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Ghasemi A, Sadr Z, Babanejad M, Rohani M, Alavi A. Copy Number Variations in Hereditary Spastic Paraplegia-Related Genes: Evaluation of an Iranian Hereditary Spastic Paraplegia Cohort and Literature Review. Mol Syndromol 2023; 14:477-484. [PMID: 38058755 PMCID: PMC10697729 DOI: 10.1159/000531507] [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: 05/11/2023] [Accepted: 06/07/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction In human genetic disorders, copy number variations (CNVs) are considered a considerable underlying cause. CNVs are generally detected by array-based methods but can also be discovered by read-depth analysis of whole-exome sequencing (WES) data. We performed WES-based CNV identification in a cohort of 35 Iranian families with hereditary spastic paraplegia (HSP) patients. Methods Thirty-five patients whose routine single-nucleotide variants (SNVs) and insertion/deletion analyses from exome data were unrevealing underwent a pipeline of CNV analysis using the read-depth detection method. Subsequently, a comprehensive search about the existence of CNVs in all 84 known HSP-causing genes was carried out in all reported HSP cases, so far. Results and Discussion CNV analysis of exome data indicated that 1 patient harbored a heterozygous deletion in exon 17 of the SPAST gene. Multiplex ligation-dependent probe amplification analysis confirmed this deletion in the proband and his affected father. Literature review demonstrated that, to date, pathogenic CNVs have been identified in 30 out of 84 HSP-causing genes (∼36%). However, CNVs in only 17 of these genes were specifically associated with the HSP phenotype. Among them, CNVs were more common in L1CAM, PLP1, SPAST, SPG7, SPG11, and REEP1 genes. The identification of the CNV in 1 of our patients suggests that WES allows the detection of both SNVs and CNVs from a single method without additional costs and execution time. However, because of intrinsic issues of WES in the detection of large rearrangements, it may not yet be exploited to replace the CNV detection methods in standard clinical practice.
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Affiliation(s)
- Aida Ghasemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zahra Sadr
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Iran University of Medical Sciences, Hazrat Rasool Hospital, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Fussiger H, Pereira BLDS, Padilha JPD, Donis KC, Siebert M, Brusius-Facchin AC, Baldo G, Saute JAM, Chen K, Virmond LA, Silva MFB, Minillo RM, Almeida TF, Pelegrino KO, Ferreira AFM, Colichio GBC, Oliveira APA, Teixeira ACB, Carlos CD, da Matta MC, Lima MM, Yamada RY, Cintra VP, Campilongo GP, Camargo SK, Oliveira TFG, Coelho AVC, de Albuquerque RS, de Souza EA, Júnior MAP, Caraciolo MP, Cervato MC, Gomes CS, Moura LMS, Guedes RLM, Barreiro RAS, Reis RS, Val FC, Oliveira JB, Siebert M, Brusius‐Facchin AC, Baldo G, Saute JAM. Copy number variations in SPAST and ATL1 are rare among Brazilians. Clin Genet 2022; 103:580-584. [PMID: 36537231 DOI: 10.1111/cge.14280] [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: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Copy number variations (CNV) may represent a significant proportion of SPG4 and SPG3A diagnosis, the most frequent autosomal dominant subtypes of hereditary spastic paraplegias (HSP). We aimed to assess the frequency of CNVs in SPAST and ATL1 and to update the molecular epidemiology of HSP families in southern Brazil. A cohort study that included 95 Brazilian index cases with clinical suspicion of HSP was conducted between April 2011 and September 2022. Multiplex Ligation Dependent Probe Amplification (MLPA) was performed in 41 cases without defined diagnosis by different massive parallel sequencing techniques (MPS). Diagnosis was obtained in 57/95 (60%) index cases, 15/57 (26.3%) being SPG4. Most frequent autosomal recessive HSP subtypes were SPG7 followed by SPG11, SPG76 and cerebrotendinous xanthomatosis. No CNVs in SPAST and ATL1 were found. Copy number variations are rare among SPG4 and SPG3A families in Brazil. Considering the possibility of CNVs detection by specific algorithms with MPS data, we consider that this is likely the most cost-effective approach to investigate CNVs in these genes in low-risk populations, with MLPA being reserved as an orthogonal confirmatory test.
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Affiliation(s)
- Helena Fussiger
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Janice Pacheco Dias Padilha
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marina Siebert
- Laboratory Research Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Guilherme Baldo
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jonas Alex Morales Saute
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marina Siebert
- Laboratory Research Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre Brazil
| | | | - Guilherme Baldo
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Jonas Alex Morales Saute
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre Brazil
- Department of Internal Medicine Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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3
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Hata T, Nan H, Koh K, Ishiura H, Tsuji S, Takiyama Y. A clinical and genetic study of SPG31 in Japan. J Hum Genet 2022; 67:421-425. [DOI: 10.1038/s10038-022-01021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/09/2022]
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Anticipation Can Be More Common in Hereditary Spastic Paraplegia with SPAST Mutations Than It Appears. Can J Neurol Sci 2021; 49:651-661. [PMID: 34353391 DOI: 10.1017/cjn.2021.188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVE Hereditary spastic paraplegia (HSP) is a heterogeneous neurodegenerative disorder with lower-limb spasticity and weakness. Different patterns of inheritance have been identified in HSP. Most autosomal-dominant HSPs (AD-HSPs) are associated with mutations of the SPAST gene (SPG4), leading to a pure form of HSP with variable age-at-onset (AAO). Anticipation, an earlier onset of disease, as well as aggravation of symptoms in successive generations, may be correlated to SPG4. Herein, we suggested that anticipation might be a relatively common finding in SPG4 families. METHODS Whole-exome sequencing was done on DNA of 14 unrelated Iranian AD-HSP probands. Data were analyzed, and candidate variants were PCR-amplified and sequenced by the Sanger method, subsequently checked in family members to co-segregation analysis. Multiplex ligation-dependent probe amplification (MLPA) was done for seven probands. Clinical features of the probands were recorded, and the probable anticipation was checked in these families. Other previous reported SPG4 families were investigated to anticipation. RESULTS Our findings showed that SPG4 was the common subtype of HSP; three families carried variants in the KIF5A, ATL1, and MFN2 genes, while five families harbored mutations in the SPAST gene. Clinical features of only SPG4 families indicated decreasing AAO in affected individuals of the successive generations, and this difference was significant (p-value <0.05). CONCLUSION It seems SPAST will be the first candidate gene in families that manifests a pure form of AD-HSP and anticipation. Therefore, it may be a powerful situation of genotype-phenotype correlation. However, the underlying mechanism of anticipation in these families is not clear yet.
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Kadnikova VA, Rudenskaya GE, Stepanova AA, Sermyagina IG, Ryzhkova OP. Mutational Spectrum of Spast (Spg4) and Atl1 (Spg3a) Genes In Russian Patients With Hereditary Spastic Paraplegia. Sci Rep 2019; 9:14412. [PMID: 31594988 PMCID: PMC6783457 DOI: 10.1038/s41598-019-50911-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/13/2019] [Indexed: 01/15/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) comprises a heterogeneous group of neurodegenerative disorders, it share common symptom - of progressive lower spastic paraparesis. The most common autosomal dominant (AD) forms of HSP are SPG4 (SPAST gene) and SPG3 (ATL1 gene). In the current research we investigated for the first time the distribution of pathogenic mutations in SPAST and ATL1 genes within a large cohort of Russian HSP patients (122 probands; 69 famillial cases). We determined the frequencies of genetic abnormalities using Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and Next Generation Sequencing (NGS) of targeted gene panels. As a result, SPG4 was diagnosed in 30.3% (37/122) of HSP cases, where the familial cases represented 37.7% (26/69) of SPG4. In total 31 pathogenic and likely pathogenic variants were detected in SPAST, with 14 new mutations. Among all detected SPAST variants, 29% were gross deletions and duplications. The proportion of SPG3 variants in Russian cohort was 8.2% (10/122) that were all familial cases. All 10 detected ATL1 mutations were missense substitutions, most of which were in the mutational hot spots of 4, 7, 8, 12 exons, with 2 novel mutations. This work will be helpful for the populational genetics of HSP understanding.
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Affiliation(s)
- V A Kadnikova
- Federal State Budgetary Institution "Research Centre For Medical Genetics", Moscow, 115478, Russia.
| | - G E Rudenskaya
- Federal State Budgetary Institution "Research Centre For Medical Genetics", Moscow, 115478, Russia
| | - A A Stepanova
- Federal State Budgetary Institution "Research Centre For Medical Genetics", Moscow, 115478, Russia
| | - I G Sermyagina
- Federal State Budgetary Institution "Research Centre For Medical Genetics", Moscow, 115478, Russia
| | - O P Ryzhkova
- Federal State Budgetary Institution "Research Centre For Medical Genetics", Moscow, 115478, Russia
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Cozma C, Hovakimyan M, Iurașcu MI, Makhseed N, Selim LA, Alhashem AM, Ben-Omran T, Mahmoud IG, Al Menabawy NM, Al-Mureikhi M, Martin M, Demuth L, Yüksel Z, Beetz C, Bauer P, Rolfs A. Genetic, clinical and biochemical characterization of a large cohort of patients with hyaline fibromatosis syndrome. Orphanet J Rare Dis 2019; 14:209. [PMID: 31455396 PMCID: PMC6712857 DOI: 10.1186/s13023-019-1183-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/16/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Hyaline fibromatosis syndrome (HFS) is a rare clinical condition in which bi-allelic variants in ANTXR2 are associated with extracellular hyaline deposits. It manifests as multiple skin nodules, patchy hyperpigmentation, joint contractures and severe pain with movement. HFS shows some clinical overlap to Farber disease (FD), a recessive lysosomal storage disorder. RESULTS We here present the largest cohort of independent, genetically confirmed HFS cases reported to date: in 19 unrelated index patients, we identified ten distinct homozygous ANTXR2 mutations, three of which are novel frame-shift variants. The associated clinical data are consistent with the previous hypothesis of non-truncating variants in the terminal exons 13-17 to confer rather mild phenotypes. The novel observation of gender-dependent disease manifestation in our cohort received support from a meta-analysis of all previously published cases. Untargeted blood-based metabolomics revealed patient samples to be biochemically distinct from control samples. Numerous potential HFS biomarker metabolites could thus be identified. We also found metabolomics profiles of HFS patients to highly overlap with those from FD patients. CONCLUSIONS Our study extends the mutational spectrum for HFS, suggests gender-dependency of manifestation, and provides pilot metabolomics data for biomarker identification and a better pathomechanistic understanding of the disorder.
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Affiliation(s)
| | | | | | - Nawal Makhseed
- Department of Pediatrics, Jahra Hospital, Ministry of Health, Jahra City, Kuwait
| | - Laila A. Selim
- Division of Neurology and Metabolism, Kasr Al Ainy School of Medicine, Cairo University Children Hospital, Cairo, Egypt
| | - Amal M. Alhashem
- Prince Sultan Military Medical City, Pediatrics, Riyadh, Saudi Arabia
- Alfaisal University, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Iman G. Mahmoud
- Division of Neurology and Metabolism, Kasr Al Ainy School of Medicine, Cairo University Children Hospital, Cairo, Egypt
| | - Nihal M. Al Menabawy
- Division of Neurology and Metabolism, Kasr Al Ainy School of Medicine, Cairo University Children Hospital, Cairo, Egypt
| | - Mariam Al-Mureikhi
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Magi Martin
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Laura Demuth
- Centogene AG, Am Strande 7, 18057 Rostock, Germany
| | - Zafer Yüksel
- Centogene AG, Am Strande 7, 18057 Rostock, Germany
| | | | - Peter Bauer
- Centogene AG, Am Strande 7, 18057 Rostock, Germany
| | - Arndt Rolfs
- Centogene AG, Am Strande 7, 18057 Rostock, Germany
- Rostock Medical University, Rostock, Germany
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Familial, long-term pollakisuria as initial manifestation of HSP4 due to the SPAST variant c.683-2A>C. J Clin Neurosci 2019; 64:4-5. [PMID: 30962061 DOI: 10.1016/j.jocn.2019.03.067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Hereditary spastic paraplegia type-IV (HSP4) is the most common of the autosomal-dominant HSPs. Though urinary dysfunction is a frequent phenotypic feature, long-term pollakisuria as the initial manifestation of HSP4 has not been reported. CASE REPORT The patient is a 56yo female with an uneventful history until age 46y, when she developed pollakisuria. After another 6y she developed a coordination disorder, recognized as difficulties with running and climbing stairs. Since 6 m prior to presentation, she recognized mild dysphagia. The further history was positive for strabismus, varicosity, hepatopathy, thiamin-deficiency, niacin-deficiency, lumbago, cutaneous borelliosis, abortive psoriasis, lumbar spondylosis, osteochondrosis L5/S1, and HLA-B27-positive rheumatoid arthritis. Clinical exam revealed mild weakness for left foot extension (M5-), a right subclonic patella tendon reflex, and mildly impaired left hook transition. Nerve conduction studies revealed subclinical polyneuropathy. Ophthalmologic investigations, and MRI of the brain and spinal cord were non-informative. Genetic work-up revealed the novel variant c.683-2A > C in the SPAST gene. The family history was positive for HSP in her mother and sister. Pure HSP4 was diagnosed. CONCLUSIONS Pure HSP4 may manifest at onset with year-long pollakisuria exclusively. HSP4 may take a mild course over years, allowing the patient to do sports and to practice a demanding job.
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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.
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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
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Zatz M, Passos-Bueno MR, Vainzof M. Neuromuscular disorders: genes, genetic counseling and therapeutic trials. Genet Mol Biol 2016; 39:339-48. [PMID: 27575431 PMCID: PMC5004840 DOI: 10.1590/1678-4685-gmb-2016-0019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/29/2016] [Indexed: 02/07/2023] Open
Abstract
Neuromuscular disorders (NMD) are a heterogeneous group of genetic conditions, with autosomal dominant, recessive, or X-linked inheritance. They are characterized by progressive muscle degeneration and weakness. Here, we are presenting our major contributions to the field during the past 30 years. We have mapped and identified several novel genes responsible for NMD. Genotype-phenotype correlations studies enhanced our comprehension on the effect of gene mutations on related proteins and their impact on clinical findings. The search for modifier factors allowed the identification of a novel "protective"; variant which may have important implication on therapeutic developments. Molecular diagnosis was introduced in the 1980s and new technologies have been incorporated since then. Next generation sequencing greatly improved our capacity to identify disease-causing mutations with important benefits for research and prevention through genetic counseling of patients' families. Stem cells researches, from and for patients, have been used as tools to study human genetic diseases mechanisms and for therapies development. The clinical effect of preclinical trials in mice and canine models for muscular dystrophies are under investigation. Finally, the integration of our researches and genetic services with our post-graduation program resulted in a significant output of new geneticists, spreading out this expertise to our large country.
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Affiliation(s)
- Mayana Zatz
- Human Genome and Research Center (HUG-CELL), Instituto de
Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Research Center (HUG-CELL), Instituto de
Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Mariz Vainzof
- Human Genome and Research Center (HUG-CELL), Instituto de
Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
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10
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Delving into the complexity of hereditary spastic paraplegias: how unexpected phenotypes and inheritance modes are revolutionizing their nosology. Hum Genet 2015; 134:511-38. [PMID: 25758904 PMCID: PMC4424374 DOI: 10.1007/s00439-015-1536-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 02/23/2015] [Indexed: 12/11/2022]
Abstract
Hereditary spastic paraplegias (HSP) are rare neurodegenerative diseases sharing the degeneration of the corticospinal tracts as the main pathological characteristic. They are considered one of the most heterogeneous neurological disorders. All modes of inheritance have been described for the 84 different loci and 67 known causative genes implicated up to now. Recent advances in molecular genetics have revealed clinico-genetic heterogeneity of these disorders including their clinical and genetic overlap with other diseases of the nervous system. The systematic analysis of a large set of genes, including exome sequencing, is unmasking unusual phenotypes or inheritance modes associated with mutations in HSP genes and related genes involved in various neurological diseases. A new nosology may emerge after integration and understanding of these new data to replace the current classification. Collectively, functions of the known genes implicate the disturbance of intracellular membrane dynamics and trafficking as the consequence of alterations of cytoskeletal dynamics, lipid metabolism and organelle structures, which represent in fact a relatively small number of cellular processes that could help to find common curative approaches, which are still lacking.
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Luo Y, Chen C, Zhan Z, Wang Y, Du J, Hu Z, Liao X, Zhao G, Wang J, Yan X, Jiang H, Pan Q, Xia K, Tang B, Shen L. Mutation and clinical characteristics of autosomal-dominant hereditary spastic paraplegias in China. NEURODEGENER DIS 2014; 14:176-83. [PMID: 25341883 DOI: 10.1159/000365513] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Hereditary spastic paraplegias constitute a heterogeneous group of inherited neurodegenerative disorders. To date, there has been no systematic mutation and clinical analysis for a large group of autosomal-dominant hereditary spastic paraplegias in China. OBJECTIVE The purpose of this study was to investigate the mutation frequencies and the clinical phenotypes of Chinese spastic paraplegia patients. METHODS Direct sequencing and a multiplex ligation-dependent probe amplification assay were applied to detect the mutations of SPAST and ATL1 in 54 autosomal-dominant hereditary spastic paraplegia probands and 66 isolated cases. Next, mutations in NIPA1, KIF5A, REEP1 and SLC33A1 were detected in the negative patients. Subsets of spastic paraplegia patients were genotyped for the modifying variants. Further, detailed clinical data regarding the genetically diagnosed families were analysed. RESULTS Altogether, 27 families were diagnosed as SPG4, 3 as SPG3A and 1 as SPG6. No mutations in KIF5A, REEP1 or SLC33A1 were found; 9 SPAST mutations were novel. There was no p.S44L or p.P45Q variant in SPAST and no p.G563A variant in HSPD1 in either the 120 spastic paraplegia patients or the 500 controls. There was a remarkable clinical difference between the SPG4 and non-SPG4 patients and even between genders among the SPG4 patients. Non-penetrance and remarkable gender difference were observed in some SPG4 and SPG3A families. CONCLUSIONS Our data confirm that hereditary spastic paraplegias in China represent a heterogeneous group of genetic neurodegenerative disorders in autosomal-dominant and apparently sporadic forms. Novel genotype-phenotype correlations were established. © 2014 S. Karger AG, Basel.
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Affiliation(s)
- Yingying Luo
- Department of Neurology, Xianga Hospital of Central South University, Changsha, China
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The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles. Am J Hum Genet 2014; 95:143-61. [PMID: 25065914 DOI: 10.1016/j.ajhg.2014.06.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/30/2014] [Indexed: 01/27/2023] Open
Abstract
Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.
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Faber I, Servelhere KR, Martinez ARM, D?Abreu A, Lopes-Cendes I, França Jr MC. Clinical features and management of hereditary spastic paraplegia. ARQUIVOS DE NEURO-PSIQUIATRIA 2014; 72:219-26. [DOI: 10.1590/0004-282x20130248] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/29/2013] [Indexed: 12/12/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a group of genetically-determined disorders characterized by progressive spasticity and weakness of lower limbs. An apparently sporadic case of adult-onset spastic paraplegia is a frequent clinical problem and a significant proportion of cases are likely to be of genetic origin. HSP is clinically divided into pure and complicated forms. The later present with a wide range of additional neurological and systemic features. To date, there are up to 60 genetic subtypes described. All modes of monogenic inheritance have been described: autosomal dominant, autosomal recessive, X-linked and mitochondrial traits. Recent advances point to abnormal axonal transport as a key mechanism leading to the degeneration of the long motor neuron axons in the central nervous system in HSP. In this review we aim to address recent advances in the field, placing emphasis on key diagnostic features that will help practicing neurologists to identify and manage these conditions.
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 423] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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França MC, Dogini DB, D'Abreu A, Teive HAG, Munhoz RP, Raskin S, Moro A, Melo CC, Gomes AP, Saute JAM, Jardim LB, Lopes-Cendes I. SPG4-related hereditary spastic paraplegia: frequency and mutation spectrum in Brazil. Clin Genet 2013; 86:194-6. [PMID: 24033003 DOI: 10.1111/cge.12252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/06/2013] [Accepted: 08/09/2013] [Indexed: 11/28/2022]
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Feng YP, Ke X, Zhai M, Xin Q, Gong YQ, Liu QJ. Novel deletion of SPAST in a Chinese family with hereditary spastic paraplegia. Singapore Med J 2013; 54:251-4. [DOI: 10.11622/smedj.2013102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Varga RE, Schüle R, Fadel H, Valenzuela I, Speziani F, Gonzalez M, Rudenskaia G, Nürnberg G, Thiele H, Altmüller J, Alvarez V, Gamez J, Garbern JY, Nürnberg P, Zuchner S, Beetz C. Do not trust the pedigree: reduced and sex-dependent penetrance at a novel mutation hotspot in ATL1 blurs autosomal dominant inheritance of spastic paraplegia. Hum Mutat 2013; 34:860-3. [PMID: 23483706 DOI: 10.1002/humu.22309] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/28/2013] [Indexed: 01/23/2023]
Abstract
The hereditary spastic paraplegias (HSPs), a group of neurodegenerative movement disorders, are among the genetically most heterogeneous clinical conditions. Still, the more than 50 forms known so far apparently explain less than 80% of cases. The present study identified two large HSP families, which seemed to show an autosomal recessive and an X-linked inheritance pattern. A set of genetic analyses including exome sequencing revealed plausible mutations only when assuming incomplete/sex-dependent penetrance of adjacent alterations in the autosomal dominant HSP gene ATL1 (c.1243C>T and c.1244G>A, respectively). By screening of additional HSP patients for the presence of these alterations, we identified three more cases and obtained additional evidence for reduced penetrance. Bisulfate sequencing and haplotype analysis indicated that c.1243C and c.1244G constitute a mutational hotspot. Our findings suggest that misinterpretation of inheritance patterns and, consequently, misselection of candidate genes to be screened in gene-focused approaches contribute to the apparently missing heritability in HSP and, potentially, in other genetically heterogeneous disorders.
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Affiliation(s)
- Rita-Eva Varga
- Department of Clinical Chemistry, Jena University Hospital, Jena, Germany
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Denora PS, Santorelli FM, Bertini E. Hereditary spastic paraplegias: one disease for many genes, and still counting. HANDBOOK OF CLINICAL NEUROLOGY 2013; 113:1899-912. [PMID: 23622413 DOI: 10.1016/b978-0-444-59565-2.00060-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hereditary spastic paraplegias (HSPs) are genetically heterogeneous Mendelian disorders characterized by spastic gait with stiffness and weakness in the legs and an associated plethora of neurological or extraneurological signs in "complicated" forms. Major advances have been made during the past two decades in our understanding of their molecular bases with the identification of a large number of gene loci and the cloning of a set of them. The combined genetic and clinical information obtained has permitted a new, molecularly-driven classification and an improved diagnosis of these conditions. This represents a prerequisite for better counseling in families and more appropriate therapeutic options. However, further heterogeneity is expected and new insight into the possible mechanisms anticipated.
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Affiliation(s)
- Paola S Denora
- Molecular Medicine and Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS-Children's Hospital Bambino Gesù, Rome, Italy
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MLPA-based evidence for sequence gain: Pitfalls in confirmation and necessity for exclusion of false positives. Anal Biochem 2012; 421:799-801. [DOI: 10.1016/j.ab.2011.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 11/17/2022]
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Sulek A, Elert E, Rajkiewicz M, Zdzienicka E, Stepniak I, Krysa W, Zaremba J. Screening for the hereditary spastic paraplaegias SPG4 and SPG3A with the multiplex ligation-dependent probe amplification technique in a large population of affected individuals. Neurol Sci 2011; 34:239-42. [DOI: 10.1007/s10072-011-0899-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 12/13/2011] [Indexed: 11/28/2022]
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Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia. Genet Med 2011; 13:582-92. [PMID: 21659953 DOI: 10.1097/gim.0b013e3182106775] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Autosomal dominant spastic paraplegia, type 4 (SPG4), a debilitating disorder of progressive spasticity and weakness of the lower limbs, results from heterozygous mutations in the SPAST gene. The full spectrum of SPAST mutations causing SPG4 and their mechanisms of formation remain to be determined. METHODS We used multiplex ligation-dependent probe amplification, locus-specific array comparative genomic hybridization, and breakpoint DNA sequencing to identify and describe genomic rearrangements in three patients with a clinical presentation of hereditary spastic paraplegia. RESULTS We describe three SPG4 patients with intragenic rearrangements in SPAST; all specifically delete the final exon, exon 17. Breakpoint sequence analyses provide evidence for Alu-specific microhomology-mediated deletion as the mechanism of exon loss; one complex rearrangement apparently occurred by multiple Alu-facilitated template switches. CONCLUSION We hypothesize that the high concentration of Alu family members in the introns and flanking sequence of SPAST may predispose to intragenic rearrangements. Thus, Alu-specific microhomology-mediated intragenic rearrangements in SPAST may be a common cause of SPG4. Furthermore, we propose that genomic deletions encompassing the final exon of SPAST may affect expression of SLC30A6, the most proximal downstream locus and a gene that has been implicated in the pathogenesis of Alzheimer disease, potentially explaining recent reports of dementia in selected SPG4 patients.
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Proukakis C, Moore D, Labrum R, Wood NW, Houlden H. Detection of novel mutations and review of published data suggests that hereditary spastic paraplegia caused by spastin (SPAST) mutations is found more often in males. J Neurol Sci 2011; 306:62-5. [PMID: 21546041 DOI: 10.1016/j.jns.2011.03.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Revised: 02/08/2011] [Accepted: 03/28/2011] [Indexed: 02/01/2023]
Abstract
BACKGROUND Hereditary spastic paraplegia (HSP) is characterised in its pure form by slowly progressive spastic paraparesis. Around 40% of autosomal dominant (AD) cases are caused by mutations in SPAST, encoding spastin. PATIENTS AND METHODS The clinical and investigation details of all patients with a SPAST mutation identified through our centre were reviewed. All published reports of SPAST mutations where the sex of patients was given were subsequently analysed in order to determine whether there is evidence of one sex being preferentially affected. RESULTS In total 22 probable pathogenic changes were detected, including 11 novel ones. One patient carried two adjacent missense mutations. The pathogenicity of a further novel missense mutation is uncertain. Most patients had a pure phenotype, although mild peripheral neuropathy was sometimes present. The total number of patients with SPAST mutations was 27, as three of the previously known mutations were present in more than one person. The excess of males over females in our population (17:10) prompted us to review all published studies where the sex of the patients was given (n=31). A significant excess of males was identified (ratio 1.29, p=0.0007). CONCLUSIONS Our results are consistent with data suggesting that SPAST mutations mostly cause a pure HSP phenotype. The excess of males in our sample and in published reports suggests that penetrance or severity may be sex-dependent, and merits further investigation as it may have important implications for counselling.
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Affiliation(s)
- Christos Proukakis
- Department of Clinical Neurosciences, University College London Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK.
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Alvarez V, Sánchez-Ferrero E, Beetz C, Díaz M, Alonso B, Corao AI, Gámez J, Esteban J, Gonzalo JF, Pascual-Pascual SI, López de Munain A, Moris G, Ribacoba R, Márquez C, Rosell J, Marín R, García-Barcina MJ, Del Castillo E, Benito C, Coto E. Mutational spectrum of the SPG4 (SPAST) and SPG3A (ATL1) genes in Spanish patients with hereditary spastic paraplegia. BMC Neurol 2010; 10:89. [PMID: 20932283 PMCID: PMC2964648 DOI: 10.1186/1471-2377-10-89] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 10/08/2010] [Indexed: 11/10/2022] Open
Abstract
Background Hereditary Spastic Paraplegias (HSP) are characterized by progressive spasticity and weakness of the lower limbs. At least 45 loci have been identified in families with autosomal dominant (AD), autosomal recessive (AR), or X-linked hereditary patterns. Mutations in the SPAST (SPG4) and ATL1 (SPG3A) genes would account for about 50% of the ADHSP cases. Methods We defined the SPAST and ATL1 mutational spectrum in a total of 370 unrelated HSP index cases from Spain (83% with a pure phenotype). Results We found 50 SPAST mutations (including two large deletions) in 54 patients and 7 ATL1 mutations in 11 patients. A total of 33 of the SPAST and 3 of the ATL1 were new mutations. A total of 141 (31%) were familial cases, and we found a higher frequency of mutation carriers among these compared to apparently sporadic cases (38% vs. 5%). Five of the SPAST mutations were predicted to affect the pre-mRNA splicing, and in 4 of them we demonstrated this effect at the cDNA level. In addition to large deletions, splicing, frameshifting, and missense mutations, we also found a nucleotide change in the stop codon that would result in a larger ORF. Conclusions In a large cohort of Spanish patients with spastic paraplegia, SPAST and ATL1 mutations were found in 15% of the cases. These mutations were more frequent in familial cases (compared to sporadic), and were associated with heterogeneous clinical manifestations.
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Affiliation(s)
- Victoria Alvarez
- Laboratory of Molecular Genetics -Genetic Unit, Hospital Universitario Central de Asturias, Oviedo, Spain.
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Partial SPAST and DPY30 deletions in a Japanese spastic paraplegia type 4 family. Neurogenetics 2010; 12:25-31. [PMID: 20857310 DOI: 10.1007/s10048-010-0260-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/01/2010] [Indexed: 01/28/2023]
Abstract
Spastic paraplegia type 4 (SPG4) is the most common autosomal dominant hereditary SPG caused by mutations in the SPAST gene. We studied the four-generation pedigree of a Japanese family with autosomal dominant hereditary SPG both clinically and genetically. Twelve available family members (ten affected; two unaffected) and two spouses were enrolled in the study. The clinical features were hyperreflexia in all four limbs, spasticity of the lower extremities, impaired vibration sense, mild cognitive impairment confirmed by the Wechsler Adult Intelligence Scale-Third Edition, and peripheral neuropathy confirmed by neurophysiological examinations. All four female patients experienced miscarriages. The cerebrospinal fluid tau levels were mildly increased in two of three patients examined. Linkage analyses revealed the highest logarithm of odds score of 2.64 at 2p23-p21 where the SPAST gene is located. Mutation scanning of the entire exonic regions of the SPAST gene by direct sequencing revealed no mutations. Exonic copy number analysis by real-time quantitative polymerase chain reaction revealed heterozygous deletion of exons 1 to 4 of the SPAST gene. Breakpoint analysis showed that the centromeric breakpoint was located within intron 4 of SPAST while the telomeric breakpoint was located within intron 3 of the neighboring DPY30 gene, causing a deletion of approximately 70 kb ranging from exons 1 to 3 of DPY30 to exons 1 to 4 of SPAST. To our knowledge, this is the first report of SPG4 associated with partial deletions of both the SPAST and DPY30 genes. The partial heterozygous deletion of DPY30 could modify the phenotypic expression of SPG4 patients with this pedigree.
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Braschinsky M, Tamm R, Beetz C, Sachez-Ferrero E, Raukas E, Lüüs SM, Gross-Paju K, Boillot C, Canzian F, Metspalu A, Haldre S. Unique spectrum of SPAST variants in Estonian HSP patients: presence of benign missense changes but lack of exonic rearrangements. BMC Neurol 2010; 10:17. [PMID: 20214791 PMCID: PMC2841126 DOI: 10.1186/1471-2377-10-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 03/09/2010] [Indexed: 11/29/2022] Open
Abstract
Background Hereditary spastic paraplegia (HSP) is a clinically and genetically heterogeneous disorder that can be an autosomal-dominant, autosomal-recessive, or X-linked disease. The most common autosomal-dominant form of the disease derives from mutations in the SPAST gene. Methods The aim of this study was to analyze 49 patients diagnosed with HSP from the Estonian population for sequence variants of the SPAST gene and to describe the associated phenotypes. Healthy control individuals (n = 100) with no family history of HSP were also analyzed. All patient samples were screened using denaturing high performance liquid chromatography (DHPLC) and multiplex ligation-dependent probe amplification (MLPA) assay. Samples with abnormal DHPLC and MLPA profiles were sequenced, with the same regions sequenced in control samples. Results Sequence variants of SPAST were identified in 19/49 HSP patients (38.8%), twelve among them had pathogenic mutations. Within the latter group there was one sporadic case. Eight patients had pure, and four - complex HSP. The twelve variants were identified: seven pathogenic (c.1174-1G>C, c.1185delA, c.1276C>T, c.1352_1356delGAGAA, c.1378C>A, c.1518_1519insTC, c.1841_1842insA) and five non-pathogenic (c.131C>T, c.484G>A, c.685A>G, c.1245+202delG, c.1245+215G>C). Only 2 of these mutations had previously been described (c.131C>T, c.1245+202delG). Three mutations, c.1174-1G>C, c.1276 C>T, c.1378C>A, showed intrafamilial segregation. Conclusion This study identified new variants of the SPAST gene which included benign missense variants and short insertions/deletions. No large rearrangements were found. Based on these data, 7 new pathogenic variants of HSP are associated with clinical phenotypes.
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Loss of phosphatidylinositol 4-kinase 2alpha activity causes late onset degeneration of spinal cord axons. Proc Natl Acad Sci U S A 2009; 106:11535-9. [PMID: 19581584 DOI: 10.1073/pnas.0903011106] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphoinositide (PI) lipids are intracellular membrane signaling intermediates and effectors produced by localized PI kinase and phosphatase activities. Although many signaling roles of PI kinases have been identified in cultured cell lines, transgenic animal studies have produced unexpected insight into the in vivo functions of specific PI 3- and 5-kinases, but no mammalian PI 4-kinase (PI4K) knockout has previously been reported. Prior studies using cultured cells implicated the PI4K2alpha isozyme in diverse functions, including receptor signaling, ion channel regulation, endosomal trafficking, and regulated secretion. We now show that despite these important functions, mice lacking PI4K2alpha kinase activity initially appear normal. However, adult Pi4k2a(GT/GT) animals develop a progressive neurological disease characterized by tremor, limb weakness, urinary incontinence, and premature mortality. Histological analysis of aged Pi4k2a(GT/GT) animals revealed lipofuscin-like deposition and gliosis in the cerebellum, and loss of Purkinje cells. Peripheral nerves are essentially normal, but massive axonal degeneration was found in the spinal cord in both ascending and descending tracts. These results reveal a previously undescribed role for aberrant PI signaling in neurological disease that resembles autosomal recessive hereditary spastic paraplegia.
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