic and non-pathogenic FGF14 repeat expansions. Nat Commun 2024; 15:7665. [PMID: 39227614 PMCID: PMC11372089 DOI: 10.1038/s41467-024-52148-1] [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: 02/08/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024] Open
Abstract
Repeat expansions in FGF14 cause autosomal dominant late-onset cerebellar ataxia (SCA27B) with estimated pathogenic thresholds of 250 (incomplete penetrance) and 300 AAG repeats (full penetrance), but the sequence of pathogenic and non-pathogenic expansions remains unexplored. Here, we demonstrate that STRling and ExpansionHunter accurately detect FGF14 expansions from short-read genome data using outlier approaches. By combining long-range PCR and nanopore sequencing in 169 patients with cerebellar ataxia and 802 controls, we compare FGF14 expansion alleles, including interruptions and flanking regions. Uninterrupted AAG expansions are significantly enriched in patients with ataxia from a lower threshold (180-200 repeats) than previously reported based on expansion size alone. Conversely, AAGGAG hexameric expansions are equally frequent in patients and controls. Distinct 5' flanking regions, interruptions and pre-repeat sequences correlate with repeat size. Furthermore, pure AAG (pathogenic) and AAGGAG (non-pathogenic) repeats form different secondary structures. Regardless of expansion size, SCA27B is a recognizable clinical entity characterized by frequent episodic ataxia and downbeat nystagmus, similar to the presentation observed in a family with a previously unreported nonsense variant (SCA27A). Overall, this study suggests that SCA27B is a major overlooked cause of adult-onset ataxia, accounting for 23-31% of unsolved patients. We strongly recommend re-evaluating pathogenic thresholds and integrating expansion sequencing into the molecular diagnostic process.
Collapse
Affiliation(s)
- Lars Mohren
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Friedrich Erdlenbruch
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Fabian Kilpert
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - G Sebastian Hönes
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andreas Thieme
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Moisés Morales de la Prida
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- Neuromuscular Unit, Neurology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- Neuromuscular Unit, Neurology Department, Bellvitge University Hospital, Barcelona, Spain
| | - Kerstin Becker
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Ulla Roggenbuck
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
| | - Matthis Synofzik
- Division Translational Genomics of Neurodegenerative Diseases, Center for Neurology & Hertie Institute for Clinical Brain Research Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Thomas Wirth
- Service de Neurologie, Département de Neurologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 1, Avenue Molière, Strasbourg, Cedex, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Mathieu Anheim
- Service de Neurologie, Département de Neurologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, 1, Avenue Molière, Strasbourg, Cedex, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stephan Klebe
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| |
Collapse
|
3
|
Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
Collapse
Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| |
Collapse
|
4
|
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 2024:10.1007/s12035-024-04307-0. [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] [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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Pilotto F, Del Bondio A, Puccio H. Hereditary Ataxias: From Bench to Clinic, Where Do We Stand? Cells 2024; 13:319. [PMID: 38391932 PMCID: PMC10886822 DOI: 10.3390/cells13040319] [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: 12/01/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
Cerebellar ataxias are a wide heterogeneous group of movement disorders. Within this broad umbrella of diseases, there are both genetics and sporadic forms. The clinical presentation of these conditions can exhibit a diverse range of symptoms across different age groups, spanning from pure cerebellar manifestations to sensory ataxia and multisystemic diseases. Over the last few decades, advancements in our understanding of genetics and molecular pathophysiology related to both dominant and recessive ataxias have propelled the field forward, paving the way for innovative therapeutic strategies aimed at preventing and arresting the progression of these diseases. Nevertheless, the rarity of certain forms of ataxia continues to pose challenges, leading to limited insights into the etiology of the disease and the identification of target pathways. Additionally, the lack of suitable models hampers efforts to comprehensively understand the molecular foundations of disease's pathophysiology and test novel therapeutic interventions. In the following review, we describe the epidemiology, symptomatology, and pathological progression of hereditary ataxia, including both the prevalent and less common forms of these diseases. Furthermore, we illustrate the diverse molecular pathways and therapeutic approaches currently undergoing investigation in both pre-clinical studies and clinical trials. Finally, we address the existing and anticipated challenges within this field, encompassing both basic research and clinical endeavors.
Collapse
Affiliation(s)
- Federica Pilotto
- Institut Neuromyogène, Pathophysiology and Genetics of Neuron and Muscle, Inserm U1315, CNRS-Université Claude Bernard Lyon 1 UMR5261, 69008 Lyon, France
| | - Andrea Del Bondio
- Institut Neuromyogène, Pathophysiology and Genetics of Neuron and Muscle, Inserm U1315, CNRS-Université Claude Bernard Lyon 1 UMR5261, 69008 Lyon, France
| | - Hélène Puccio
- Institut Neuromyogène, Pathophysiology and Genetics of Neuron and Muscle, Inserm U1315, CNRS-Université Claude Bernard Lyon 1 UMR5261, 69008 Lyon, France
| |
Collapse
|