1
|
Brankovic M, Ivanovic V, Basta I, Khang R, Lee E, Stevic Z, Ralic B, Tubic R, Seo G, Markovic V, Bozovic I, Svetel M, Marjanovic A, Veselinovic N, Mesaros S, Jankovic M, Savic-Pavicevic D, Jovin Z, Novakovic I, Lee H, Peric S. Whole exome sequencing in Serbian patients with hereditary spastic paraplegia. Neurogenetics 2024; 25:165-177. [PMID: 38499745 DOI: 10.1007/s10048-024-00755-x] [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: 12/14/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
Hereditary spastic paraplegia (HSP) is a group of neurodegenerative diseases with a high genetic and clinical heterogeneity. Numerous HSP patients remain genetically undiagnosed despite screening for known genetic causes of HSP. Therefore, identification of novel variants and genes is needed. Our previous study analyzed 74 adult Serbian HSP patients from 65 families using panel of the 13 most common HSP genes in combination with a copy number variation analysis. Conclusive genetic findings were established in 23 patients from 19 families (29%). In the present study, nine patients from nine families previously negative on the HSP gene panel were selected for the whole exome sequencing (WES). Further, 44 newly diagnosed adult HSP patients from 44 families were sent to WES directly, since many studies showed WES may be used as the first step in HSP diagnosis. WES analysis of cohort 1 revealed a likely genetic cause in five (56%) of nine HSP families, including variants in the ETHE1, ZFYVE26, RNF170, CAPN1, and WASHC5 genes. In cohort 2, possible causative variants were found in seven (16%) of 44 patients (later updated to 27% when other diagnosis were excluded), comprising six different genes: SPAST, SPG11, WASCH5, KIF1A, KIF5A, and ABCD1. These results expand the genetic spectrum of HSP patients in Serbia and the region with implications for molecular genetic diagnosis and future causative therapies. Wide HSP panel can be the first step in diagnosis, alongside with the copy number variation (CNV) analysis, while WES should be performed after.
Collapse
Affiliation(s)
- Marija Brankovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia.
| | - Vukan Ivanovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Ivana Basta
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | | | | | - Zorica Stevic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | | | - Radoje Tubic
- Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | | | - Vladana Markovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ivo Bozovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Marina Svetel
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ana Marjanovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Nikola Veselinovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Sarlota Mesaros
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Milena Jankovic
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Dusanka Savic-Pavicevic
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Zita Jovin
- Neurology Clinic, University Clinical Center of Vojvodina, Novi Sad, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
| | - Hane Lee
- 3Billion, Inc., Seoul, South Korea
| | - Stojan Peric
- Faculty of Medicine, University of Belgrade, Dr Subotica 6, Belgrade, Serbia
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| |
Collapse
|
2
|
Galatolo D, Trovato R, Scarlatti A, Rossi S, Natale G, De Michele G, Barghigiani M, Cioffi E, Filla A, Bilancieri G, Casali C, Santorelli FM, Silvestri G, Tessa A. Power of NGS-based tests in HSP diagnosis: analysis of massively parallel sequencing in clinical practice. Neurogenetics 2023; 24:147-160. [PMID: 37131039 DOI: 10.1007/s10048-023-00717-9] [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: 10/13/2022] [Accepted: 04/24/2023] [Indexed: 05/04/2023]
Abstract
Hereditary spastic paraplegia (HSP) refers to a group of heterogeneous neurological disorders mainly characterized by corticospinal degeneration (pure forms), but sometimes associated with additional neurological and extrapyramidal features (complex HSP). The advent of next-generation sequencing (NGS) has led to huge improvements in knowledge of HSP genetics and made it possible to clarify the genetic etiology of hundreds of "cold cases," accelerating the process of reaching a molecular diagnosis. The different NGS-based strategies currently employed as first-tier approaches most commonly involve the use of targeted resequencing panels and exome sequencing, whereas genome sequencing remains a second-tier approach because of its high costs. The question of which approach is the best is still widely debated, and many factors affect the choice. Here, we aim to analyze the diagnostic power of different NGS techniques applied in HSP, by reviewing 38 selected studies in which different strategies were applied in different-sized cohorts of patients with genetically uncharacterized HSP.
Collapse
Affiliation(s)
| | - Rosanna Trovato
- Molecular Medicine, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Arianna Scarlatti
- Molecular Medicine, IRCCS Stella Maris Foundation, Pisa, Italy
- Laboratory of Biology, BIO@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Salvatore Rossi
- UOC Neurologia, Fondazione Policlinico Universitario 'A. Gemelli' IRCCS, Rome, Italy
| | - Gemma Natale
- Molecular Medicine, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Giovanna De Michele
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | | | - Ettore Cioffi
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Alessandro Filla
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | | | - Carlo Casali
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | | | - Gabriella Silvestri
- UOC Neurologia, Fondazione Policlinico Universitario 'A. Gemelli' IRCCS, Rome, Italy
| | | |
Collapse
|
3
|
Doleckova K, Roth J, Stellmachova J, Gescheidt T, Sigut V, Houska P, Jech R, Zech M, Vyhnalek M, Vyhnalkova E, Seeman P, Meszarosova AU. SPG11: clinical and genetic features of seven Czech patients and literature review. Neurol Res 2022; 44:379-389. [DOI: 10.1080/01616412.2021.1975224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kristyna Doleckova
- Department of Neurology and Center of Clinical Neuroscience First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague
| | - Jan Roth
- Department of Neurology and Center of Clinical Neuroscience First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague
| | - Julia Stellmachova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czechia
| | - Tomas Gescheidt
- Department of Neurology, St. Anne´s University Hospital, Brno, Czechia
| | | | - Pavel Houska
- Department of Neurology, Strakonice Hospital, Strakonice, Czechia
| | - Robert Jech
- Department of Neurology and Center of Clinical Neuroscience First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Martin Vyhnalek
- Department of Neurology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague
| | - Emilie Vyhnalkova
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague
| | - Pavel Seeman
- Department of Paediatric Neurology, Neurogenetic Laboratory, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague
| | - Anna Uhrova Meszarosova
- Department of Paediatric Neurology, Neurogenetic Laboratory, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague
| |
Collapse
|
4
|
Gómez-González C, Pizarro-Sánchez C, Rodríguez-Antolín C, Pascual-Pascual I, Garcia-Romero M, Rodriguez-Jiménez C, de Sancho-Martín R, Del Pozo-Mate Á, Solís-López M, Prior-de Castro C, Torres RJ. Hereditary spastic paraplegia associated with a novel homozygous intronic noncanonical splice site variant in the AP4B1 gene. Ann Hum Genet 2021; 86:109-118. [PMID: 34927723 DOI: 10.1111/ahg.12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 11/27/2022]
Abstract
Pathogenic variants in the AP4B1 gene lead to a rare form of hereditary spastic paraplegia (HSP) known as SPG47. We report on a patient with a clinical suspicion of complicated HSP of the lower limbs with intellectual disability, as well as a novel homozygous noncanonical splice site variant in the AP4B1 gene, in which the effect on splicing was validated by RNA analysis. We sequenced 152 genes associated with HSP using Next-Generation Sequencing (NGS). We isolated total RNA from peripheral blood and generated cDNA using reverse transcription-polymerase chain reaction (RT-PCR). A region of AP4B1 mRNA was amplified by PCR and the fragments obtained were purified from the agarose gel and sequenced. We found a homozygous variant of uncertain significance in the AP4B1 gene NM_006594.4: c.1511-6C>G in the proband. Two different AP4B1 mRNA fragments were obtained in the patient and his carrier parents. The shorter fragment was the predominant fragment in the patient and revealed a deletion with skipping of the AP4B1 exon 10. The patient's longer fragment corresponded to an insertion of the last five nucleotides of AP4B1 intron 9. We confirmed that this variant affects the normal splicing of RNA, sustaining the molecular diagnosis of SPG47 in the patient.
Collapse
Affiliation(s)
- Clara Gómez-González
- Department of Molecular Genetics, INGEMM, La Paz University Hospital, Madrid, Spain
| | | | - Carlos Rodríguez-Antolín
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain.,Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | | | - Mar Garcia-Romero
- Department of Paediatric Neurology, La Paz University Hospital, Madrid, Spain
| | | | | | | | - Mario Solís-López
- Department of Bioinformatics, INGEMM, La Paz University Hospital, Madrid, Spain
| | | | - Rosa J Torres
- Biochemistry Laboratory, La Paz University Hospital Health Research Institute (FIBHULP), IdiPAZ, Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Spain
| |
Collapse
|
5
|
Dragašević-Mišković N, Stanković I, Milovanović A, Kostić VS. Autosomal recessive adult onset ataxia. J Neurol 2021; 269:504-533. [PMID: 34499204 DOI: 10.1007/s00415-021-10763-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
Autosomal recessive ataxias (ARCA) represent a complex group of diseases ranging from primary ataxias to rare and complex metabolic disorders in which ataxia is a part of the clinical picture. Small number of ARCA manifest exclusively in adulthood, while majority of typical childhood onset ARCA may also start later with atypical clinical presentation. We have systematically searched the literature for ARCA with adult onset, both in the group of primary ataxias including those that are less frequently described in isolated or in a small number of families, and also in the group of complex and metabolic diseases in which ataxia is only part of the clinical picture. We propose an algorithm that could be used when encountering a patient with adult onset sporadic or recessive ataxia in whom the acquired causes are excluded. ARCA are frequently neglected in the differential diagnosis of adult-onset ataxias. Rising awareness of their clinical significance is important, not only because some of these disorders may be potentially treatable, but also for prognostic implications and inclusion of patients to future clinical trials with disease modifying agents.
Collapse
Affiliation(s)
- Nataša Dragašević-Mišković
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia.
| | - Iva Stanković
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
| | - Andona Milovanović
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
| | - Vladimir S Kostić
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr Subotića 6, 11000, Belgrade, Serbia
| |
Collapse
|
6
|
Saputra L, Kumar KR. Challenges and Controversies in the Genetic Diagnosis of Hereditary Spastic Paraplegia. Curr Neurol Neurosci Rep 2021; 21:15. [PMID: 33646413 PMCID: PMC7921051 DOI: 10.1007/s11910-021-01099-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
Purpose of Review The hereditary spastic paraplegias (HSPs) are a group of disorders characterised by progressive lower limb weakness and spasticity. We address the challenges and controversies involved in the genetic diagnosis of HSP. Recent Findings There is a large and rapidly expanding list of genes implicated in HSP, making it difficult to keep gene testing panels updated. There is also a high degree of phenotypic overlap between HSP and other disorders, leading to problems in choosing the right panel to analyse. We discuss genetic testing strategies for overcoming these diagnostic hurdles, including the use of targeted sequencing gene panels, whole-exome sequencing and whole-genome sequencing. Personalised treatments for HSP are on the horizon, and a genetic diagnosis may hold the key to access these treatments. Summary Developing strategies to overcome the challenges and controversies in HSP may hold the key to a rapid and accurate genetic diagnosis.
Collapse
Affiliation(s)
- Lydia Saputra
- Northern Beaches Hospital, Frenchs Forest, New South Wales, Australia
| | - Kishore Raj Kumar
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia. .,Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, Sydney, New South Wales, Australia. .,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia. .,Institute of Precision Medicine & Bioinformatics, Sydney Local Health District, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.
| |
Collapse
|
7
|
Wali G, Kumar KR, Liyanage E, Davis RL, Mackay-Sim A, Sue CM. Mitochondrial Function in Hereditary Spastic Paraplegia: Deficits in SPG7 but Not SPAST Patient-Derived Stem Cells. Front Neurosci 2020; 14:820. [PMID: 32973427 PMCID: PMC7469654 DOI: 10.3389/fnins.2020.00820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022] Open
Abstract
Mutations in SPG7 and SPAST are common causes of hereditary spastic paraplegia (HSP). While some SPG7 mutations cause paraplegin deficiency, other SPG7 mutations cause increased paraplegin expression. Mitochondrial function has been studied in models that are paraplegin-deficient (human, mouse, and Drosophila models with large exonic deletions, null mutations, or knockout models) but not in models of mutations that express paraplegin. Here, we evaluated mitochondrial function in olfactory neurosphere-derived cells, derived from patients with a variety of SPG7 mutations that express paraplegin and compared them to cells derived from healthy controls and HSP patients with SPAST mutations, as a disease control. We quantified paraplegin expression and an extensive range of mitochondrial morphology measures (fragmentation, interconnectivity, and mass), mitochondrial function measures (membrane potential, oxidative phosphorylation, and oxidative stress), and cell proliferation. Compared to control cells, SPG7 patient cells had increased paraplegin expression, fragmented mitochondria with low interconnectivity, reduced mitochondrial mass, decreased mitochondrial membrane potential, reduced oxidative phosphorylation, reduced ATP content, increased mitochondrial oxidative stress, and reduced cellular proliferation. Mitochondrial dysfunction was specific to SPG7 patient cells and not present in SPAST patient cells, which displayed mitochondrial functions similar to control cells. The mitochondrial dysfunction observed here in SPG7 patient cells that express paraplegin was similar to the dysfunction reported in cell models without paraplegin expression. The p.A510V mutation was common to all patients and was the likely species associated with increased expression, albeit seemingly non-functional. The lack of a mitochondrial phenotype in SPAST patient cells indicates genotype-specific mechanisms of disease in these HSP patients.
Collapse
Affiliation(s)
- Gautam Wali
- Department of Neurogenetics, Royal North Shore Hospital, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Kishore Raj Kumar
- Department of Neurogenetics, Royal North Shore Hospital, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Department of Neurology, Concord Hospital, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia
| | - Erandhi Liyanage
- Department of Neurogenetics, Royal North Shore Hospital, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Ryan L Davis
- Department of Neurogenetics, Royal North Shore Hospital, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Alan Mackay-Sim
- Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
| | - Carolyn M Sue
- Department of Neurogenetics, Royal North Shore Hospital, Kolling Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Department of Neurology, Royal North Shore Hospital, Northern Sydney Local Health District, Sydney, NSW, Australia
| |
Collapse
|
8
|
Chou CT, Soong BW, Lin KP, Tsai YS, Jih KY, Liao YC, Lee YC. Clinical characteristics of Taiwanese patients with Hereditary spastic paraplegia type 5. Ann Clin Transl Neurol 2020; 7:486-496. [PMID: 32202070 PMCID: PMC7187706 DOI: 10.1002/acn3.51019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/03/2022] Open
Abstract
Objectives To investigate the clinical, electrophysiological, neuroimaging characteristics and genetic features of SPG5 in Taiwan. Methods Mutational analysis of the coding regions of CYP7B1 was performed by utilizing targeted resequencing analysis of the 187 unrelated Taiwanese HSP patients. The diagnosis of SPG5 was ascertained by the presence of biallelic CYP7B1 mutations. The SPG5 patients received clinical, electrophysiological, and neuroimaging evaluations. Disease severity was assessed by using the Spastic Paraplegia Rating Scale (SPRS) and the disability score. Two microsatellite markers as well as 18 single‐nucleotide polymorphism (SNP) markers flanking CYP7B1 were genotyped to assess the founder effect of the CYP7B1 p.R112* mutation. Results Nineteen SPG5 patients from 17 families were identified. They typically presented an insidious onset progressive spastic paraparesis with proprioception involvement beginning at age 8 to 40 years. Their MRIs often showed white matter abnormalities in bilateral occipito‐parietal regions, spinal cord atrophy, and mild cerebellar atrophy. Six different mutations in CYP7B1 were recognized, including three novel ones (p.N131Ifs*4, p.A295V, and p.L439R). CYP7B1 p.R112* was the most common mutation and present in 88.2% of the 17 SPG5 pedigrees. The patients with homozygous CYP7B1 p.R112* mutations had a milder clinical severity. Detailed haplotype analyses demonstrated a shared haplotype in the 25 individuals carrying at least one single allele of CYP7B1 p.R112*, suggesting a founder effect. Interpretation This study delineates the distinct clinical and genetic features of SPG5 in Taiwan and provides useful information for the diagnosis and management of SPG5, especially in patients of Chinese descent.
Collapse
Affiliation(s)
- Cheng-Ta Chou
- Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Department of Neurology, Neurological Institute, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Bing-Wen Soong
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, Taipei Neuroscience Institute, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan
| | - Kon-Ping Lin
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Yu-Shuen Tsai
- Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
| | - Kang-Yang Jih
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Yi-Chu Liao
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Brain Research Center, National Yang-Ming University School of Medicine, Taipei, Taiwan
| |
Collapse
|
9
|
Meszarosova AU, Seeman P, Jencik J, Drabova J, Cibochova R, Stellmachova J, Safka Brozkova D. Two types of recessive hereditary spastic paraplegia in Roma patients in compound heterozygous state; no ethnically prevalent variant found. Neurosci Lett 2020; 721:134800. [PMID: 32007496 DOI: 10.1016/j.neulet.2020.134800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 01/09/2020] [Accepted: 01/29/2020] [Indexed: 10/25/2022]
Abstract
Hereditary spastic paraplegia (HSP or SPG) is a group of rare upper motor neuron diseases. As some ethnically-specific, disease-causing homozygous variants were described in the Czech Roma population, we hypotesised that some prevalent HSP-causing variant could exist in this population. Eight Czech Roma patients were found in a large group of Czech patients with suspected HSP and were tested using gene panel massively parallel sequencing (MPS). Two of the eight were diagnosed with SPG11 and SPG77, respectively. The SPG77 patient manifests a pure HSP phenotype, which is unusual for this SPG type. Both patients are compound heterozygotes for two different variants in the SPG11 (c.1603-1G>A and del ex. 16-18) and FARS2 (c.1082C>T and del ex.1-2) genes respectively; the three variants are novel. In order to find a potential ethnically-specific, disease-causing variant for HSP, we tested the heterozygote frequency of these variants among 130 anonymised DNA samples of Czech Roma individuals without clinical signs of HSP (HPS-negative). A novel deletion of ex.16-18 in the SPG11 gene was found in a heterozygous state in one individual in the HSP-negative group. Haplotype analysis showed that this individual and the patient with SPG11 shared the same haplotype. This supports the assumption that the identified SPG11 deletion could be a founder mutation in the Czech Roma population. In some Roma patients the disease may also be caused by two different biallelic pathogenic mutations.
Collapse
Affiliation(s)
- Anna Uhrova Meszarosova
- DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic.
| | - Pavel Seeman
- DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Jencik
- DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jana Drabova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic
| | - Renata Cibochova
- Department of Paediatric Neurology, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic
| | - Julia Stellmachova
- Department of Medical Genetics, Palacky University Hospital, Olomouc, Czech Republic
| | - Dana Safka Brozkova
- DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine Charles University and University Hospital Motol, Prague, Czech Republic
| |
Collapse
|
10
|
Kang C, Liang C, Ahmad KE, Gu Y, Siow SF, Colebatch JG, Whyte S, Ng K, Cremer PD, Corbett AJ, Davis RL, Roscioli T, Cowley MJ, Park JS, Sue CM, Kumar KR. High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia. THE CEREBELLUM 2019; 18:137-146. [PMID: 30078120 DOI: 10.1007/s12311-018-0969-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic testing strategies such as next-generation sequencing (NGS) panels and whole genome sequencing (WGS) can be applied to the hereditary cerebellar ataxias (HCAs), but their exact role in the diagnostic pathway is unclear. We aim to determine the yield from genetic testing strategies and the genetic and phenotypic spectrum of HCA in Australia by analysing real-world data. We performed a retrospective review on 87 HCA cases referred to the Neurogenetics Clinic at the Royal North Shore Hospital, Sydney, Australia. Probands underwent triplet repeat expansion testing; those that tested negative had NGS-targeted panels and WGS testing when available. In our sample, 58.6% were male (51/87), with an average age at onset of 37.1 years. Individuals with sequencing variants had a prolonged duration of illness compared to those with a triplet repeat expansion. The detection rate in probands for routine repeat expansion panels was 13.8% (11/80). NGS-targeted panels yielded a further 11 individuals (11/32, 34.4%), with WGS yielding 1 more diagnosis (1/3, 33.3%). NGS panels and WGS improved the overall diagnostic rate to 28.8% (23/80) in 14 known HCA loci. The genetic findings included novel variants in ANO10, CACNA1A, PRKCG and SPG7. Our findings highlight the genetic heterogeneity of HCAs and support the use of NGS approaches for individuals who were negative on repeat expansion testing. In comparison to repeat disorders, individuals with sequencing variants may have a prolonged duration of illness, consistent with slower progression of disease.
Collapse
Affiliation(s)
- Ce Kang
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia
| | - Christina Liang
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kate E Ahmad
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Yufan Gu
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Sue-Faye Siow
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - James G Colebatch
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, Australia
| | - Scott Whyte
- Department of Neurology, Gosford Hospital, Gosford, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Philip D Cremer
- Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Alastair J Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, Australia
| | - Ryan L Davis
- Faculty of Medicine and Health, Kolling Institute of Medical Research, University of Sydney Northern Clinical School, St Leonards, Australia.,Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia
| | - Tony Roscioli
- Prince of Wales Clinical School and Neuroscience Research Australia, University of New South Wales, Randwick, Australia.,Department of Clinical Genetics, Sydney Children's Hospital, Randwick, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Jin-Sung Park
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Experimental Animal Research, Seoul National University Hospital, Biomedical Research Institute, Seoul, Republic of Korea
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia.,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, University of Sydney and Northern Sydney Local Health District, St Leonards, Australia. .,Department of Neurology, Royal North Shore Hospital, St Leonards, Australia. .,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
| |
Collapse
|
11
|
Increased Diagnostic Yield of Spastic Paraplegia with or Without Cerebellar Ataxia Through Whole-Genome Sequencing. THE CEREBELLUM 2019; 18:781-790. [DOI: 10.1007/s12311-019-01038-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
12
|
Elert-Dobkowska E, Stepniak I, Krysa W, Ziora-Jakutowicz K, Rakowicz M, Sobanska A, Pilch J, Antczak-Marach D, Zaremba J, Sulek A. Next-generation sequencing study reveals the broader variant spectrum of hereditary spastic paraplegia and related phenotypes. Neurogenetics 2019; 20:27-38. [PMID: 30778698 PMCID: PMC6411833 DOI: 10.1007/s10048-019-00565-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/11/2019] [Indexed: 12/18/2022]
Abstract
Hereditary spastic paraplegias (HSPs) are clinically and genetically heterogeneous neurodegenerative disorders. Numerous genes linked to HSPs, overlapping phenotypes between HSP subtypes and other neurodegenerative disorders and the HSPs’ dual mode of inheritance (both dominant and recessive) make the genetic diagnosis of HSPs complex and difficult. Out of the original HSP cohort comprising 306 index cases (familial and isolated) who had been tested according to “traditional workflow/guidelines” by Multiplex Ligation-dependent Probe Amplification (MLPA) and Sanger sequencing, 30 unrelated patients (all familial cases) with unsolved genetic diagnoses were tested using next-generation sequencing (NGS). One hundred thirty-two genes associated with spastic paraplegias, hereditary ataxias and related movement disorders were analysed using the Illumina TruSight™ One Sequencing Panel. The targeted NGS data showed pathogenic variants, likely pathogenic variants and those of uncertain significance (VUS) in the following genes: SPAST (spastin, SPG4), ATL1 (atlastin 1, SPG3), WASHC5 (SPG8), KIF5A (SPG10), KIF1A (SPG30), SPG11 (spatacsin), CYP27A1, SETX and ITPR1. Out of the nine genes mentioned above, three have not been directly associated with the HSP phenotype to date. Considering the phenotypic overlap and joint cellular pathways of the HSP, spinocerebellar ataxia (SCA) and amyotrophic lateral sclerosis (ALS) genes, our findings provide further evidence that common genetic testing may improve the diagnostics of movement disorders with a spectrum of ataxia-spasticity signs.
Collapse
Affiliation(s)
- Ewelina Elert-Dobkowska
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland
| | - Iwona Stepniak
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland
| | - Wioletta Krysa
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland
| | - Karolina Ziora-Jakutowicz
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland
| | - Maria Rakowicz
- Department of Clinical Neurophysiology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Anna Sobanska
- Department of Clinical Neurophysiology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Jacek Pilch
- Department of Paediatric Neurology, Medical University of Silesia, Katowice, Poland
| | - Dorota Antczak-Marach
- Clinic of Neurology of Children and Adolescents, Institute of Mother and Child, Warsaw, Poland
| | - Jacek Zaremba
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland.,Division Five of Medical Sciences, Polish Academy of Science, Warsaw, Poland
| | - Anna Sulek
- Department of Genetics, Institute of Psychiatry and Neurology, Sobieskiego 9 Street, 02-957, Warsaw, Poland.
| |
Collapse
|
13
|
D'Amore A, Tessa A, Casali C, Dotti MT, Filla A, Silvestri G, Antenora A, Astrea G, Barghigiani M, Battini R, Battisti C, Bruno I, Cereda C, Dato C, Di Iorio G, Donadio V, Felicori M, Fini N, Fiorillo C, Gallone S, Gemignani F, Gigli GL, Graziano C, Guerrini R, Gurrieri F, Kariminejad A, Lieto M, Marques LourenḈo C, Malandrini A, Mandich P, Marcotulli C, Mari F, Massacesi L, Melone MAB, Mignarri A, Milone R, Musumeci O, Pegoraro E, Perna A, Petrucci A, Pini A, Pochiero F, Pons MR, Ricca I, Rossi S, Seri M, Stanzial F, Tinelli F, Toscano A, Valente M, Federico A, Rubegni A, Santorelli FM. Next Generation Molecular Diagnosis of Hereditary Spastic Paraplegias: An Italian Cross-Sectional Study. Front Neurol 2018; 9:981. [PMID: 30564185 PMCID: PMC6289125 DOI: 10.3389/fneur.2018.00981] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Hereditary spastic paraplegia (HSP) refers to a group of genetically heterogeneous neurodegenerative motor neuron disorders characterized by progressive age-dependent loss of corticospinal motor tract function, lower limb spasticity, and weakness. Recent clinical use of next generation sequencing (NGS) methodologies suggests that they facilitate the diagnostic approach to HSP, but the power of NGS as a first-tier diagnostic procedure is unclear. The larger-than-expected genetic heterogeneity-there are over 80 potential disease-associated genes-and frequent overlap with other clinical conditions affecting the motor system make a molecular diagnosis in HSP cumbersome and time consuming. In a single-center, cross-sectional study, spanning 4 years, 239 subjects with a clinical diagnosis of HSP underwent molecular screening of a large set of genes, using two different customized NGS panels. The latest version of our targeted sequencing panel (SpastiSure3.0) comprises 118 genes known to be associated with HSP. Using an in-house validated bioinformatics pipeline and several in silico tools to predict mutation pathogenicity, we obtained a positive diagnostic yield of 29% (70/239), whereas variants of unknown significance (VUS) were found in 86 patients (36%), and 83 cases remained unsolved. This study is among the largest screenings of consecutive HSP index cases enrolled in real-life clinical-diagnostic settings. Its results corroborate NGS as a modern, first-step procedure for molecular diagnosis of HSP. It also disclosed a significant number of new mutations in ultra-rare genes, expanding the clinical spectrum, and genetic landscape of HSP, at least in Italy.
Collapse
Affiliation(s)
- Angelica D'Amore
- Molecular Medicine, Pisa, Italy.,Department of Biology, University of Pisa, Pisa, Italy
| | | | - Carlo Casali
- Department of Medical and Surgical Sciences and Biotechnologies, University of Rome Sapienza, Latina, Italy
| | - Maria Teresa Dotti
- Department of Medicine, Surgery and Neurosciences, Medical School, University of Siena, Siena, Italy
| | - Alessandro Filla
- Department of Neurosciences, Reproductive and Odontostomatologic Sciences, Federico II University, Naples, Italy
| | - Gabriella Silvestri
- IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy.,Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonella Antenora
- Department of Neurosciences, Reproductive and Odontostomatologic Sciences, Federico II University, Naples, Italy
| | | | | | | | - Carla Battisti
- Department of Medicine, Surgery and Neurosciences, Medical School, University of Siena, Siena, Italy
| | - Irene Bruno
- Department of Pediatrics, Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Clemente Dato
- Second Division of Neurology, Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, University of Luigi Vanvitelli, Naples, Italy
| | - Giuseppe Di Iorio
- Second Division of Neurology, Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, University of Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Donadio
- IRCCS Istituto delle Scienze Neurologiche di Bologna-UOC Clinica Neurologica, Bologna, Italy
| | - Monica Felicori
- Istituto delle Scienze Neurologiche di Bologna-UOC Neuropsichiatria Infantile, Bologna, Italy
| | - Nicola Fini
- Department of Neurosciences, Sant'Agostino-Estense Hospital, Azienda Ospedaliero Universitaria di Modena, Modena, Italy
| | - Chiara Fiorillo
- Pediatric Neurology and Neuromuscular Disorders, University of Genoa and Istituto Giannina Gaslini, Genova, Italy
| | - Salvatore Gallone
- Neurology I, Department of Neuroscience and Mental Health, AOU Città della Salute e della Scienza, Turin, Italy
| | | | - Gian Luigi Gigli
- Neurology Clinic, Azienda Ospedaliero Universitaria Santa Maria della Misericordia, Udine, Italy
| | - Claudio Graziano
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit, Children's Hospital A. Meyer, University of Firenze, Florence, Italy
| | - Fiorella Gurrieri
- Institute of Genomic Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Ariana Kariminejad
- Clinical Genetics, Kariminejad-Najmabadi Pathology & Genetics Research Center, Tehran, Iran
| | - Maria Lieto
- Department of Neurosciences, Reproductive and Odontostomatologic Sciences, Federico II University, Naples, Italy
| | - Charles Marques LourenḈo
- Neurogenetics Division, Clinics Hospital of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Alessandro Malandrini
- Department of Medicine, Surgery and Neurosciences, Medical School, University of Siena, Siena, Italy
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Section of Medical Genetics, University of Genoa, Genoa, Italy.,Medical Genetics Unit, Department of Diagnosis, Pathology and Treatments of High Technological Complexity, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Christian Marcotulli
- Department of Medical and Surgical Sciences and Biotechnologies, University of Rome Sapienza, Latina, Italy
| | - Francesco Mari
- Pediatric Neurology Unit, Children's Hospital A. Meyer, University of Firenze, Florence, Italy
| | - Luca Massacesi
- Department of Neurosciences Drugs and Child Health, University of Florence, Florence, Italy
| | - Maria A B Melone
- Second Division of Neurology, Department of Medical, Surgical, Neurological, Metabolic and Aging Sciences, University of Luigi Vanvitelli, Naples, Italy
| | - Andrea Mignarri
- Department of Medicine, Surgery and Neurosciences, Medical School, University of Siena, Siena, Italy
| | - Roberta Milone
- Child Neuropsychiatry, ULSS 7 Pedemontana, Vicenza, Italy
| | - Olimpia Musumeci
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Alessia Perna
- IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy.,Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | | | - Antonella Pini
- Istituto delle Scienze Neurologiche di Bologna-UOC Neuropsichiatria Infantile, Bologna, Italy
| | - Francesca Pochiero
- Metabolic and Muscular Unit, Neuroscience Department, Meyer Children's Hospital, Florence, Italy
| | - Maria Roser Pons
- First Department of Pediatrics, Aghia Sophia Children's Hospital, University of Athens, Athens, Greece
| | | | - Salvatore Rossi
- IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy.,Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Marco Seri
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Franco Stanzial
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Antonio Toscano
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Mariarosaria Valente
- Neurology Clinic, Azienda Ospedaliero Universitaria Santa Maria della Misericordia, Udine, Italy
| | - Antonio Federico
- Department of Medicine, Surgery and Neurosciences, Medical School, University of Siena, Siena, Italy
| | | | | |
Collapse
|
14
|
Mancini C, Giorgio E, Rubegni A, Pradotto L, Bagnoli S, Rubino E, Prontera P, Cavalieri S, Di Gregorio E, Ferrero M, Pozzi E, Riberi E, Ferrero P, Nigro P, Mauro A, Zibetti M, Tessa A, Barghigiani M, Antenora A, Sirchia F, Piacentini S, Silvestri G, De Michele G, Filla A, Orsi L, Santorelli FM, Brusco A. Prevalence and phenotype of the c.1529C>T SPG7 variant in adult-onset cerebellar ataxia in Italy. Eur J Neurol 2018; 26:80-86. [PMID: 30098094 DOI: 10.1111/ene.13768] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND PURPOSE Hereditary ataxias are heterogeneous groups of neurodegenerative disorders, characterized by cerebellar syndromes associated with dysarthria, oculomotor and corticospinal signs, neuropathy and cognitive impairment. Recent reports have suggested mutations in the SPG7 gene, causing the most common form of autosomal recessive spastic paraplegia (MIM#607259), as a main cause of ataxias. The majority of described patients were homozygotes or compound heterozygotes for the c.1529C>T (p.Ala510Val) change. We screened a cohort of 895 Italian patients with ataxia for p.Ala510Val in order to define the prevalence and genotype-phenotype correlation of this variant. METHODS We set up a rapid assay for c.1529C>T using restriction enzyme analysis after polymerase chain reaction amplification. We confirmed the diagnosis with Sanger sequencing. RESULTS We identified eight homozygotes and 13 compound heterozygotes, including two novel variants affecting splicing. Mutated patients showed a pure cerebellar ataxia at onset, evolving in mild spastic ataxia (alternatively) associated with dysarthria (~80% of patients), urinary urgency (~30%) and pyramidal signs (~70%). Comparing homozygotes and compound heterozygotes, we noted a difference in age at onset and Scale for the Assessment and Rating of Ataxia score between the two groups, supporting an earlier and more severe phenotype in compound heterozygotes versus homozygotes. CONCLUSIONS The SPG7 c.1529C>T (p.Ala510Val) mutants accounted for 2.3% of cerebellar ataxia cases in Italy, suggesting that this variant should be considered as a priority test in the presence of late-onset pure ataxia. Moreover, the heterozygous/homozygous genotype appeared to predict the onset of clinical manifestation and disease progression.
Collapse
Affiliation(s)
- C Mancini
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - A Rubegni
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - L Pradotto
- Division of Neurology and Neurorehabilitation, San Giuseppe Hospital, IRCCS Istituto Auxologico Italiano, Piancavallo, Italy
| | - S Bagnoli
- Department of Neuroscience, Psychology, Drug Research and Child's Health, University of Florence, Florence, Italy
| | - E Rubino
- Department of Neuroscience and Mental Health, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Prontera
- Medical Genetics Unit, Hospital S. Maria della Misericordia, Perugia, Italy
| | - S Cavalieri
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Di Gregorio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - M Ferrero
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Pozzi
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - E Riberi
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - P Ferrero
- Department of Neuroscience and Mental Health, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Nigro
- Clinica Neurologica, Azienda Ospedaliera - Università di Perugia, Perugia, Italy
| | - A Mauro
- Department of Neurosciences, University of Torino, Turin, Italy
| | - M Zibetti
- Department of Neuroscience and Mental Health, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - A Tessa
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - M Barghigiani
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - A Antenora
- Department of Neurosciences, Federico II University, Naples, Italy
| | - F Sirchia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - S Piacentini
- Department of Neuroscience, Psychology, Drug Research and Child's Health, University of Florence, Florence, Italy
| | - G Silvestri
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
| | - G De Michele
- Department of Neurosciences, Federico II University, Naples, Italy
| | - A Filla
- Department of Neurosciences, Federico II University, Naples, Italy
| | - L Orsi
- Department of Neuroscience and Mental Health, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - F M Santorelli
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - A Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza Hospital, Turin, Italy
| |
Collapse
|
15
|
Targeted gene capture sequencing in diagnosis of dystonia patients. J Neurol Sci 2018; 390:36-41. [PMID: 29801903 DOI: 10.1016/j.jns.2018.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/27/2018] [Accepted: 04/04/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Dystonia is a movement disorder with high clinical and genetic heterogeneity. Molecular diagnosis is important for an accurate diagnosis of dystonia. Targeted gene capture sequencing has been an effective method for screening multiple candidate genes simultaneously. This method, however, has been rarely reported to be used with dystonia patients. OBJECTIVES AND METHODS To assess the effectiveness of the targeted gene capture sequencing in dystonia, we performed custom target gene capture followed by next-generation sequencing in dystonia patients from China. Sanger sequencing was utilized to substantiate the findings. The effects of identified variants were classified according to the American College of Medical Genetics and Genomics (ACMG) standards and guidelines. RESULTS A total of 65 patients (34 female and 31 male) were recruited in this study. The mean age at onset was 22.7 ± 13.3 years ranging from 2 to 59 years. According to ACMG standards and guidelines, of 65 patients, 12 were identified with pathogenic variants (12/65, 18.5%) in gene TOR1A, PANK2 or ATP1A3, and another four were identified with likely-pathogenic variants (4/65, 6.2%) in gene PRRT2, GCH1 or THAP1. In total, 24.6% of patients in this cohort were detected to have a genetic cause of dystonia. Another four patients (4/65, 6.2%) were identified with variants which were considered to be VUS (Variants of Uncertain Significance) in gene SGCE, TH, ANO3 and ATP1A3 respectively. The most common detected gene was TOR1A, known to be causative for DYT1 (8/65, 12.3%). CONCLUSIONS The study demonstrates that targeted gene capture sequencing is an effective tool for identifying the genetic cause of heterogeneous dystonia patients.
Collapse
|
16
|
Schöls L, Rattay TW, Martus P, Meisner C, Baets J, Fischer I, Jägle C, Fraidakis MJ, Martinuzzi A, Saute JA, Scarlato M, Antenora A, Stendel C, Höflinger P, Lourenco CM, Abreu L, Smets K, Paucar M, Deconinck T, Bis DM, Wiethoff S, Bauer P, Arnoldi A, Marques W, Jardim LB, Hauser S, Criscuolo C, Filla A, Züchner S, Bassi MT, Klopstock T, De Jonghe P, Björkhem I, Schüle R. Hereditary spastic paraplegia type 5: natural history, biomarkers and a randomized controlled trial. Brain 2017; 140:3112-3127. [PMID: 29126212 PMCID: PMC5841036 DOI: 10.1093/brain/awx273] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/22/2017] [Accepted: 08/26/2017] [Indexed: 12/31/2022] Open
Abstract
Spastic paraplegia type 5 (SPG5) is a rare subtype of hereditary spastic paraplegia, a highly heterogeneous group of neurodegenerative disorders defined by progressive neurodegeneration of the corticospinal tract motor neurons. SPG5 is caused by recessive mutations in the gene CYP7B1 encoding oxysterol-7α-hydroxylase. This enzyme is involved in the degradation of cholesterol into primary bile acids. CYP7B1 deficiency has been shown to lead to accumulation of neurotoxic oxysterols. In this multicentre study, we have performed detailed clinical and biochemical analysis in 34 genetically confirmed SPG5 cases from 28 families, studied dose-dependent neurotoxicity of oxysterols in human cortical neurons and performed a randomized placebo-controlled double blind interventional trial targeting oxysterol accumulation in serum of SPG5 patients. Clinically, SPG5 manifested in childhood or adolescence (median 13 years). Gait ataxia was a common feature. SPG5 patients lost the ability to walk independently after a median disease duration of 23 years and became wheelchair dependent after a median 33 years. The overall cross-sectional progression rate of 0.56 points on the Spastic Paraplegia Rating Scale per year was slightly lower than the longitudinal progression rate of 0.80 points per year. Biochemically, marked accumulation of CYP7B1 substrates including 27-hydroxycholesterol was confirmed in serum (n = 19) and cerebrospinal fluid (n = 17) of SPG5 patients. Moreover, 27-hydroxycholesterol levels in serum correlated with disease severity and disease duration. Oxysterols were found to impair metabolic activity and viability of human cortical neurons at concentrations found in SPG5 patients, indicating that elevated levels of oxysterols might be key pathogenic factors in SPG5. We thus performed a randomized placebo-controlled trial (EudraCT 2015-000978-35) with atorvastatin 40 mg/day for 9 weeks in 14 SPG5 patients with 27-hydroxycholesterol levels in serum as the primary outcome measure. Atorvastatin, but not placebo, reduced serum 27-hydroxycholesterol from 853 ng/ml [interquartile range (IQR) 683-1113] to 641 (IQR 507-694) (-31.5%, P = 0.001, Mann-Whitney U-test). Similarly, 25-hydroxycholesterol levels in serum were reduced. In cerebrospinal fluid 27-hydroxycholesterol was reduced by 8.4% but this did not significantly differ from placebo. As expected, no effects were seen on clinical outcome parameters in this short-term trial. In this study, we define the mutational and phenotypic spectrum of SPG5, examine the correlation of disease severity and progression with oxysterol concentrations, and demonstrate in a randomized controlled trial that atorvastatin treatment can effectively lower 27-hydroxycholesterol levels in serum of SPG5 patients. We thus demonstrate the first causal treatment strategy in hereditary spastic paraplegia.
Collapse
Affiliation(s)
- Ludger Schöls
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Tim W Rattay
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Peter Martus
- Institute for Clinical Epidemiology and Applied Biostatistics, Eberhard-Karls-University, 72076 Tübingen, Germany
| | - Christoph Meisner
- Institute for Clinical Epidemiology and Applied Biostatistics, Eberhard-Karls-University, 72076 Tübingen, Germany
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Imma Fischer
- Institute for Clinical Epidemiology and Applied Biostatistics, Eberhard-Karls-University, 72076 Tübingen, Germany
| | - Christine Jägle
- Center for Rare Diseases and Institute of Human Genetics and Applied Genomics, Eberhard-Karls-University, 72076 Tübingen, Germany
| | - Matthew J Fraidakis
- Rare Neurological Diseases Unit, Department of Neurology, University Hospital ‘Attikon’, Medical School of the University of Athens, 12462 Athens, Greece
| | - Andrea Martinuzzi
- Scientific Institute IRCCS E. Medea, Conegliano Research Center, 31015 Conegliano, Italy
| | - Jonas Alex Saute
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Genetics Identification Laboratory, Hospital de Clínicas de Porto Alegre, 90035 Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), 90040 Porto Alegre, Brazil
| | - Marina Scarlato
- Neurology Department and INSPE, San Raffaele Hospital, 20132 Milan, Italy
| | - Antonella Antenora
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University Naples, 80131 Naples, Italy
| | - Claudia Stendel
- Department of Neurology, Friedrich Baur Institute, Ludwig-Maximilians-University, 80336 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Philip Höflinger
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Charles Marques Lourenco
- Departamento de Neurologia, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, 14049 Ribeirao Preto, Brazil
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul (UFRGS), 90040 Porto Alegre, Brazil
| | - Lisa Abreu
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
| | - Katrien Smets
- Neurogenetics Group, Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Martin Paucar
- Department of Neurology, Karolinska University Hospital Huddinge and Department of Clinical Neuroscience, Karolinska Institute, 14152 Huddinge, Sweden
| | - Tine Deconinck
- Neurogenetics Group, Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Dana M Bis
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
| | - Sarah Wiethoff
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, Eberhard-Karls-University, 72076 Tübingen, Germany
- CENTOGENE AG, 18057 Rostock, Germany
| | - Alessia Arnoldi
- Laboratory of Molecular Biology, Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, Italy
| | - Wilson Marques
- Departamento de Neurologia, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, 14049 Ribeirao Preto, Brazil
| | - Laura Bannach Jardim
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Genetics Identification Laboratory, Hospital de Clínicas de Porto Alegre, 90035 Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), 90040 Porto Alegre, Brazil
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul (UFRGS), 90040 Porto Alegre, Brazil
| | - Stefan Hauser
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Chiara Criscuolo
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University Naples, 80131 Naples, Italy
| | - Alessandro Filla
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University Naples, 80131 Naples, Italy
| | - Stephan Züchner
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, 33136 Miami, Florida, USA
| | - Maria Teresa Bassi
- Laboratory of Molecular Biology, Scientific Institute IRCCS E. Medea, 23842 Bosisio Parini, Italy
| | - Thomas Klopstock
- Department of Neurology, Friedrich Baur Institute, Ludwig-Maximilians-University, 80336 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, 2610 Antwerp, Belgium
| | - Ingemar Björkhem
- Karolinska University Hospital Huddinge, Karolinska Institute, 14152 Stockholm, Sweden
| | - Rebecca Schüle
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard-Karls-University, 72076 Tübingen, Germany
- German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| |
Collapse
|
17
|
Burguez D, Polese-Bonatto M, Scudeiro LAJ, Björkhem I, Schöls L, Jardim LB, Matte U, Saraiva-Pereira ML, Siebert M, Saute JAM. Clinical and molecular characterization of hereditary spastic paraplegias: A next-generation sequencing panel approach. J Neurol Sci 2017; 383:18-25. [DOI: 10.1016/j.jns.2017.10.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/22/2017] [Accepted: 10/06/2017] [Indexed: 01/19/2023]
|
18
|
Morais S, Raymond L, Mairey M, Coutinho P, Brandão E, Ribeiro P, Loureiro JL, Sequeiros J, Brice A, Alonso I, Stevanin G. Massive sequencing of 70 genes reveals a myriad of missing genes or mechanisms to be uncovered in hereditary spastic paraplegias. Eur J Hum Genet 2017; 25:1217-1228. [PMID: 28832565 PMCID: PMC5643959 DOI: 10.1038/ejhg.2017.124] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 06/09/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
Hereditary spastic paraplegias (HSP) are neurodegenerative disorders characterized by lower limb spasticity and weakness that can be complicated by other neurological or non-neurological signs. Despite a high genetic heterogeneity (>60 causative genes), 40–70% of the families remain without a molecular diagnosis. Analysis of one of the pioneer cohorts of 193 HSP families generated in the early 1990s in Portugal highlighted that SPAST and SPG11 are the most frequent diagnoses. We have now explored 98 unsolved families from this series using custom next generation sequencing panels analyzing up to 70 candidate HSP genes. We identified the likely disease-causing variant in 20 of the 98 families with KIF5A being the most frequently mutated gene. We also found 52 variants of unknown significance (VUS) in 38% of the cases. These new diagnoses resulted in 42% of solved cases in the full Portuguese cohort (81/193). Segregation of the variants was not always compatible with the presumed inheritance, indicating that the analysis of all HSP genes regardless of the inheritance mode can help to explain some cases. Our results show that there is still a large set of unknown genes responsible for HSP and most likely novel mechanisms or inheritance modes leading to the disease to be uncovered, but this will require international collaborative efforts, particularly for the analysis of VUS.
Collapse
Affiliation(s)
- Sara Morais
- UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.,INSERM, U 1127, Paris, France.,CNRS, UMR 7225, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Laure Raymond
- INSERM, U 1127, Paris, France.,CNRS, UMR 7225, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Mathilde Mairey
- INSERM, U 1127, Paris, France.,CNRS, UMR 7225, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Paula Coutinho
- UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Eva Brandão
- Serviço de Neurologia, Centro Hospitalar de Entre o Douro e Vouga, Santa Maria da Feira, Portugal
| | - Paula Ribeiro
- Serviço de Neurologia, Centro Hospitalar de Entre o Douro e Vouga, Santa Maria da Feira, Portugal
| | - José Leal Loureiro
- UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Serviço de Neurologia, Centro Hospitalar de Entre o Douro e Vouga, Santa Maria da Feira, Portugal
| | - Jorge Sequeiros
- UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Alexis Brice
- INSERM, U 1127, Paris, France.,CNRS, UMR 7225, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Isabel Alonso
- UnIGENe, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Giovanni Stevanin
- INSERM, U 1127, Paris, France.,CNRS, UMR 7225, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France.,APHP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| |
Collapse
|
19
|
Iqbal Z, Rydning SL, Wedding IM, Koht J, Pihlstrøm L, Rengmark AH, Henriksen SP, Tallaksen CME, Toft M. Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia. PLoS One 2017; 12:e0174667. [PMID: 28362824 PMCID: PMC5375131 DOI: 10.1371/journal.pone.0174667] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/13/2017] [Indexed: 12/24/2022] Open
Abstract
Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed. Here, we have assessed molecular diagnosis by gene panel sequencing in 105 early and late-onset hereditary ataxia and spastic paraplegia probands, in whom extensive previous investigations had failed to identify the genetic cause of disease. Pathogenic and likely-pathogenic variants were identified in 20 probands (19%) and variants of uncertain significance in ten probands (10%). Together these accounted for 30 probands (29%) and involved 18 different genes. Among several interesting findings, dominantly inherited KIF1A variants, p.(Val8Met) and p.(Ile27Thr) segregated in two independent families, both presenting with a pure spastic paraplegia phenotype. Two homozygous missense variants, p.(Gly4230Ser) and p.(Leu4221Val) were found in SACS in one consanguineous family, presenting with spastic ataxia and isolated cerebellar atrophy. The average disease duration in probands with pathogenic and likely-pathogenic variants was 31 years, ranging from 4 to 51 years. In conclusion, this study confirmed and expanded the clinical phenotypes associated with known disease genes. The results demonstrate that gene panel sequencing and similar sequencing approaches can serve as efficient diagnostic tools for different heterogeneous disorders. Early use of such strategies may help to reduce both costs and time of the diagnostic process.
Collapse
Affiliation(s)
- Zafar Iqbal
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- * E-mail:
| | - Siri L. Rydning
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Iselin M. Wedding
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jeanette Koht
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Chantal M. E. Tallaksen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
20
|
Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants. Mol Diagn Ther 2017; 21:303-313. [DOI: 10.1007/s40291-017-0268-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
21
|
Kumar KR, Wali GM, Kamate M, Wali G, Minoche AE, Puttick C, Pinese M, Gayevskiy V, Dinger ME, Roscioli T, Sue CM, Cowley MJ. Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing. Neurogenetics 2016; 17:265-270. [PMID: 27679996 PMCID: PMC5061846 DOI: 10.1007/s10048-016-0495-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/12/2016] [Indexed: 12/20/2022]
Abstract
We performed whole genome sequencing (WGS) in nine families from India with early-onset hereditary spastic paraplegia (HSP). We obtained a genetic diagnosis in 4/9 (44 %) families within known HSP genes (DDHD2 and CYP2U1), as well as perixosomal biogenesis disorders (PEX16) and GM1 gangliosidosis (GLB1). In the remaining patients, no candidate structural variants, copy number variants or predicted splice variants affecting an extended candidate gene list were identified. Our findings demonstrate the efficacy of using WGS for diagnosing early-onset HSP, particularly in consanguineous families (4/6 diagnosed), highlighting that two of the diagnoses would not have been made using a targeted approach.
Collapse
Affiliation(s)
- Kishore R Kumar
- Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, St Leonards, 2065, Australia. .,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.
| | - G M Wali
- Neurospecialities Centre, Belgaum, India
| | - Mahesh Kamate
- Department of Paediatrics, KLE University's Jawaharlal Nehru J N Medical College, Belgaum, India
| | - Gautam Wali
- Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, St Leonards, 2065, Australia
| | - André E Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Clare Puttick
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Mark Pinese
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Tony Roscioli
- Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, St Leonards, 2065, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, Australia.,Department of Medical Genetics, Sydney Children's Hospital, Randwick, Australia
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute of Medical Research, Royal North Shore Hospital and University of Sydney, St Leonards, 2065, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| |
Collapse
|
22
|
Lu C, Zheng YC, Dong Y, Li HF. Identification of novel senataxin mutations in Chinese patients with autosomal recessive cerebellar ataxias by targeted next-generation sequencing. BMC Neurol 2016; 16:179. [PMID: 27644330 PMCID: PMC5029030 DOI: 10.1186/s12883-016-0696-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/07/2016] [Indexed: 11/21/2022] Open
Abstract
Background Autosomal recessive cerebellar ataxias (ARCA) are a group of neurodegenerative disorders characterized by early onset of gait impairment, disturbed limb coordination, dysarthria, and eye movement abnormalities, most likely due to the degeneration of cerebellum, brainstem, and spinal cord. Despite of the rarity, ARCA are both clinically and genetically heterogeneous. To date, more than 30 culprit genes have been identified in ARCA. Unraveling the specific causative mutation in cases with ARCA remains challenging so far. Methods Three ARCA pedigrees of Chinese ancestry were recruited. Clinical features were evaluated and peripheral blood was collected after obtaining the written inform. Laboratory examinations, brain MRI, and EMG were performed for all the affected individuals. Genomic DNA was extracted, followed by the screening of GAA repeat expansion in FXN gene to exclude Friedreich’s ataxia. Targeted next-generation sequencing combining Sanger sequencing was performed in each proband of these families. Results Compound heterozygous mutations, c.3190G > T (p.E1064X) and c.4883C > G (p.S1628X) of senataxin (SETX) gene were identified in one family with two affected cases. Both of the patients presented with early onset of unsteady walk, dysarthria, and diplopia. EMG test revealed decreased conduction velocity and evoked potential of both motor and sensory nerve. Moreover, elevated serum alpha-fetoprotein (AFP) and apparent cerebellar atrophy were observed. These features were typical features of ataxia with oculomotor apraxia type 2 (AOA2) and in line with the genetic results. However, no specific mutation was identified in the other two pedigrees. Conclusions We identified novel compound heterozygous mutations of SETX in Chinese AOA2 pedigree, which broaden the mutation spectrum of SETX. To our knowledge, this is the first report concerning Chinese AOA2 cases with SETX mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12883-016-0696-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cong Lu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.,Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yi-Cen Zheng
- The High School Affiliated to Fudan University-WLSA Fudan Academy, Shanghai, China
| | - Yi Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China
| | - Hong-Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and the Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, 88 Jiefang Road, Hangzhou, 310009, China.
| |
Collapse
|
23
|
Wang Y, Peng W, Guo HY, Li H, Tian J, Shi YJ, Yang X, Yang Y, Zhang WQ, Liu X, Liu GN, Deng T, Sun YM, Xing WL, Cheng J, Feng ZC. Next-generation sequencing-based molecular diagnosis of neonatal hypotonia in Chinese Population. Sci Rep 2016; 6:29088. [PMID: 27353517 PMCID: PMC4926250 DOI: 10.1038/srep29088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/14/2016] [Indexed: 12/20/2022] Open
Abstract
Neonatal hypotonia is extremely challenging to diagnose because numerous disorders present similar clinical manifestations. Two panels for diagnosing neonatal hypotonia were developed, which enriches 35 genes corresponding to 61 neonatal hypotonia-related disorders. A cohort of 214 neonates with hypotonia was recruited from 2012 to 2014 in China for this study. Of these subjects, twenty-eight neonates with hypotonia were eliminated according to exclusion criteria and 97 were confirmed using traditional detection methods. The clinical diagnoses of the remaining 89 neonates with hypotonia were approached by targeted next-generation sequencing (NGS). Among the 89 tested neonates, 25 potentially pathogenic variants in nine genes (RYR1, MECP2, MUT, CDKL5, MPZ, PMM2, MTM1, LAMA2 and DMPK) were identified in 22 patients. Six of these pathogenic variants were novel. Of the 186 neonates with hypotonia, we identified the genetic causes for 117 neonates by the traditional detection methods and targeted NGS, achieving a high solving rate of 62.9%. In addition, we found seven neonates with RETT syndrome carrying five mutations, thus expanding the mutation profiles in Chinese neonates with hypotonia. Our study highlights the utility of comprehensive molecular genetic testing, which provides the advantage of speed and diagnostic specificity without invasive procedures.
Collapse
Affiliation(s)
- Yan Wang
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Wei Peng
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Hong-Yan Guo
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Hui Li
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Jie Tian
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Yu-Jing Shi
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Xiao Yang
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Yao Yang
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Wan-Qiao Zhang
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Xin Liu
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| | - Guan-Nan Liu
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Tao Deng
- Beijing CapitalBio Medical Laboratory, Beijing, 101111, P.R. China
| | - Yi-Min Sun
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China
| | - Wan-Li Xing
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China.,Department of Biomedical Engineering, Tsinghua University School of Medicine, Beijing, 100084, P.R. China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P.R. China.,CapitalBio Corporation, Beijing, 102206, P.R. China.,Department of Biomedical Engineering, Tsinghua University School of Medicine, Beijing, 100084, P.R. China
| | - Zhi-Chun Feng
- BaYi Children's Hospital, Beijing Military General Hospital, Beijing, 100700, P.R. China
| |
Collapse
|
24
|
Masciullo M, Tessa A, Perazza S, Santorelli FM, Perna A, Silvestri G. Hereditary spastic paraplegia: Novel mutations and expansion of the phenotype variability in SPG56. Eur J Paediatr Neurol 2016; 20:444-8. [PMID: 26936192 DOI: 10.1016/j.ejpn.2016.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/13/2016] [Accepted: 02/03/2016] [Indexed: 11/27/2022]
Abstract
We describe a novel sporadic case of SPG56, a rare complicated form of HSP, that expands the clinical and molecular spectrum of the disease, being associated to novel mutations in CYP2U1 and showing as novel feature dorsal hydromyelia at spinal cord MRI. The patient presented an early-onset, slowly progressive paraparesis associated with mild mental retardation. Neurological assessments included the Spastic Paraplegia Rating Scale (SPRS), Mental Deterioration Battery (MDB), and Wechsler Adult Intelligence Scale (WAIS), neurophysiological and neuroimaging studies. Targeted next-generation sequencing panels for the whole set of genes associated with HSP were performed in the probands and her relatives. Neuroimaging studies showed dorsal hydromyelia but no brain MRI abnormalities. Targeted next-generation identified two novel mutations: the c.5C > A/p.S2* on the maternal allele in compound heterozygosity with the paternally-inherited c.1288+5G > C in CYP2U1. Both mutations predict early protein truncation and a loss of function. So far, only few SPG56 cases have been reported. This case, expands and further characterize the clinical and molecular spectrum of SPG56. In this regard, in consideration of the putative gene function in neurodevelopment, we suggest a causal association between CYP2U1 mutations and hydromyelia in our patient.
Collapse
Affiliation(s)
| | - A Tessa
- IRCCS Stella Maris, Pisa, Italy
| | - S Perazza
- IRCCS Stella Maris, Pisa, Italy; Advanced Sciences and Technologies in Rehabilitation Medicine and Sports, Tor Vergata University (SP), Rome, Italy
| | | | - A Perna
- Department of Geriatrics, Neurosciences and Orthopedics, Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - G Silvestri
- Department of Geriatrics, Neurosciences and Orthopedics, Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy.
| |
Collapse
|
25
|
Genetic background of the hereditary spastic paraplegia phenotypes in Hungary - An analysis of 58 probands. J Neurol Sci 2016; 364:116-21. [PMID: 27084228 DOI: 10.1016/j.jns.2016.03.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND Hereditary spastic paraplegias (HSPs) are a clinically and genetically heterogeneous group of neurodegenerative diseases with progressive lower limb spasticity and weakness. The aim of this study is to determine the frequency of different SPG mutations in Hungarian patients, and to provide further genotype-phenotype correlations for the known HSP causing genes. METHODS We carried out genetic testing for 58 probands with clinical characteristics of HSP. For historical reasons, three different approaches were followed in different patients: 1) Sanger sequencing of ATL1 and SPAST genes, 2) whole exome, and 3) targeted panel sequencing by next generation sequencing. RESULTS Genetic diagnosis was established for 20 probands (34.5%). We detected nine previously unreported mutations with high confidence for pathogenicity. The most frequently affected gene was SPAST with pathogenic or likely pathogenic mutations in 10 probands. The most frequently detected variant in our cohort was the SPG7 p.Leu78*, observed in four probands. Altogether five probands were diagnosed with SPG7. Additional mutations were detected in SPG11, ATL1, NIPA1, and ABCD1. CONCLUSION This is the first comprehensive genetic epidemiological study of patients with HSP in Hungary. Next generation sequencing improved the yield of genetic diagnostics in this disease group even when the phenotype was atypical. However, considering the frequency of the HSP-causing gene defects, SPG4, the most common form of the disease, should be tested first to be cost effective in this economic region.
Collapse
|
26
|
Olgiati S, Quadri M, Bonifati V. Genetics of movement disorders in the next-generation sequencing era. Mov Disord 2016; 31:458-70. [DOI: 10.1002/mds.26521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/29/2015] [Indexed: 12/15/2022] Open
Affiliation(s)
- Simone Olgiati
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
| | - Marialuisa Quadri
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics; Erasmus MC; Rotterdam The Netherlands
| |
Collapse
|
27
|
Mignarri A, Rubegni A, Tessa A, Stefanucci S, Malandrini A, Cardaioli E, Meschini MC, Stromillo ML, Doccini S, Federico A, Santorelli FM, Dotti MT. Mitochondrial dysfunction in hereditary spastic paraparesis with mutations in DDHD1/SPG28. J Neurol Sci 2016; 362:287-91. [PMID: 26944165 DOI: 10.1016/j.jns.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 01/12/2016] [Accepted: 02/02/2016] [Indexed: 12/22/2022]
Abstract
Mutations in DDHD1 cause the SPG28 subtype of hereditary spastic paraplegia (HSP). Recent studies suggested that mitochondrial dysfunction occurs in SPG28. Here we describe two siblings with SPG28, and report evidence of mitochondrial impairment in skeletal muscle and skin fibroblasts. Patient 1 (Pt1) was a 35-year-old man with spastic paraparesis and urinary incontinence, while his 25-year-old brother (Pt2) had gait spasticity and motor axonal neuropathy. In these patients we identified the novel homozygous c.1429C>T/p.R477* mutation in DDHD1, using a next-generation sequencing (NGS) approach. Histochemical analyses in muscle showed mitochondrial alterations, and multiple mitochondrial DNA (mtDNA) deletions were evident. In Pt1, respiratory chain enzyme activities were altered in skeletal muscle, mitochondrial ATP levels reduced, and analysis of skin fibroblasts revealed mitochondrial fragmentation. It seems possible that the novel nonsense mutation identified abolishes DDHD1 protein function thus altering oxidative metabolism. Qualitative alterations of mtDNA could have a pathogenetic significance. We suggest to perform DDHD1 analysis in patients with multiple mtDNA deletions.
Collapse
Affiliation(s)
- Andrea Mignarri
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | - Anna Rubegni
- Unit of Molecular Medicine, IRCCS Stella Maris, Pisa, Italy
| | | | | | - Alessandro Malandrini
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | - Elena Cardaioli
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | | | - Maria Laura Stromillo
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | | | - Antonio Federico
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | | | - Maria Teresa Dotti
- Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| |
Collapse
|
28
|
Choquet K, Tétreault M, Yang S, La Piana R, Dicaire MJ, Vanstone MR, Mathieu J, Bouchard JP, Rioux MF, Rouleau GA, Boycott KM, Majewski J, Brais B. SPG7 mutations explain a significant proportion of French Canadian spastic ataxia cases. Eur J Hum Genet 2015; 24:1016-21. [PMID: 26626314 DOI: 10.1038/ejhg.2015.240] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 10/01/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022] Open
Abstract
Hereditary cerebellar ataxias and hereditary spastic paraplegias are clinically and genetically heterogeneous and often overlapping neurological disorders. Mutations in SPG7 cause the autosomal recessive spastic paraplegia type 7 (SPG7), but recent studies indicate that they are also one of the most common causes of recessive cerebellar ataxia. In Quebec, a significant number of patients affected with cerebellar ataxia and spasticity remain without a molecular diagnosis. We performed whole-exome sequencing in three French Canadian (FC) patients affected with spastic ataxia and uncovered compound heterozygous variants in SPG7 in all three. Sanger sequencing of SPG7 exons and exon/intron boundaries was used to screen additional patients. In total, we identified recessive variants in SPG7 in 22 FC patients belonging to 12 families (38.7% of the families screened), including two novel variants. The p.(Ala510Val) variant was the most common in our cohort. Cerebellar features, including ataxia, were more pronounced than spasticity in this cohort. These results strongly suggest that variants affecting the function of SPG7 are the fourth most common form of recessive ataxia in FC patients. Thus, we propose that SPG7 mutations explain a significant proportion of FC spastic ataxia cases and that this gene should be considered in unresolved patients.
Collapse
Affiliation(s)
- Karine Choquet
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.,Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Martine Tétreault
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.,McGill University and Genome Quebec Innovation Center, Montreal, Québec, Canada
| | - Sharon Yang
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Roberta La Piana
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Marie-Josée Dicaire
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean Mathieu
- Complexe Hospitalier de la Sagamie et Faculté de Médecine et des Sciences de la Santé de l'Université de Sherbrooke, Jonquière, Québec, Canada
| | - Jean-Pierre Bouchard
- Hôpital Enfant-Jésus, CHU de Québec et Département des Sciences Neurologiques, Faculté de Médecine de l'Université Laval, Québec, Québec, Canada
| | - Marie-France Rioux
- Centre Hospitalier Universitaire de Sherbrooke - Hôpital Fleurimont, Sherbrooke, Québec, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital and Department of Neurology and Neurosurgery, McGill University, Montreal, Québec, Canada
| | | | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Jacek Majewski
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.,McGill University and Genome Quebec Innovation Center, Montreal, Québec, Canada
| | - Bernard Brais
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.,Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| |
Collapse
|
29
|
Kumar KR, Vulinovic F, Lohmann K, Park JS, Schaake S, Sue CM, Klein C. Mutations in TUBB4A and spastic paraplegia. Mov Disord 2015; 30:1857-8. [PMID: 26477786 DOI: 10.1002/mds.26444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/30/2015] [Accepted: 08/03/2015] [Indexed: 12/23/2022] Open
Affiliation(s)
- Kishore R Kumar
- Department of Neurogenetics, Kolling Institute of Medical Research and Royal North Shore Hospital, The University of Sydney, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, Australia
| | - Franca Vulinovic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jin-Sung Park
- Department of Neurogenetics, Kolling Institute of Medical Research and Royal North Shore Hospital, The University of Sydney, Australia
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute of Medical Research and Royal North Shore Hospital, The University of Sydney, Australia
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| |
Collapse
|
30
|
Lynch DS, Koutsis G, Tucci A, Panas M, Baklou M, Breza M, Karadima G, Houlden H. Hereditary spastic paraplegia in Greece: characterisation of a previously unexplored population using next-generation sequencing. Eur J Hum Genet 2015; 24:857-63. [PMID: 26374131 DOI: 10.1038/ejhg.2015.200] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/04/2015] [Accepted: 08/07/2015] [Indexed: 11/09/2022] Open
Abstract
Hereditary Spastic Paraplegia (HSP) is a syndrome characterised by lower limb spasticity, occurring alone or in association with other neurological manifestations, such as cognitive impairment, seizures, ataxia or neuropathy. HSP occurs worldwide, with different populations having different frequencies of causative genes. The Greek population has not yet been characterised. The purpose of this study was to describe the clinical presentation and molecular epidemiology of the largest cohort of HSP in Greece, comprising 54 patients from 40 families. We used a targeted next-generation sequencing (NGS) approach to genetically assess a proband from each family. We made a genetic diagnosis in >50% of cases and identified 11 novel variants. Variants in SPAST and KIF5A were the most common causes of autosomal dominant HSP, whereas SPG11 and CYP7B1 were the most common cause of autosomal recessive HSP. We identified a novel variant in SPG11, which led to disease with later onset and may be unique to the Greek population and report the first nonsense mutation in KIF5A. Interestingly, the frequency of HSP mutations in the Greek population, which is relatively isolated, was very similar to other European populations. We confirm that NGS approaches are an efficient diagnostic tool and should be employed early in the assessment of HSP patients.
Collapse
Affiliation(s)
- David S Lynch
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, London, UK.,The Leonard Wolfson Experimental Neurology Centre, The National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, London, UK
| | - Georgios Koutsis
- Neurogenetics Unit, 1st Department of Neurology, School of Medicine, University of Athens, Athens, Greece
| | - Arianna Tucci
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, London, UK.,Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Marios Panas
- Neurogenetics Unit, 1st Department of Neurology, School of Medicine, University of Athens, Athens, Greece
| | - Markella Baklou
- Neurogenetics Unit, 1st Department of Neurology, School of Medicine, University of Athens, Athens, Greece
| | - Marianthi Breza
- Neurogenetics Unit, 1st Department of Neurology, School of Medicine, University of Athens, Athens, Greece
| | - Georgia Karadima
- Neurogenetics Unit, 1st Department of Neurology, School of Medicine, University of Athens, Athens, Greece
| | - Henry Houlden
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, London, UK.,Neurogenetics Laboratory, The National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, London, UK
| |
Collapse
|
31
|
Castro-Fernández C, Arias M, Blanco-Arias P, Santomé-Collazo L, Amigo J, Carracedo Á, Sobrido MJ. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11. Appl Transl Genom 2015; 5:33-6. [PMID: 26937357 PMCID: PMC4745395 DOI: 10.1016/j.atg.2015.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/30/2015] [Indexed: 12/12/2022]
Abstract
Next generation sequencing (NGS) is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.
Collapse
Affiliation(s)
- Cristina Castro-Fernández
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Spain
| | - Manuel Arias
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Servicio de Neurología, Complejo Hospitalario de Santiago de Compostela, Spain
| | - Patricia Blanco-Arias
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Spain
| | - Luis Santomé-Collazo
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Fundación Pública Galega de Medicina Xenómica, Spain
| | - Jorge Amigo
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Spain
| | - Ángel Carracedo
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Spain; Center of Excellence in Genomic Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maria-Jesús Sobrido
- Instituto de Investigación Sanitaria de Santiago-IDIS, Spain; Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Spain
| |
Collapse
|
32
|
Kumar KR, Blair NF, Sue CM. An Update on the Hereditary Spastic Paraplegias: New Genes and New Disease Models. Mov Disord Clin Pract 2015; 2:213-223. [PMID: 30838228 DOI: 10.1002/mdc3.12184] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/24/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023] Open
Abstract
Aims The hereditary spastic paraplegias (HSPs) are a heterogeneous group of disorders characterized by spasticity in the lower limbs. We provide an overview of HSP with an emphasis on recent developments. Methods A PubMed search using the term "hereditary spastic paraplegia" and "hereditary spastic paraparesis" was conducted for a period from January 2012 to January 2015. We discuss and critique the major studies in the field over this 36-month period. Results A total of 346 publications were identified, of which 47 were selected for review. We provide an update of the common forms of HSP and include patient videos. We also discuss how next-generation sequencing (NGS) has led to the accelerated discovery of new HSP genes, including B4GALNT1,DDHD1, C19orf12,GBA2,TECPR2,DDHD2, C12orf65,REEP2, and IBA57. Moreover, a single study alone identified 18 previously unknown putative HSP genes and created a model for the protein interactions of HSP, called the "HSPome." Many of the newly reported genes cause rare, complicated, autosomal recessive forms of HSP. NGS also has important clinical applications by facilitating the molecular diagnosis of HSP. Furthermore, common genetic forms of HSP have been studied using new disease models, such as neurons derived from induced pluripotent stem cells. These models have been used to elucidate important disease mechanisms and have served as platforms to screen for candidate drug compounds. Conclusion The field of HSP research has been progressing at a rapid pace. The challenge remains in translating these advances into new targeted disease therapies.
Collapse
Affiliation(s)
- Kishore R Kumar
- Departments of Neurology and Neurogenetics Kolling Institute of Medical Research and Royal North Shore Hospital University of Sydney Sydney New South Wales Australia
| | - Nicholas F Blair
- Departments of Neurology and Neurogenetics Kolling Institute of Medical Research and Royal North Shore Hospital University of Sydney Sydney New South Wales Australia
| | - Carolyn M Sue
- Departments of Neurology and Neurogenetics Kolling Institute of Medical Research and Royal North Shore Hospital University of Sydney Sydney New South Wales Australia
| |
Collapse
|
33
|
Klebe S, Stevanin G, Depienne C. Clinical and genetic heterogeneity in hereditary spastic paraplegias: from SPG1 to SPG72 and still counting. Rev Neurol (Paris) 2015; 171:505-30. [PMID: 26008818 DOI: 10.1016/j.neurol.2015.02.017] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/10/2015] [Accepted: 02/19/2015] [Indexed: 12/11/2022]
Abstract
Hereditary spastic paraplegias (HSPs) are genetically determined neurodegenerative disorders characterized by progressive weakness and spasticity of lower limbs, and are among the most clinically and genetically heterogeneous human diseases. All modes of inheritance have been described, and the recent technological revolution in molecular genetics has led to the identification of 76 different spastic gait disease-loci with 59 corresponding spastic paraplegia genes. Autosomal recessive HSP are usually associated with diverse additional features (referred to as complicated forms), contrary to autosomal dominant HSP, which are mostly pure. However, the identification of additional mutations and families has considerably enlarged the clinical spectra, and has revealed a huge clinical variability for almost all HSP; complicated forms have also been described for primary pure HSP subtypes, adding further complexity to the genotype-phenotype correlations. In addition, the introduction of next generation sequencing in clinical practice has revealed a genetic and phenotypic overlap with other neurodegenerative disorders (amyotrophic lateral sclerosis, neuropathies, cerebellar ataxias, etc.) and neurodevelopmental disorders, including intellectual disability. This review aims to describe the most recent advances in the field and to provide genotype-phenotype correlations that could help clinical diagnoses of this heterogeneous group of disorders.
Collapse
Affiliation(s)
- S Klebe
- Department of neurology, university hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany
| | - G Stevanin
- Sorbonne universités, UPMC université Paris 06, 91-105, boulevard de l'Hôpital, 75013 Paris, France; ICM, CNRS UMR 7225, Inserm U 1127, 47/83, boulevard de l'Hôpital, 75013 Paris, France; École pratique des hautes études, 4-14, rue Ferrus, 75014 Paris, France; Département de génétique, AP-HP, hôpital Pitié-Salpêtrière, 47/83, boulevard de l'Hôpital, 75013 Paris, France
| | - C Depienne
- Sorbonne universités, UPMC université Paris 06, 91-105, boulevard de l'Hôpital, 75013 Paris, France; ICM, CNRS UMR 7225, Inserm U 1127, 47/83, boulevard de l'Hôpital, 75013 Paris, France; Département de génétique, AP-HP, hôpital Pitié-Salpêtrière, 47/83, boulevard de l'Hôpital, 75013 Paris, France.
| |
Collapse
|
34
|
Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A, Spears MD, Beckman K, Silverstein KAT, Thyagarajan B. Clinical validation of targeted next-generation sequencing for inherited disorders. Arch Pathol Lab Med 2015; 139:204-10. [PMID: 25611102 DOI: 10.5858/arpa.2013-0625-oa] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Although next-generation sequencing (NGS) can revolutionize molecular diagnostics, several hurdles remain in the implementation of this technology in clinical laboratories. OBJECTIVES To validate and implement an NGS panel for genetic diagnosis of more than 100 inherited diseases, such as neurologic conditions, congenital hearing loss and eye disorders, developmental disorders, nonmalignant diseases treated by hematopoietic cell transplantation, familial cancers, connective tissue disorders, metabolic disorders, disorders of sexual development, and cardiac disorders. The diagnostic gene panels ranged from 1 to 54 genes with most of panels containing 10 genes or fewer. DESIGN We used a liquid hybridization-based, target-enrichment strategy to enrich 10 067 exons in 568 genes, followed by NGS with a HiSeq 2000 sequencing system (Illumina, San Diego, California). RESULTS We successfully sequenced 97.6% (9825 of 10 067) of the targeted exons to obtain a minimum coverage of 20× at all bases. We demonstrated 100% concordance in detecting 19 pathogenic single-nucleotide variations and 11 pathogenic insertion-deletion mutations ranging in size from 1 to 18 base pairs across 18 samples that were previously characterized by Sanger sequencing. Using 4 pairs of blinded, duplicate samples, we demonstrated a high degree of concordance (>99%) among the blinded, duplicate pairs. CONCLUSIONS We have successfully demonstrated the feasibility of using the NGS platform to multiplex genetic tests for several rare diseases and the use of cloud computing for bioinformatics analysis as a relatively low-cost solution for implementing NGS in clinical laboratories.
Collapse
Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis (Drs Yohe, Wilson, Zhou, Spears, and Thyagarajan); the University of Minnesota Genomics Center (Mr Hauge, Mss Bunjer and Deshpande, and Dr Beckman); the Molecular Diagnostics Laboratory, Fairview-University of Minnesota Medical Center (Ms Kemmer and Messrs Bower and Schomaker); the Division of Genetics and Metabolism, University of Minnesota (Mr Bower); and the Minnesota Supercomputing Institute, University of Minnesota (Drs Onsongo and Silverstein and Mr Erdmann)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Ylikallio E, Kim D, Isohanni P, Auranen M, Kim E, Lönnqvist T, Tyynismaa H. Dominant transmission of de novo KIF1A motor domain variant underlying pure spastic paraplegia. Eur J Hum Genet 2015; 23:1427-30. [PMID: 25585697 DOI: 10.1038/ejhg.2014.297] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/05/2014] [Accepted: 12/17/2014] [Indexed: 12/27/2022] Open
Abstract
Variants in family 1 kinesin (KIF1A), which encodes a kinesin axonal motor protein, have been described to cause variable neurological manifestations. Recessive missense variants have led to spastic paraplegia, and recessive truncations to sensory and autonomic neuropathy. De novo missense variants cause developmental delay or intellectual disability, cerebellar atrophy and variable spasticity. We describe a family with father-to-son transmission of de novo variant in the KIF1A motor domain, in a phenotype of pure spastic paraplegia. Structural modeling of the predicted p.(Ser69Leu) amino acid change suggested that it impairs the stable binding of ATP to the KIF1A protein. Our study reports the first dominantly inherited KIF1A variant and expands the spectrum of phenotypes caused by heterozygous KIF1A motor domain variants to include pure spastic paraplegia. We conclude that KIF1A should be considered a candidate gene for hereditary paraplegias regardless of inheritance pattern.
Collapse
Affiliation(s)
- Emil Ylikallio
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Doyoun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Korea
| | - Pirjo Isohanni
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Child Neurology, Children's Hospital, Helsinki University Central Hospital, Helsinki, Finland
| | - Mari Auranen
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Korea.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital, Helsinki University Central Hospital, Helsinki, Finland
| | - Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| |
Collapse
|
36
|
Toft M. Advances in genetic diagnosis of neurological disorders. Acta Neurol Scand 2014:20-5. [PMID: 24588502 DOI: 10.1111/ane.12232] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2013] [Indexed: 12/13/2022]
Abstract
Neurogenetics has developed enormously in recent years, and the genetic basis of human disorders is being unravelled rapidly. Many neurological disorders are Mendelian disorders, caused by mutations in genes involved in normal function of the brain, spinal cord, peripheral nerves or muscles. Due to high costs and time-consuming procedures, genetic tests have normally been performed late in the diagnostic process, when clinical examination and other tests have indicated a specific gene as the likely disease cause. Many neurological phenotypes are genetically very heterogeneous, and testing of all possible disease genes has been impossible. As a result, many patients with genetic neurological disorders have remained without a specific diagnosis, even when the disease is caused by mutations in known disease genes. Recent technological advances, in particular next-generation DNA sequencing techniques, have resulted in rapid identification of genes involved in Mendelian disorders and provided new possibilities for diagnostic genetic testing. The development of methods for coupling targeted capture and massively parallel DNA sequencing has made it possible to examine a large number of genes in a single reaction. Diagnostic genetic testing can today be performed by the use of gene panels and exome sequencing. This allows a more precise diagnosis of many neurological disorders, and genetic testing should now be considered earlier in the diagnostic procedure.
Collapse
Affiliation(s)
- M. Toft
- Department of Neurology; Oslo University Hospital - Rikshospitalet; Oslo Norway
| |
Collapse
|
37
|
|
38
|
Lo Giudice T, Lombardi F, Santorelli FM, Kawarai T, Orlacchio A. Hereditary spastic paraplegia: clinical-genetic characteristics and evolving molecular mechanisms. Exp Neurol 2014; 261:518-39. [PMID: 24954637 DOI: 10.1016/j.expneurol.2014.06.011] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/07/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a group of clinically and genetically heterogeneous neurological disorders characterized by pathophysiologic hallmark of length-dependent distal axonal degeneration of the corticospinal tracts. The prominent features of this pathological condition are progressive spasticity and weakness of the lower limbs. To date, 72 spastic gait disease-loci and 55 spastic paraplegia genes (SPGs) have been identified. All modes of inheritance (autosomal dominant, autosomal recessive, and X-linked) have been described. Recently, a late onset spastic gait disorder with maternal trait of inheritance has been reported, as well as mutations in genes not yet classified as spastic gait disease. Several cellular processes are involved in its pathogenesis, such as membrane and axonal transport, endoplasmic reticulum membrane modeling and shaping, mitochondrial function, DNA repair, autophagy, and abnormalities in lipid metabolism and myelination processes. Moreover, recent evidences have been found about the impairment of endosome membrane trafficking in vesicle formation and about the involvement of oxidative stress and mtDNA polymorphisms in the onset of the disease. Interactome networks have been postulated by bioinformatics and biological analyses of spastic paraplegia genes, which would contribute to the development of new therapeutic approaches.
Collapse
Affiliation(s)
- Temistocle Lo Giudice
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy; Dipartimento di Medicina dei Sistemi, Università di Roma "Tor Vergata", Rome, Italy
| | - Federica Lombardi
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | - Filippo Maria Santorelli
- Unità Operativa Complessa di Medicina Molecolare, Neurogenetica e Malattie Neurodegenerative, IRCCS Stella Maris, Pisa, Italy
| | - Toshitaka Kawarai
- Department of Clinical Neuroscience, Institute of Health Biosciences, Graduate School of Medicine, University of Tokushima, Tokushima, Japan
| | - Antonio Orlacchio
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy; Dipartimento di Medicina dei Sistemi, Università di Roma "Tor Vergata", Rome, Italy.
| |
Collapse
|
39
|
Esteves T, Durr A, Mundwiller E, Loureiro J, Boutry M, Gonzalez M, Gauthier J, El-Hachimi K, Depienne C, Muriel MP, Acosta Lebrigio R, Gaussen M, Noreau A, Speziani F, Dionne-Laporte A, Deleuze JF, Dion P, Coutinho P, Rouleau G, Zuchner S, Brice A, Stevanin G, Darios F. Loss of association of REEP2 with membranes leads to hereditary spastic paraplegia. Am J Hum Genet 2014; 94:268-77. [PMID: 24388663 DOI: 10.1016/j.ajhg.2013.12.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/09/2013] [Indexed: 01/05/2023] Open
Abstract
Hereditary spastic paraplegias (HSPs) are clinically and genetically heterogeneous neurological conditions. Their main pathogenic mechanisms are thought to involve alterations in endomembrane trafficking, mitochondrial function, and lipid metabolism. With a combination of whole-genome mapping and exome sequencing, we identified three mutations in REEP2 in two families with HSP: a missense variant (c.107T>A [p.Val36Glu]) that segregated in the heterozygous state in a family with autosomal-dominant inheritance and a missense change (c.215T>A [p.Phe72Tyr]) that segregated in trans with a splice site mutation (c.105+3G>T) in a family with autosomal-recessive transmission. REEP2 belongs to a family of proteins that shape the endoplasmic reticulum, an organelle that was altered in fibroblasts from an affected subject. In vitro, the p.Val36Glu variant in the autosomal-dominant family had a dominant-negative effect; it inhibited the normal binding of wild-type REEP2 to membranes. The missense substitution p.Phe72Tyr, in the recessive family, decreased the affinity of the mutant protein for membranes that, together with the splice site mutation, is expected to cause complete loss of REEP2 function. Our findings illustrate how dominant and recessive inheritance can be explained by the effects and nature of mutations in the same gene. They have also important implications for genetic diagnosis and counseling in clinical practice because of the association of various modes of inheritance to this new clinico-genetic entity.
Collapse
|