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Newton T, Allison R, Edgar JR, Lumb JH, Rodger CE, Manna PT, Rizo T, Kohl Z, Nygren AOH, Arning L, Schüle R, Depienne C, Goldberg L, Frahm C, Stevanin G, Durr A, Schöls L, Winner B, Beetz C, Reid E. Mechanistic basis of an epistatic interaction reducing age at onset in hereditary spastic paraplegia. Brain 2019; 141:1286-1299. [PMID: 29481671 PMCID: PMC5917785 DOI: 10.1093/brain/awy034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022] Open
Abstract
Many genetic neurological disorders exhibit variable expression within affected families, often exemplified by variations in disease age at onset. Epistatic effects (i.e. effects of modifier genes on the disease gene) may underlie this variation, but the mechanistic basis for such epistatic interactions is rarely understood. Here we report a novel epistatic interaction between SPAST and the contiguous gene DPY30, which modifies age at onset in hereditary spastic paraplegia, a genetic axonopathy. We found that patients with hereditary spastic paraplegia caused by genomic deletions of SPAST that extended into DPY30 had a significantly younger age at onset. We show that, like spastin, the protein encoded by SPAST, the DPY30 protein controls endosomal tubule fission, traffic of mannose 6-phosphate receptors from endosomes to the Golgi, and lysosomal ultrastructural morphology. We propose that additive effects on this pathway explain the reduced age at onset of hereditary spastic paraplegia in patients who are haploinsufficient for both genes.
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Affiliation(s)
- Timothy Newton
- Department of Medical Genetics and Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Rachel Allison
- Department of Medical Genetics and Cambridge Institute for Medical Research, University of Cambridge, UK
| | - James R Edgar
- Department of Clinical Biochemistry and Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jennifer H Lumb
- Department of Medical Genetics and Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Catherine E Rodger
- Department of Medical Genetics and Cambridge Institute for Medical Research, University of Cambridge, UK
| | - Paul T Manna
- Department of Clinical Biochemistry and Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Tania Rizo
- Department of Stem Cell Biology, Friedrich-Alexander University Erlangen-Nuernberg (FAU), Erlangen, Germany
| | - Zacharias Kohl
- Department of Molecular Neurology, Friedrich-Alexander University Erlangen-Nuernberg (FAU), Erlangen, Germany
| | | | - Larissa Arning
- Department of Human Genetics, Ruhr-University, Bochum, Germany
| | - 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
| | - Christel Depienne
- ICM Brain and Spine Institute, INSERM U1127, CNRS UMR7225, Sorbonne Universites, UPMC Univ Paris VI UMR_S1127, Paris, France.,APHP, Genetic Department, Pitie-Salpêtrière University Hospital, Paris, France
| | - Lisa Goldberg
- Department of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Christiane Frahm
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Giovanni Stevanin
- ICM Brain and Spine Institute, INSERM U1127, CNRS UMR7225, Sorbonne Universites, UPMC Univ Paris VI UMR_S1127, Paris, France.,APHP, Genetic Department, Pitie-Salpêtrière University Hospital, Paris, France.,Ecole Pratique des Hautes Etudes, PSL Research University, Paris, France
| | - Alexandra Durr
- ICM Brain and Spine Institute, INSERM U1127, CNRS UMR7225, Sorbonne Universites, UPMC Univ Paris VI UMR_S1127, Paris, France.,APHP, Genetic Department, Pitie-Salpêtrière University Hospital, Paris, France
| | - 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
| | - Beate Winner
- Department of Molecular Neurology, Friedrich-Alexander University Erlangen-Nuernberg (FAU), Erlangen, Germany
| | - Christian Beetz
- Department of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Evan Reid
- Department of Medical Genetics and Cambridge Institute for Medical Research, University of Cambridge, UK
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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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Racis L, Storti E, Pugliatti M, Agnetti V, Tessa A, Santorelli FM. Novel SPAST deletion and reduced DPY30 expression in a Spastic Paraplegia type 4 kindred. BMC MEDICAL GENETICS 2014; 15:39. [PMID: 24690193 PMCID: PMC3974227 DOI: 10.1186/1471-2350-15-39] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/12/2014] [Indexed: 11/12/2022]
Abstract
BACKGROUND The hereditary spastic paraplegias (HSPs) are pleiomorphic disorders of motor pathway and a large number of affected genes have been discovered. Yet, mutations in SPG4/SPAST represent the most frequent molecular etiology in autosomal dominant (AD) patients and sporadic cases. We describe a large, AD-HSP Sardinian family where 5 out of several living members harbored a novel deletion affecting also the 5'UTR of SPAST and resulting in reduced expression of DPY30, the gene located upstream SPAST in a head-to-head manner. CASE PRESENTATION A 54-year-old woman manifested leg stiffness at age 39 and required a cane to walk at age 50. Neurological examination disclosed mild spasticity and weakness in the legs, hyperreflexia in all limbs, and bilateral Babinski sign. She also complained of urinary urgency, but no additional neurological symptoms or signs were detected at examination. The clinical examination of 24 additional relatives disclosed three further affected individuals, two men and one woman. In the four symptomatic patients the initial manifestations were walking abnormalities and leg stiffness with a mean age at onset (SD) of 46.75 (5.44) years (range 39-51). The mean disease duration was 13.2 (13.4) years (range 6-35), and it correlated well with clinical severity (SPRS score) (r = 0.975, p = 0.005). One patient was confined to bed and displayed knee and ankle contractures, another case needed a cane to walk, and two individuals were able to walk without aids. Interestingly, a patient had also had a miscarriage during her first pregnancy.Gene testing revealed an heterozygous deletion spanning from the 5'-UTR to intron 4 of SPAST in the affected individuals and in one clinically unaffected woman. In three affected patients, the deletion also determined low mRNA levels of SPAST and DPY30, a component of the Set1-like multiprotein histone methyltransferase complex located upstream, head-to-head with SPAST. CONCLUSION Together with data described in a Japanese family, our findings seem to suggest that genes close to spastin might be candidates in modulating the clinical phenotype. This report endorses future research on the role of neighboring genes as potential players in SPG4 disease variability.
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Affiliation(s)
- Loretta Racis
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Eugenia Storti
- IRCCS Stella Maris, via dei Giacinti 2, 56028 Pisa, Italy
| | - Maura Pugliatti
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Virgilio Agnetti
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
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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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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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McDermott CJ, Shaw PJ. Chapter 17 Hereditary spastic paraparesis. HANDBOOK OF CLINICAL NEUROLOGY 2007; 82:327-352. [PMID: 18808902 DOI: 10.1016/s0072-9752(07)80020-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Depienne C, Fedirko E, Forlani S, Cazeneuve C, Ribaï P, Feki I, Tallaksen C, Nguyen K, Stankoff B, Ruberg M, Stevanin G, Durr A, Brice A. Exon deletions of SPG4 are a frequent cause of hereditary spastic paraplegia. J Med Genet 2006; 44:281-4. [PMID: 17098887 PMCID: PMC2598038 DOI: 10.1136/jmg.2006.046425] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Point mutations in SPG4, the gene encoding spastin, are a frequent cause of autosomal dominant hereditary spastic paraplegia (AD-HSP). However, standard methods for genetic analyses fail to detect exonic microdeletions. METHODS 121 mutation-negative probands were screened for rearrangements in SPG4 by multiplex ligation-dependent probe amplification. RESULTS 24 patients with 16 different heterozygotic exon deletions in SPG4 (20%) were identified, ranging from one exon to the whole coding sequence. Comparison with 78 patients with point mutations showed a similar clinical picture but an earlier age at onset. CONCLUSIONS Exon deletions in SPG4 are as frequent as point mutations, and SPG4 is responsible for 40% of AD-HSP.
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Basri R, Yabe I, Soma H, Takei A, Nishimura H, Machino Y, Kokubo Y, Kosugi M, Okada R, Yukitake M, Tachibana H, Kuroda Y, Kuzuhara S, Sasaki H. Four mutations of the spastin gene in Japanese families with spastic paraplegia. J Hum Genet 2006; 51:711-715. [PMID: 16788734 DOI: 10.1007/s10038-006-0412-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 04/07/2006] [Indexed: 10/24/2022]
Abstract
Hereditary spastic paraplegia (HSP) is a group of genetically heterogeneous neurodegenerative disorders characterized by slowly progressive spasticity and weakness of the lower limbs. HSP is caused by failure of development or selective degeneration of the corticospinal tracts, which contain the longest axons in humans. The most common form of HSP is caused by mutations of the spastin gene (SPAST), located on chromosome 2p21-p22, which encodes spastin, one of the ATPases associated with diverse cellular activities (AAA). In this study, we detected four causative mutations of SPAST among 14 unrelated patients with spastic paraplegia. Two missense mutations (1447A-->G, 1207C-->G) and two deletion mutations (1465delT, 1475-1476delAA) were located in the AAA cassette region. Three of these four mutations were novel. Previous reports and our results suggest that the frequency of SPAST mutations is higher among Japanese patients with autosomal dominant HSP, although SPAST mutations are also observed in patients with sporadic spastic paraplegia.
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Affiliation(s)
- Rehana Basri
- Department of Neurology, Graduate School of Medicine, Hokkaido University, Kita-ku, Sapporo, 060-8368, Japan
| | - Ichiro Yabe
- Department of Neurology, Graduate School of Medicine, Hokkaido University, Kita-ku, Sapporo, 060-8368, Japan
| | - Hiroyuki Soma
- Department of Neurology, Graduate School of Medicine, Hokkaido University, Kita-ku, Sapporo, 060-8368, Japan
| | - Asako Takei
- Hokuyukai Neurology Hospital, Sapporo, Japan
| | - Hiroyuki Nishimura
- Department of Internal Medicine, Division of Neurology and Stroke Care Unit, Hyogo College of Medicine, Nishinomiya, Japan
| | - Yuka Machino
- Department of Neurology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Yasumasa Kokubo
- Department of Neurology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Masafumi Kosugi
- Department of Neurology, Graduate School of Medicine, Saga University, Saga, Japan
| | - Ryuichirou Okada
- Department of Neurology, Graduate School of Medicine, Saga University, Saga, Japan
| | - Motohiro Yukitake
- Department of Neurology, Graduate School of Medicine, Saga University, Saga, Japan
| | - Hisao Tachibana
- Department of General Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Yasuo Kuroda
- Department of Neurology, Graduate School of Medicine, Saga University, Saga, Japan
| | - Shigeki Kuzuhara
- Department of Neurology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Hidenao Sasaki
- Department of Neurology, Graduate School of Medicine, Hokkaido University, Kita-ku, Sapporo, 060-8368, Japan.
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