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Vegezzi E, Ishiura H, Bragg DC, Pellerin D, Magrinelli F, Currò R, Facchini S, Tucci A, Hardy J, Sharma N, Danzi MC, Zuchner S, Brais B, Reilly MM, Tsuji S, Houlden H, Cortese A. Neurological disorders caused by novel non-coding repeat expansions: clinical features and differential diagnosis. Lancet Neurol 2024; 23:725-739. [PMID: 38876750 DOI: 10.1016/s1474-4422(24)00167-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 06/16/2024]
Abstract
Nucleotide repeat expansions in the human genome are a well-known cause of neurological disease. In the past decade, advances in DNA sequencing technologies have led to a better understanding of the role of non-coding DNA, that is, the DNA that is not transcribed into proteins. These techniques have also enabled the identification of pathogenic non-coding repeat expansions that cause neurological disorders. Mounting evidence shows that adult patients with familial or sporadic presentations of epilepsy, cognitive dysfunction, myopathy, neuropathy, ataxia, or movement disorders can be carriers of non-coding repeat expansions. The description of the clinical, epidemiological, and molecular features of these recently identified non-coding repeat expansion disorders should guide clinicians in the diagnosis and management of these patients, and help in the genetic counselling for patients and their families.
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Affiliation(s)
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Pellerin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Stefano Facchini
- IRCCS Mondino Foundation, Pavia, Italy; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Arianna Tucci
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - John Hardy
- Department of Neurogedengerative Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Matt C Danzi
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
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Aryal S, Chen S, Burbach KF, Yang Y, Capano LS, Kim WK, Bragg DC, Yoo A. SAK3 confers neuroprotection in the neurodegeneration model of X-linked Dystonia-Parkinsonism. RESEARCH SQUARE 2024:rs.3.rs-4068432. [PMID: 38746402 PMCID: PMC11092809 DOI: 10.21203/rs.3.rs-4068432/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background X-linked Dystonia-Parkinsonism(XDP) is an adult-onset neurodegenerative disorder that results in the loss of striatal medium spiny neurons (MSNs). XDP is associated with disease-specific mutations in and around the TAF1 gene. This study highlights the utility of directly reprogrammed MSNs from fibroblasts of affected XDP individuals as a platform that captures cellular and epigenetic phenotypes associated with XDP-related neurodegeneration. In addition, the current study demonstrates the neuroprotective effect of SAK3 currently tested in other neurodegenerative diseases. Methods XDP fibroblasts from three independent patients as well as age- and sex-matched control fibroblasts were used to generate MSNs by direct neuronal reprogramming using miRNA-9/9*-124 and thetranscription factors CTIP2 , DLX1 -P2A- DLX2 , and MYT1L . Neuronal death, DNA damage, and mitochondrial health assays were carried out to assess the neurodegenerative state of directly reprogrammed MSNs from XDP patients (XDP-MSNs). RNA sequencing and ATAC sequencing were performed to infer changes in the transcriptomic and chromatin landscapesof XDP-MSNs compared to those of control MSNs (Ctrl-MSNs). Results Our results show that XDP patient fibroblasts can be successfully reprogrammed into MSNs and XDP-MSNs display several degenerative phenotypes, including neuronal death, DNA damage, and mitochondrial dysfunction, compared to Ctrl-MSNs reprogrammed from age- and sex-matched control individuals' fibroblasts. In addition, XDP-MSNs showed increased vulnerability to TNFα -toxicity compared to Ctrl-MSNs. To dissect the altered cellular state in XDP-MSNs, we conducted transcriptomic and chromatin accessibility analyses using RNA- and ATAC-seq. Our results indicate that pathways related to neuronal function, calcium signaling, and genes related to other neurodegenerative diseases are commonly altered in XDP-MSNs from multiple patients. Interestingly, we found that SAK3, a T-type calcium channel activator, that may have therapeutic values in other neurodegenerative disorders, protected XDP-MSNs from neuronal death. Notably, we found that SAK3-mediated alleviation of neurodegeneration in XDP-MSNs was accompanied by gene expression changes toward Ctrl-MSNs.
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Leid J, Gray R, Rakita P, Koenig AL, Tripathy R, Fitzpatrick JAJ, Kaufman C, Solnica-Krezel L, Lavine KJ. Deletion of taf1 and taf5 in zebrafish capitulate cardiac and craniofacial abnormalities associated with TAFopathies through perturbations in metabolism. Biol Open 2023; 12:bio059905. [PMID: 37746814 PMCID: PMC10354717 DOI: 10.1242/bio.059905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 09/26/2023] Open
Abstract
Intellectual disability is a neurodevelopmental disorder that affects 2-3% of the general population. Syndromic forms of intellectual disability frequently have a genetic basis and are often accompanied by additional developmental anomalies. Pathogenic variants in components of TATA-binding protein associated factors (TAFs) have recently been identified in a subset of patients with intellectual disability, craniofacial hypoplasia, and congenital heart disease. This syndrome has been termed as a TAFopathy and includes mutations in TATA binding protein (TBP), TAF1, TAF2, and TAF6. The underlying mechanism by which TAFopathies give rise to neurodevelopmental, craniofacial, and cardiac abnormalities remains to be defined. Through a forward genetic screen in zebrafish, we have recovered a recessive mutant phenotype characterized by craniofacial hypoplasia, ventricular hypoplasia, heart failure at 96 h post-fertilization and lethality, and show it is caused by a nonsense mutation in taf5. CRISPR/CAS9 mediated gene editing revealed that these defects where phenocopied by mutations in taf1 and taf5. Mechanistically, taf5-/- zebrafish displayed misregulation in metabolic gene expression and metabolism as evidenced by RNA sequencing, respiration assays, and metabolite studies. Collectively, these findings suggest that the TAF complex may contribute to neurologic, craniofacial, and cardiac development through regulation of metabolism.
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Affiliation(s)
- Jamison Leid
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ryan Gray
- Departments of Nutritional Sciences, Dell Pediatrics Research Institute, University of Texas at Austin, Austin, TX 78723, USA
| | - Peter Rakita
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L. Koenig
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rohan Tripathy
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James A. J. Fitzpatrick
- Departments of Neuroscience and Cell Biology, Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles Kaufman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Immunology and Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
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D'Ignazio L, Jacomini RS, Qamar B, Benjamin KJM, Arora R, Sawada T, Evans TA, Diffenderfer KE, Pankonin AR, Hendriks WT, Hyde TM, Kleinman JE, Weinberger DR, Bragg DC, Paquola ACM, Erwin JA. Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism. eNeuro 2022; 9:ENEURO.0129-22.2022. [PMID: 35868859 PMCID: PMC9428949 DOI: 10.1523/eneuro.0129-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/14/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022] Open
Abstract
X-linked Dystonia-Parkinsonism (XDP) is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. The mechanisms underlying regional differences in degeneration and adult onset are unknown. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due, in part, to a partial loss of TAF1 function. A disease-specific SINE-VNTR-Alu (SVA) retrotransposon insertion occurs within intron 32 of TAF1, a subunit of TFIID involved in transcription initiation. While all XDP males are usually clinically affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight iPSC lines from three XDP female carrier individuals for X chromosome inactivation status and identified clonal lines that express either the wild-type X or XDP haplotype. Furthermore, we characterized XDP-relevant transcript expression in neurotypical humans, and found that SVA-F expression decreases after 30 years of age in the brain and that TAF1 is decreased in most female samples. Uniquely in the caudate nucleus, TAF1 expression is not sexually dimorphic and decreased after adolescence. These findings indicate that regional-, age- and sex-specific mechanisms regulate TAF1, highlighting the importance of disease-relevant models and postmortem tissue. We propose that the decreased TAF1 expression in the adult caudate may synergize with the XDP-specific partial loss of TAF1 function in patients, thereby passing a minimum threshold of TAF1 function, and triggering degeneration in the neostriatum.Significance StatementXDP is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due to a partial loss of TAF1 function. While all XDP males are usually affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight stem cell lines from XDP female carrier individuals. Furthermore, we found that, uniquely in the caudate nucleus, TAF1 expression decreases after adolescence in healthy humans. We hypothesize that the decrease of TAF1 after adolescence in human caudate, in general, may underlie the vulnerability of the adult neostriatum in XDP.
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Affiliation(s)
- Laura D'Ignazio
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ricardo S Jacomini
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Bareera Qamar
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ria Arora
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Biology, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taylor A Evans
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Aimee R Pankonin
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William T Hendriks
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University Baltimore, MD 21205, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Apua C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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Li X, Gao X, Huang S, Han M, Kang D, Yang J, Wu X, Zheng Q, Yuan Y, Dai P, Wang G. Establishment of an iPSC line (CPGHi005-A) from a patient with Waardenburg syndrome carrying a heterozygous SVA-F retrotransposon insertion into SOX10. Stem Cell Res 2022; 62:102831. [DOI: 10.1016/j.scr.2022.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/05/2022] [Indexed: 10/18/2022] Open
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Campion LN, Mejia Maza A, Yadav R, Penney EB, Murcar MG, Correia K, Gillis T, Fernandez-Cerado C, Velasco-Andrada MS, Legarda GP, Ganza-Bautista NG, Lagarde JBB, Acuña PJ, Multhaupt-Buell T, Aldykiewicz G, Supnet ML, De Guzman JK, Go C, Sharma N, Munoz EL, Ang MC, Diesta CCE, Bragg DC, Ozelius LJ, Wheeler VC. Tissue-specific and repeat length-dependent somatic instability of the X-linked dystonia parkinsonism-associated CCCTCT repeat. Acta Neuropathol Commun 2022; 10:49. [PMID: 35395816 PMCID: PMC8994295 DOI: 10.1186/s40478-022-01349-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a progressive adult-onset neurodegenerative disorder caused by insertion of a SINE-VNTR-Alu (SVA) retrotransposon in the TAF1 gene. The SVA retrotransposon contains a CCCTCT hexameric repeat tract of variable length, whose length is inversely correlated with age at onset. This places XDP in a broader class of repeat expansion diseases, characterized by the instability of their causative repeat mutations. Here, we observe similar inverse correlations between CCCTCT repeat length with age at onset and age at death and no obvious correlation with disease duration. To gain insight into repeat instability in XDP we performed comprehensive quantitative analyses of somatic instability of the XDP CCCTCT repeat in blood and in seventeen brain regions from affected males. Our findings reveal repeat length-dependent and expansion-based instability of the XDP CCCTCT repeat, with greater levels of expansion in brain than in blood. The brain exhibits regional-specific patterns of instability that are broadly similar across individuals, with cerebellum exhibiting low instability and cortical regions exhibiting relatively high instability. The spectrum of somatic instability in the brain includes a high proportion of moderate repeat length changes of up to 5 repeats, as well as expansions of ~ 20- > 100 repeats and contractions of ~ 20–40 repeats at lower frequencies. Comparison with HTT CAG repeat instability in postmortem Huntington’s disease brains reveals similar brain region-specific profiles, indicating common trans-acting factors that contribute to the instability of both repeats. Analyses in XDP brains of expansion of a different SVA-associated CCCTCT located in the LIPG gene, and not known to be disease-associated, reveals repeat length-dependent expansion at overall lower levels relative to the XDP CCCTCT repeat, suggesting that expansion propensity may be modified by local chromatin structure. Together, the data support a role for repeat length-dependent somatic expansion in the process(es) driving the onset of XDP and prompt further investigation into repeat dynamics and the relationship to disease.
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Marsili L, Duque KR, Bode RL, Kauffman MA, Espay AJ. Uncovering Essential Tremor Genetics: The Promise of Long-Read Sequencing. Front Neurol 2022; 13:821189. [PMID: 35401394 PMCID: PMC8983820 DOI: 10.3389/fneur.2022.821189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/25/2022] [Indexed: 12/23/2022] Open
Abstract
Long-read sequencing (LRS) technologies have been recently introduced to overcome intrinsic limitations of widely-used next-generation sequencing (NGS) technologies, namely the sequencing limited to short-read fragments (150–300 base pairs). Since its introduction, LRS has permitted many successes in unraveling hidden mutational mechanisms. One area in clinical neurology in need of rethinking as it applies to genetic mechanisms is essential tremor (ET). This disorder, among the most common in neurology, is a syndrome often exhibiting an autosomal dominant pattern of inheritance whose large phenotypic spectrum suggest a multitude of genetic etiologies. Exome sequencing has revealed the genetic etiology only in rare ET families (FUS, SORT1, SCN4A, NOS3, KCNS2, HAPLN4/BRAL2, and USP46). We hypothesize that a reason for this shortcoming may be non-classical genetic mechanism(s) underpinning ET, among them trinucleotide, tetranucleotide, or pentanucleotide repeat disorders. In support of this hypothesis, trinucleotide (e.g., GGC repeats in NOTCH2NLC) and pentanucleotide repeat disorders (e.g., ATTTC repeats in STARD7) have been revealed as pathogenic in patients with a past history of what has come to be referred to as “ET plus,” bilateral hand tremor associated with epilepsy and/or leukoencephalopathy. A systematic review of LRS in neurodegenerative disorders showed that 10 of the 22 (45%) genetic etiologies ascertained by LRS include tremor in their phenotypic spectrum, suggesting that future clinical applications of LRS for tremor disorders may uncover genetic subtypes of familial ET that have eluded NGS, particularly those with associated leukoencephalopathy or family history of epilepsy. LRS provides a pathway for potentially uncovering novel genes and genetic mechanisms, helping narrow the large proportion of “idiopathic” ET.
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Affiliation(s)
- Luca Marsili
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Kevin R. Duque
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Rachel L. Bode
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Marcelo A. Kauffman
- Consultorio y Laboratorio de Neurogenética, Centro Universitario de Neurología José María Ramos Mejía, Buenos Aires, Argentina
| | - Alberto J. Espay
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Alberto J. Espay
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Lüth T, Laβ J, Schaake S, Wohlers I, Pozojevic J, Jamora RDG, Rosales RL, Brüggemann N, Saranza G, Diesta CCE, Schlüter K, Tse R, Reyes CJ, Brand M, Busch H, Klein C, Westenberger A, Trinh J. Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing. Genes (Basel) 2022; 13:genes13010126. [PMID: 35052466 PMCID: PMC8775018 DOI: 10.3390/genes13010126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)n domain that acts as a genetic modifier of disease onset and expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach. Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus. Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Joshua Laβ
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Susen Schaake
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Inken Wohlers
- Medical Systems Biology Division, Luebeck Institute of Experimental Dermatology, University of Luebeck, 23538 Luebeck, Germany; (I.W.); (H.B.)
- Institute for Cardiogenetics, University of Luebeck, 23538 Luebeck, Germany
| | - Jelena Pozojevic
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Roland Dominic G. Jamora
- Department of Neurosciences, College of Medicine, Philippine General Hospital, University of the Philippines Manila, Manila 1000, Philippines;
| | - Raymond L. Rosales
- Department of Neurology and Psychiatry, The Hospital Neuroscience Institute, University of Santo Tomas, Manila 1008, Philippines;
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
- Department of Neurology, University of Luebeck, 23538 Luebeck, Germany
| | - Gerard Saranza
- Section of Neurology, Department of Internal Medicine, Chong Hua Hospital, Cebu City 6000, Philippines;
| | - Cid Czarina E. Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati 1229, Philippines;
| | - Kathleen Schlüter
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Ronnie Tse
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Charles Jourdan Reyes
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Max Brand
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Hauke Busch
- Medical Systems Biology Division, Luebeck Institute of Experimental Dermatology, University of Luebeck, 23538 Luebeck, Germany; (I.W.); (H.B.)
- Institute for Cardiogenetics, University of Luebeck, 23538 Luebeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Ana Westenberger
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
- Correspondence:
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Pozojevic J, Cruz JN, Westenberger A. X-linked dystonia-parkinsonism: over and above a repeat disorder. MED GENET-BERLIN 2021; 33:319-324. [PMID: 38835428 PMCID: PMC11006257 DOI: 10.1515/medgen-2021-2105] [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: 04/29/2021] [Accepted: 11/24/2021] [Indexed: 06/06/2024]
Abstract
X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative movement disorder, caused by a founder retrotransposon insertion in an intron of the TAF1 gene. This insertion contains a polymorphic hexanucleotide repeat (CCCTCT)n, the length of which inversely correlates with the age at disease onset (AAO) and other clinical parameters, aligning XDP with repeat expansion disorders. Nevertheless, many other pathogenic mechanisms are conceivably at play in XDP, indicating that in contrast to other repeat disorders, the (CCCTCT)n repeat may not be the actual (or only) disease cause. Here, we summarize and discuss genetic and molecular aspects of XDP, highlighting the role of the hexanucleotide repeat in age-related disease penetrance and expressivity.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Joseph Neos Cruz
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Disease Molecular Biology and Epigenetics Laboratory, University of the Philippines Diliman, Quezon City, Philippines
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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