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Rosenkrantz JL, Brandorff JE, Raghib S, Kapadia A, Vaine CA, Bragg DC, Farmiloe G, Jacobs FMJ. ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP). Proc Natl Acad Sci U S A 2024; 121:e2401217121. [PMID: 39102544 PMCID: PMC11331120 DOI: 10.1073/pnas.2401217121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative disorder resulting from an inherited intronic SINE-Alu-VNTR (SVA) retrotransposon in the TAF1 gene that causes dysregulation of TAF1 transcription. The specific mechanism underlying this dysregulation remains unclear, but it is hypothesized to involve the formation of G-quadruplexes (G4) structures within the XDP-SVA that impede transcription. In this study, we show that ZNF91, a critical repressor of SVA retrotransposons, specifically binds to G4-forming DNA sequences. Further, we found that genetic deletion of ZNF91 exacerbates the molecular phenotype associated with the XDP-SVA insertion in patient cells, while no difference was observed when ZNF91 was deleted from isogenic control cells. Additionally, we observed a significant age-related reduction in ZNF91 expression in whole blood and brain, indicating a progressive loss of repression of the XDP-SVA in XDP. These findings indicate that ZNF91 plays a crucial role in controlling the molecular phenotype associated with XDP. Since ZNF91 binds to G4-forming DNA sequences in SVAs, this suggests that interactions between ZNF91 and G4-forming sequences in the XDP-SVA minimize the severity of the molecular phenotype. Our results showing that ZNF91 expression levels significantly decrease with age provide a potential explanation for the age-related progressive neurodegenerative character of XDP. Collectively, our study provides important insights into the protective role of ZNF91 in XDP pathogenesis and suggests that restoring ZNF91 expression, destabilization of G4s, or targeted repression of the XDP-SVA could be future therapeutic strategies to prevent or treat XDP.
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Affiliation(s)
- Jimi L. Rosenkrantz
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - J. Elias Brandorff
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Sanaz Raghib
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Ashni Kapadia
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Christine A. Vaine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA02129
| | - D. Cristopher Bragg
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA02129
| | - Grace Farmiloe
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
| | - Frank M. J. Jacobs
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam1098 XH, The Netherlands
- Faculty of Science, Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam1098 XH, The Netherlands
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2
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Crombie EM, Korecki AJ, Cleverley K, Adair BA, Cunningham TJ, Lee WC, Lengyell TC, Maduro C, Mo V, Slade LM, Zouhair I, Fisher EMC, Simpson EM. Taf1 knockout is lethal in embryonic male mice and heterozygous females show weight and movement disorders. Dis Model Mech 2024; 17:dmm050741. [PMID: 38804708 PMCID: PMC11261634 DOI: 10.1242/dmm.050741] [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: 02/01/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
The TATA box-binding protein-associated factor 1 (TAF1) is a ubiquitously expressed protein and the largest subunit of the basal transcription factor TFIID, which plays a key role in initiation of RNA polymerase II-dependent transcription. TAF1 missense variants in human males cause X-linked intellectual disability, a neurodevelopmental disorder, and TAF1 is dysregulated in X-linked dystonia-parkinsonism, a neurodegenerative disorder. However, this field has lacked a genetic mouse model of TAF1 disease to explore its mechanism in mammals and treatments. Here, we generated and validated a conditional cre-lox allele and the first ubiquitous Taf1 knockout mouse. We discovered that Taf1 deletion in male mice was embryonically lethal, which may explain why no null variants have been identified in humans. In the brains of Taf1 heterozygous female mice, no differences were found in gross structure, overall expression and protein localisation, suggesting extreme skewed X inactivation towards the non-mutant chromosome. Nevertheless, these female mice exhibited a significant increase in weight, weight with age, and reduced movement, suggesting that a small subset of neurons was negatively impacted by Taf1 loss. Finally, this new mouse model may be a future platform for the development of TAF1 disease therapeutics.
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Affiliation(s)
- Elisa M. Crombie
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Andrea J. Korecki
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Karen Cleverley
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Bethany A. Adair
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z3, Canada
| | | | - Weaverly Colleen Lee
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Tess C. Lengyell
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Cheryl Maduro
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Victor Mo
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Liam M. Slade
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Ines Zouhair
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Elizabeth M. C. Fisher
- Department of Neuromuscular Diseases, UCL Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z3, Canada
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3
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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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4
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Petrozziello T, Motlagh NJ, Monsanto RZB, Lei D, Murcar MG, Penney EB, Bragg DC, Fernandez-Cerado C, Legarda GP, Sy M, Muñoz E, Ang MC, Diesta CCE, Zhang C, Tanzi RE, Qureshi IA, Chen JW, Sadri-Vakili G. Targeting myeloperoxidase to reduce neuroinflammation in X-linked dystonia parkinsonism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.25.24309481. [PMID: 38978657 PMCID: PMC11230314 DOI: 10.1101/2024.06.25.24309481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Although the genetic locus of X-linked dystonia parkinsonism (XDP), a neurodegenerative disease endemic in the Philippines, is well-characterized, the exact molecular mechanisms leading to neuronal loss are not yet fully understood. Recently, we demonstrated a significant increase in astrogliosis and microgliosis together with an increase in myeloperoxidase (MPO) levels in XDP post-mortem prefrontal cortex (PFC), suggesting a role for neuroinflammation in XDP pathogenesis. Here, we demonstrated a significant increase in MPO activity in XDP PFC using a novel specific MPO-activatable fluorescent agent (MAFA). Additionally, we demonstrated a significant increase in reactive oxygen species (ROS) in XDP-derived fibroblasts as well as in SH-SY5Y cells treated with post-mortem XDP PFC, further supporting a role for MPO in XDP. To determine whether increases in MPO activity were linked to increases in ROS, MPO content was immuno-depleted from XDP PFC [MPO(-)], which resulted in a significant decrease in ROS in SH-SY5Y cells. Consistently, the treatment with verdiperstat, a potent and selective MPO inhibitor, significantly decreased ROS in both XDP-derived fibroblasts and XDP PFC-treated SH-SY5Y cells. Collectively, our results suggest that MPO inhibition mitigates oxidative stress and may provide a novel therapeutic strategy for XDP treatment. Highlights MPO activity is increased in XDP post-mortem prefrontal cortex.MPO activity is increased in cellular models of XDP.MPO increases reactive oxygen species (ROS) in vitro.Inhibiting MPO mitigates ROS in XDP.The MPO inhibitor, verdiperstat, dampens ROS suggesting a potential therapeutic strategy for XDP.
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5
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Horváth V, Garza R, Jönsson ME, Johansson PA, Adami A, Christoforidou G, Karlsson O, Castilla Vallmanya L, Koutounidou S, Gerdes P, Pandiloski N, Douse CH, Jakobsson J. Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease. Nat Struct Mol Biol 2024:10.1038/s41594-024-01320-8. [PMID: 38834915 DOI: 10.1038/s41594-024-01320-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
SVA (SINE (short interspersed nuclear element)-VNTR (variable number of tandem repeats)-Alu) retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized and how their regulatory impact is constrained by an innate epigenetic defense system.
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Affiliation(s)
- Vivien Horváth
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Pia A Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Georgia Christoforidou
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Laura Castilla Vallmanya
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Symela Koutounidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ninoslav Pandiloski
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christopher H Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden.
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6
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Fröhlich A, Pfaff AL, Middlehurst B, Hughes LS, Bubb VJ, Quinn JP, Koks S. Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression. Sci Rep 2024; 14:10932. [PMID: 38740892 DOI: 10.1038/s41598-024-61753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are transposable elements which represent a source of genetic variation. We previously demonstrated that the presence/absence of a human-specific SVA, termed SVA_67, correlated with the progression of Parkinson's disease (PD). In the present study, we demonstrate that SVA_67 acts as expression quantitative trait loci, thereby exhibiting a strong regulatory effect across the genome using whole genome and transcriptomic data from the Parkinson's progression markers initiative cohort. We further show that SVA_67 is polymorphic for its variable number tandem repeat domain which correlates with both regulatory properties in a luciferase reporter gene assay in vitro and differential expression of multiple genes in vivo. Additionally, this variation's utility as a biomarker is reflected in a correlation with a number of PD progression markers. These experiments highlight the plethora of transcriptomic and phenotypic changes associated with SVA_67 polymorphism which should be considered when investigating the missing heritability of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren S Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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7
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Prasuhn J, Henkel J, Algodon SM, Uter J, Rosales RL, Klein C, Steinhardt J, Diesta CC, Brüggemann N. Neuroenergetic Changes in Patients with X-Linked Dystonia-Parkinsonism and Female Carriers. Mov Disord Clin Pract 2024; 11:550-555. [PMID: 38404049 PMCID: PMC11078482 DOI: 10.1002/mdc3.14001] [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: 06/14/2023] [Revised: 01/03/2024] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND X-linked dystonia-parkinsonism (XDP) is a rare movement disorder characterized by profound neurodegeneration in the basal ganglia. The molecular consequences and the bioenergetic state of affected individuals remain largely unexplored. OBJECTIVES To investigate the bioenergetic state in male patients with XDP and female carriers using 31phosphorus magnetic resonance spectroscopy imaging and to correlate these findings with clinical manifestations. METHODS We examined the levels of high-energy phosphorus-containing metabolites (HEP) in the basal ganglia and cerebellum of five male patients with XDP, 10 asymptomatic female heterozygous carriers, and 10 SVA-insertion-free controls. RESULTS HEP levels were reduced in the basal ganglia of patients with XDP (PwXDP) compared to controls, but increased in the cerebellum of both male patients and female carriers. CONCLUSIONS Our findings suggest a potential compensatory mechanism in the cerebellum of female carriers regardless of sex. Our study highlights alterations in HEP levels in PwXDP patients and female carriers.
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Affiliation(s)
- Jannik Prasuhn
- Department of NeurologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Julia Henkel
- Department of NeurologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Jan Uter
- Department of NeurologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Raymond L. Rosales
- Department of Neurology and PsychiatryUniversity of Santo ThomasManilaPhilippines
| | | | - Julia Steinhardt
- Department of NeurologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
| | - Cid C. Diesta
- Makati Medical CenterMakati CityPhilippines
- Asian Hospital and Medical CenterManilaPhilippines
| | - Norbert Brüggemann
- Department of NeurologyUniversity Medical Center Schleswig‐HolsteinLübeckGermany
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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8
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Miano-Burkhardt A, Alvarez Jerez P, Daida K, Bandres Ciga S, Billingsley KJ. The Role of Structural Variants in the Genetic Architecture of Parkinson's Disease. Int J Mol Sci 2024; 25:4801. [PMID: 38732020 PMCID: PMC11084710 DOI: 10.3390/ijms25094801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) significantly impacts millions of individuals worldwide. Although our understanding of the genetic foundations of PD has advanced, a substantial portion of the genetic variation contributing to disease risk remains unknown. Current PD genetic studies have primarily focused on one form of genetic variation, single nucleotide variants (SNVs), while other important forms of genetic variation, such as structural variants (SVs), are mostly ignored due to the complexity of detecting these variants with traditional sequencing methods. Yet, these forms of genetic variation play crucial roles in gene expression and regulation in the human brain and are causative of numerous neurological disorders, including forms of PD. This review aims to provide a comprehensive overview of our current understanding of the involvement of coding and noncoding SVs in the genetic architecture of PD.
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Affiliation(s)
- Abigail Miano-Burkhardt
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Sara Bandres Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
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9
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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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10
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Kulski JK, Suzuki S, Shiina T, Pfaff AL, Kõks S. Regulatory SVA retrotransposons and classical HLA genotyped-transcripts associated with Parkinson's disease. Front Immunol 2024; 15:1349030. [PMID: 38590523 PMCID: PMC10999589 DOI: 10.3389/fimmu.2024.1349030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/06/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction Parkinson's disease (PD) is a neurodegenerative and polygenic disorder characterised by the progressive loss of neural dopamine and onset of movement disorders. We previously described eight SINE-VNTR-Alu (SVA) retrotransposon-insertion-polymorphisms (RIPs) located and expressed within the Human Leucocyte Antigen (HLA) genomic region of chromosome 6 that modulate the differential co-expression of 71 different genes including the HLA classical class I and class II genes in a Parkinson's Progression Markers Initiative (PPMI) cohort. Aims and methods In the present study, we (1) reanalysed the PPMI genomic and transcriptomic sequencing data obtained from whole blood of 1521 individuals (867 cases and 654 controls) to infer the genotypes of the transcripts expressed by eight classical HLA class I and class II genes as well as DRA and the DRB3/4/5 haplotypes, and (2) examined the statistical differences between three different PD subgroups (cases) and healthy controls (HC) for the HLA and SVA transcribed genotypes and inferred haplotypes. Results Significant differences for 57 expressed HLA alleles (21 HLA class I and 36 HLA class II alleles) up to the three-field resolution and four of eight expressed SVA were detected at p<0.05 by the Fisher's exact test within one or other of three different PD subgroups (750 individuals with PD, 57 prodromes, 60 individuals who had scans without evidence of dopamine deficits [SWEDD]), when compared against a group of 654 HCs within the PPMI cohort and when not corrected by the Bonferroni test for multiple comparisons. Fourteen of 20 significant alleles were unique to the PD-HC comparison, whereas 31 of the 57 alleles overlapped between two or more different subgroup comparisons. Only the expressed HLA-DRA*01:01:01 and -DQA1*03:01:01 protective alleles (PD v HC), the -DQA1*03:03:01 risk (HC v Prodrome) or protective allele (PD v Prodrome), the -DRA*01:01:02 and -DRB4*01:03:02 risk alleles (SWEDD v HC), and the NR_SVA_381 present genotype (PD v HC) at a 5% homozygous insertion frequency near HLA-DPA1, were significant (Pc<0.1) after Bonferroni corrections. The homologous NR_SVA_381 insertion significantly decreased the transcription levels of HLA-DPA1 and HLA-DPB1 in the PPMI cohort and its presence as a homozygous genotype is a risk factor (Pc=0.012) for PD. The most frequent NR_SVA_381 insertion haplotype in the PPMI cohort was NR_SVA_381/DPA1*02/DPB1*01 (3.7%). Although HLA C*07/B*07/DRB5*01/DRB1*15/DQB1*06 was the most frequent HLA 5-loci phased-haplotype (n, 76) in the PPMI cohort, the NR_SVA_381 insertion was present in only six of them (8%). Conclusions These data suggest that expressed SVA and HLA gene alleles in circulating white blood cells are coordinated differentially in the regulation of immune responses and the long-term onset and progression of PD, the mechanisms of which have yet to be elucidated.
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Affiliation(s)
- Jerzy K. Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Health and Medical Science, Division of Immunology and Microbiology, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
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11
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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12
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Alonto AHD, Jamora RDG. A scoping review on the diagnosis and treatment of X-linked dystonia-parkinsonism. Parkinsonism Relat Disord 2024; 119:105949. [PMID: 38072720 DOI: 10.1016/j.parkreldis.2023.105949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 01/21/2024]
Abstract
INTRODUCTION X-linked dystonia-parkinsonism (XDP) is a progressive neurodegenerative disorder that has been studied well in recent years. OBJECTIVES This scoping review aimed to describe the current state of knowledge about the diagnosis and treatment of XDP, to provide clinicians with a concise and up-to-date overview. METHODS We conducted a scoping review of pertinent literature on the diagnosis and treatment of XDP using Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidelines. RESULTS There were 24 articles on diagnostic methods and 20 articles on therapeutic interventions for XDP, with 7 review articles describing both. The detection of the SVA retrotransposon insertion within the TAF1 gene is confirmatory for XDP. Oral medications are marginally effective. Chemodenervation with botulinum toxin is an effective treatment. Pallidal deep brain stimulation (DBS) has been shown to provide significant improvement in the dystonia and quality of life of patients with XDP for a longer time. A less invasive surgical option is the transcranial magnetic resonance-guided focused ultrasound (tcMRgFUS), which has shown promising effects with the limited number of case reports available. CONCLUSION XDP is a geneti disorder characterized by striatal symptoms and pathology on neuroimaging. No effective oral medications are available for the management of XDP. The use of botulinum toxin is limited by its cost and duration of effects. As of now, pallidal DBS is deemed to be the best option. Another promising option is the tcMRgFUS but still has limited studies on its safety and efficacy in XDP.
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Affiliation(s)
- Anisah Hayaminnah D Alonto
- Department of Neurosciences, College of Medicine and Philippine General Hospital, University of the Philippines Manila, Manila, Philippines.
| | - Roland Dominic G Jamora
- Department of Neurosciences, College of Medicine and Philippine General Hospital, University of the Philippines Manila, Manila, Philippines; Institute for Neurosciences, St. Luke's Medical Center, Quezon City & Global City, Philippines.
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13
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Singh S, Borkar MR, Bhatt LK. Transposable Elements: Emerging Therapeutic Targets in Neurodegenerative Diseases. Neurotox Res 2024; 42:9. [PMID: 38270797 DOI: 10.1007/s12640-024-00688-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are characterized by the progressive loss of neuronal function and structure. While several genetic and environmental factors have been implicated in the pathogenesis of these disorders, emerging evidence suggests that transposable elements (TEs), once considered "junk DNA," play a significant role in their development and progression. TEs are mobile genetic elements capable of moving within the genome, and their dysregulation has been associated with genomic instability, altered gene expression, and neuroinflammation. This review provides an overview of TEs, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs), mechanisms of repression and derepression, and their potential impact on neurodegeneration. The evidence linking TEs to AD, PD, and ALS by shedding light on the complex interactions between TEs and neurodegeneration has been discussed. Furthermore, the therapeutic potential of targeting TEs in neurodegenerative diseases has been explored. Understanding the role of TEs in neurodegeneration holds promise for developing novel therapeutic strategies aimed at mitigating disease progression and preserving neuronal health.
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Affiliation(s)
- Shrishti Singh
- Department of Pharmacology, Bhanuben Nanavati College of Pharmacy, SVKM's DrVile Parle (W), Mumbai, India
| | - Maheshkumar R Borkar
- Department of Pharmaceutical Chemistry, SVKM's Dr, Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, Bhanuben Nanavati College of Pharmacy, SVKM's DrVile Parle (W), Mumbai, India.
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14
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Thomsen M, Lange LM, Zech M, Lohmann K. Genetics and Pathogenesis of Dystonia. ANNUAL REVIEW OF PATHOLOGY 2024; 19:99-131. [PMID: 37738511 DOI: 10.1146/annurev-pathmechdis-051122-110756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Dystonia is a clinically and genetically highly heterogeneous neurological disorder characterized by abnormal movements and postures caused by involuntary sustained or intermittent muscle contractions. A number of groundbreaking genetic and molecular insights have recently been gained. While they enable genetic testing and counseling, their translation into new therapies is still limited. However, we are beginning to understand shared pathophysiological pathways and molecular mechanisms. It has become clear that dystonia results from a dysfunctional network involving the basal ganglia, cerebellum, thalamus, and cortex. On the molecular level, more than a handful of, often intertwined, pathways have been linked to pathogenic variants in dystonia genes, including gene transcription during neurodevelopment (e.g., KMT2B, THAP1), calcium homeostasis (e.g., ANO3, HPCA), striatal dopamine signaling (e.g., GNAL), endoplasmic reticulum stress response (e.g., EIF2AK2, PRKRA, TOR1A), autophagy (e.g., VPS16), and others. Thus, different forms of dystonia can be molecularly grouped, which may facilitate treatment development in the future.
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Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
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15
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Tshilenge KT, Bons J, Aguirre CG, Geronimo-Olvera C, Shah S, Rose J, Gerencser AA, Mak SK, Ehrlich ME, Bragg DC, Schilling B, Ellerby LM. Proteomic analysis of X-linked dystonia parkinsonism disease striatal neurons reveals altered RNA metabolism and splicing. Neurobiol Dis 2024; 190:106367. [PMID: 38042508 PMCID: PMC11103251 DOI: 10.1016/j.nbd.2023.106367] [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: 09/22/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a rare neurodegenerative disease endemic to the Philippines. The genetic cause for XDP is an insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within intron 32 of TATA-binding protein associated factor 1 (TAF1) that causes an alteration of TAF1 splicing, partial intron retention, and decreased transcription. Although TAF1 is expressed in all organs, medium spiny neurons (MSNs) within the striatum are one of the cell types most affected in XDP. To define how mutations in the TAF1 gene lead to MSN vulnerability, we carried out a proteomic analysis of human XDP patient-derived neural stem cells (NSCs) and MSNs derived from induced pluripotent stem cells. NSCs and MSNs were grown in parallel and subjected to quantitative proteomic analysis in data-independent acquisition mode on the Orbitrap Eclipse Tribrid mass spectrometer. Subsequent functional enrichment analysis demonstrated that neurodegenerative disease-related pathways, such as Huntington's disease, spinocerebellar ataxia, cellular senescence, mitochondrial function and RNA binding metabolism, were highly represented. We used weighted coexpression network analysis (WGCNA) of the NSC and MSN proteomic data set to uncover disease-driving network modules. Three of the modules significantly correlated with XDP genotype when compared to the non-affected control and were enriched for DNA helicase and nuclear chromatin assembly, mitochondrial disassembly, RNA location and mRNA processing. Consistent with aberrant mRNA processing, we found splicing and intron retention of TAF1 intron 32 in XDP MSN. We also identified TAF1 as one of the top enriched transcription factors, along with YY1, ATF2, USF1 and MYC. Notably, YY1 has been implicated in genetic forms of dystonia. Overall, our proteomic data set constitutes a valuable resource to understand mechanisms relevant to TAF1 dysregulation and to identify new therapeutic targets for XDP.
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Affiliation(s)
| | - Joanna Bons
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Carlos Galicia Aguirre
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - Samah Shah
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Jacob Rose
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Akos A Gerencser
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Sally K Mak
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA, USA
| | - Birgit Schilling
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
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16
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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17
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Zhang J, Tang J, Li G, Li N, Wang J, Yao R, Yu T. SINE-VNTR-Alu retrotransposon insertion as a novel mutational event underlying Glanzmann thrombasthenia. J Thromb Haemost 2023; 21:3597-3607. [PMID: 37604334 DOI: 10.1016/j.jtha.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Glanzmann thrombasthenia (GT) is an autosomal recessive platelet aggregation disorder caused by mutations in ITGA2B or ITGB3. OBJECTIVES We aimed to assess the phenotype and investigate the genetic etiology of a GT pedigree. METHODS A patient with bleeding manifestations and mild mental retardation was enrolled. Complete blood count, coagulation, and platelet aggregation tests were performed. Causal mutations were identified via whole exome and genome sequencing and subsequently confirmed through polymerase chain reaction and Sanger sequencing. The transcription of ITGB3 was characterized using RNA sequencing and reverse transcription polymerase chain reaction. The αⅡb and β3 biosynthesis was investigated via whole blood flow cytometry and in vitro studies. RESULTS GT was diagnosed in a patient with defective platelet aggregation. Novel compound heterozygous ITGB3 variants were identified, with a maternal nonsense mutation (c.2222G>A, p.Trp741∗) and a paternal SINE-VNTR-Alu (SVA) retrotransposon insertion. The 5' truncated SVA element was inserted in a sense orientation in intron 11 of ITGB3, resulting in aberrant splicing of ITGB3 and significantly reducing β3 protein content. Meanwhile, both the expression and transportation of β3 were damaged by the ITGB3 c.2222G>A. Almost no αⅡb and β3 expressions were detected on the patient's platelets surface. CONCLUSION Novel compound heterozygous ITGB3 mutations were identified in the GT pedigree, resulting in defects of αⅡbβ3 biosynthesis. This is the first report of SVA retrotransposon insertion in the genetic pathogenesis of GT. Our study highlights the importance of combining multiple high-throughput sequencing technologies for the molecular diagnosis of genetic disorders.
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Affiliation(s)
- Jiasheng Zhang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Tang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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18
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Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res 2023; 51:11453-11465. [PMID: 37823611 PMCID: PMC10681720 DOI: 10.1093/nar/gkad821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are evolutionarily young and still-active transposable elements (TEs) in the human genome. Several pathogenic SVA insertions have been identified that directly mutate host genes to cause neurodegenerative and other types of diseases. However, due to their sequence heterogeneity and complex structures as well as limitations in sequencing techniques and analysis, SVA insertions have been less well studied compared to other mobile element insertions. Here, we identified polymorphic SVA insertions from 3646 whole-genome sequencing (WGS) samples of >150 diverse populations and constructed a polymorphic SVA insertion reference catalog. Using 20 long-read samples, we also assembled reference and polymorphic SVA sequences and characterized the internal hexamer/variable-number-tandem-repeat (VNTR) expansions as well as differing SVA activity for SVA subfamilies and human populations. In addition, we developed a module to annotate both reference and polymorphic SVA copies. By characterizing the landscape of both reference and polymorphic SVA retrotransposons, our study enables more accurate genotyping of these elements and facilitate the discovery of pathogenic SVA insertions.
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Eric W Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Antuan Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Natalie I Ho
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
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Fröhlich A, Hughes LS, Middlehurst B, Pfaff AL, Bubb VJ, Koks S, Quinn JP. CRISPR deletion of a SINE-VNTR- Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol 2023; 14:1273036. [PMID: 37840928 PMCID: PMC10570551 DOI: 10.3389/fneur.2023.1273036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Background SINE-VNTR-Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specific SVA element, termed SVA_67, was associated with differential expression of several genes at the MAPT locus, a locus associated with Parkinson's Disease (PD) and frontotemporal dementia. However, we were not able to demonstrate that causation of differential gene expression was directed by the SVA due to lack of functional validation. Methods We performed CRISPR to delete SVA_67 in the HEK293 cell line. Quantification of target gene expression was performed using qPCR to assess the effects on expression in response to the deletion of SVA_67. Differences between CRISPR edit and control cell lines were analysed using two-tailed t-test with a minimum 95% confidence interval to determine statistical significance. Results In this study, we provide data highlighting the SVA-specific effect on differential gene expression. We demonstrate that the hemizygous deletion of the endogenous SVA_67 in CRISPR edited cell lines was associated with differential expression of several genes at the MAPT locus associated with neurodegenerative diseases including KANSL1, MAPT and LRRC37A. Discussion This data is consistent with our previous bioinformatic work of differential gene expression analysis using transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) cohort. As SVAs have regulatory influences on gene expression, and insertion polymorphisms contribute to interpersonal differences in expression patterns, these results highlight the potential contribution of these elements to complex diseases with potentially many genetic components, such as PD.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Lauren S. Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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21
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Jagota P, Ugawa Y, Aldaajani Z, Ibrahim NM, Ishiura H, Nomura Y, Tsuji S, Diesta C, Hattori N, Onodera O, Bohlega S, Al-Din A, Lim SY, Lee JY, Jeon B, Pal PK, Shang H, Fujioka S, Kukkle PL, Phokaewvarangkul O, Lin CH, Shambetova C, Bhidayasiri R. Nine Hereditary Movement Disorders First Described in Asia: Their History and Evolution. J Mov Disord 2023; 16:231-247. [PMID: 37309109 PMCID: PMC10548072 DOI: 10.14802/jmd.23065] [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: 03/31/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
Clinical case studies and reporting are important to the discovery of new disorders and the advancement of medical sciences. Both clinicians and basic scientists play equally important roles leading to treatment discoveries for both cures and symptoms. In the field of movement disorders, exceptional observation of patients from clinicians is imperative, not just for phenomenology but also for the variable occurrences of these disorders, along with other signs and symptoms, throughout the day and the disease course. The Movement Disorders in Asia Task Force (TF) was formed to help enhance and promote collaboration and research on movement disorders within the region. As a start, the TF has reviewed the original studies of the movement disorders that were preliminarily described in the region. These include nine disorders that were first described in Asia: Segawa disease, PARK-Parkin, X-linked dystonia-parkinsonism, dentatorubral-pallidoluysian atrophy, Woodhouse-Sakati syndrome, benign adult familial myoclonic epilepsy, Kufor-Rakeb disease, tremulous dystonia associated with mutation of the calmodulin-binding transcription activator 2 gene, and paroxysmal kinesigenic dyskinesia. We hope that the information provided will honor the original researchers and help us learn and understand how earlier neurologists and basic scientists together discovered new disorders and made advances in the field, which impact us all to this day.
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Affiliation(s)
- Priya Jagota
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Yoshikazu Ugawa
- Department of Human Neurophysiology, Faculty of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Zakiyah Aldaajani
- Neurology Unit, King Fahad Military Medical Complex, Dhahran, Saudi Arabia
| | - Norlinah Mohamed Ibrahim
- Neurology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hiroyuki Ishiura
- Department of Neurology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshiko Nomura
- Yoshiko Nomura Neurological Clinic for Children, Tokyo, Japan
| | - Shoji Tsuji
- Institute of Medical Genomics, International University of Health and Welfare, Narita, Chiba, Japan
| | - Cid Diesta
- Section of Neurology, Department of Neuroscience, Makati Medical Center, NCR, Makati City, Philippines
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Saeed Bohlega
- Department of Neurosciences, King Faisal Specialist Hospital & Research Center, Riyad, Saudi Arabia
| | - Amir Al-Din
- Mid Yorkshire Hospitals National Health Services Trust, Wakefield, UK
| | - Shen-Yang Lim
- Division of Neurology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- The Mah Pooi Soo & Tan Chin Nam Centre for Parkinson’s & Related Disorders, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jee-Young Lee
- Department of Neurology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center & Seoul National University Medical College, Seoul, Korea
| | - Beomseok Jeon
- Department of Neurology, Seoul National University, Seoul, Korea
- Movement Disorder Center, Seoul National University Hospital, Seoul, Korea
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health & Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shinsuke Fujioka
- Department of Neurology, Fukuoka University, Faculty of Medicine, Fukuoka, Japan
| | - Prashanth Lingappa Kukkle
- Center for Parkinson’s Disease and Movement Disorders, Manipal Hospital, Bangalore, India
- Parkinson's Disease and Movement Disorders Clinic, Bangalore, India
| | - Onanong Phokaewvarangkul
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Roongroj Bhidayasiri
- Chulalongkorn Centre of Excellence for Parkinson’s Disease and Related Disorders, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- The Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
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22
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Fröhlich A, Pfaff AL, Bubb VJ, Quinn JP, Koks S. Reference LINE-1 insertion polymorphisms correlate with Parkinson's disease progression and differential transcript expression in the PPMI cohort. Sci Rep 2023; 13:13857. [PMID: 37620405 PMCID: PMC10449770 DOI: 10.1038/s41598-023-41052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023] Open
Abstract
Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons make up 17% of the human genome. They represent one class of transposable elements with the capacity to both mobilize autonomously and in trans via the mobilization of other elements, primarily Alu and SVA elements. Reference LINE-1 elements are, by definition, found in the reference genome, however, due to the polymorphic nature of these elements, variation for presence or absence is present within the population. We used a combination of clinical and transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) and applied matrix expression quantitative trait loci analysis and linear mixed-effects models involving 114 clinical, biochemical and imaging data from the PPMI cohort to elucidate the role of reference LINE-1 insertion polymorphism on both gene expression genome-wide and progression of Parkinson's disease (PD). We demonstrate that most LINE-1 insertion polymorphisms are capable of regulating gene expression, preferentially in trans, including previously identified PD risk loci. In addition, we show that 70 LINE-1 elements were associated with longitudinal changes of at least one PD progression marker, including ipsilateral count density ratio and UPDRS scores which are indicators of degeneration and severity. In conclusion, this study highlights the effect of the polymorphic nature of LINE-1 retrotransposons on gene regulation and progression of PD which underlines the importance of analyzing transposable elements within complex diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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23
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Maalouf KE, Vaine CA, Frederick DM, Yoshinaga A, Obuchi W, Mahjoum S, Nieland L, Al Ali J, Bragg DC, Breakefield XO, Breyne K. Tracking human neurologic disease status in mouse brain/plasma using reporter-tagged, EV-associated biomarkers. Mol Ther 2023; 31:2206-2219. [PMID: 37198883 PMCID: PMC10362415 DOI: 10.1016/j.ymthe.2023.05.011] [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: 11/02/2022] [Revised: 04/17/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disease caused by a retrotransposon insertion in intron 32 of the TAF1 gene. This insertion causes mis-splicing of intron 32 (TAF1-32i) and reduced TAF1 levels. TAF1-32i transcript is unique to XDP patient cells and can be detected in their extracellular vesicles (EVs). We engrafted patient and control iPSC-derived neural progenitor cells (hNPCs) into the striatum of mice. To track TAF1-32i transcript spread by EVs, we transduced the brain-implanted hNPCs with a lentiviral construct called ENoMi, which consists of a re-engineered tetraspanin scaffold tagged with bioluminescent and fluorescent reporter proteins under an EF-1α promoter. Alongside this improved detection in ENoMi-hNPCs-derived EVs, their surface allows specific immunocapture purification, thereby facilitating TAF1-32i analysis. Using this ENoMi-labeling method, TAF1-32i was demonstrated in EVs released from XDP hNPCs implanted in mouse brains. Post-implantation of ENoMi-XDP hNPCs, TAF1-32i transcript was retrieved in EVs isolated from mouse brain and blood, and levels increased over time in plasma. We compared and combined our EV isolation technique to analyze XDP-derived TAF1-32i with other techniques, including size exclusion chromatography and Exodisc. Overall, our study demonstrates the successful engraftment of XDP patient-derived hNPCs in mice as a tool for monitoring disease markers with EVs.
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Affiliation(s)
- Katia E Maalouf
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Christine A Vaine
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Dawn M Frederick
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Akiko Yoshinaga
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Wataru Obuchi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Shadi Mahjoum
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lisa Nieland
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jamal Al Ali
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Xandra O Breakefield
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA; Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02114, USA.
| | - Koen Breyne
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02114, USA.
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24
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Mätlik K, Baffuto M, Kus L, Deshmukh AL, Davis DA, Paul MR, Carroll TS, Caron MC, Masson JY, Pearson CE, Heintz N. Cell Type Specific CAG Repeat Expansions and Toxicity of Mutant Huntingtin in Human Striatum and Cerebellum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538082. [PMID: 37333326 PMCID: PMC10274669 DOI: 10.1101/2023.04.24.538082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Brain region-specific degeneration and somatic expansions of the mutant Huntingtin (mHTT) CAG tract are key features of Huntington's disease (HD). However, the relationships between CAG expansions, death of specific cell types, and molecular events associated with these processes are not established. Here we employed fluorescence-activated nuclear sorting (FANS) and deep molecular profiling to gain insight into the properties of cell types of the human striatum and cerebellum in HD and control donors. CAG expansions arise in striatal medium spiny neurons (MSNs) and cholinergic interneurons, in cerebellar Purkinje neurons, and at mATXN3 in MSNs from SCA3 donors. CAG expansions in MSNs are associated with higher levels of MSH2 and MSH3 (forming MutSβ), which can inhibit nucleolytic excision of CAG slip-outs by FAN1 in a concentration-dependent manner. Our data indicate that ongoing CAG expansions are not sufficient for cell death, and identify transcriptional changes associated with somatic CAG expansions and striatal toxicity.
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25
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Acuna P, Supnet-Wells ML, Spencer NA, de Guzman JK, Russo M, Hunt A, Stephen C, Go C, Carr S, Ganza NG, Lagarde JB, Begalan S, Multhaupt-Buell T, Aldykiewicz G, Paul L, Ozelius L, Bragg DC, Perry B, Green JR, Miller JW, Sharma N. Establishing a natural history of X-linked dystonia parkinsonism. Brain Commun 2023; 5:fcad106. [PMID: 37265597 PMCID: PMC10231801 DOI: 10.1093/braincomms/fcad106] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 08/10/2024] Open
Abstract
X-linked dystonia parkinsonism is a neurodegenerative movement disorder that affects men whose mothers originate from the island of Panay, Philippines. Current evidence indicates that the most likely cause is an expansion in the TAF1 gene that may be amenable to treatment. To prepare for clinical trials of therapeutic candidates for X-linked dystonia parkinsonism, we focused on the identification of quantitative phenotypic measures that are most strongly associated with disease progression. Our main objective is to establish a comprehensive, quantitative assessment of movement dysfunction and bulbar motor impairments that are sensitive and specific to disease progression in persons with X-linked dystonia parkinsonism. These measures will set the stage for future treatment trials. We enrolled patients with X-linked dystonia parkinsonism and performed a comprehensive oromotor, speech and neurological assessment. Measurements included patient-reported questionnaires regarding daily living activities and both neurologist-rated movement scales and objective quantitative measures of bulbar function and nutritional status. Patients were followed for 18 months from the date of enrollment and evaluated every 6 months during that period. We analysed a total of 87 men: 29 were gene-positive and had symptoms at enrollment, seven were gene-positive and had no symptoms at enrollment and 51 were gene-negative. We identified measures that displayed a significant change over the study. We used principal variables analysis to identify a minimal battery of 21 measures that explains 67.3% of the variance over the course of the study. These measures included patient-reported, clinician-rated and objective quantitative outcomes that may serve as endpoints in future clinical trials.
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Affiliation(s)
- Patrick Acuna
- 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
- Sunshine Care Foundation, The Health Centrum, Roxas City, Capiz 5800Philippines
| | - Melanie Leigh Supnet-Wells
- 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
| | - Neil A Spencer
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Jan Kristoper de Guzman
- Department of Neurology, Jose Reyes Memorial Medical Center, Manila, Metro Manila, 1012Philippines
- Sunshine Care Foundation, The Health Centrum, Roxas City, Capiz 5800Philippines
| | - Massimiliano Russo
- Division of Pharmacoepidemiology and Pharmacoeconomics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ann Hunt
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christopher Stephen
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Criscely Go
- Department of Neurology, Jose Reyes Memorial Medical Center, Manila, Metro Manila, 1012Philippines
| | - Samuel Carr
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Niecy Grace Ganza
- Sunshine Care Foundation, The Health Centrum, Roxas City, Capiz 5800Philippines
| | | | - Shin Begalan
- Sunshine Care Foundation, The Health Centrum, Roxas City, Capiz 5800Philippines
| | - Trisha Multhaupt-Buell
- 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
| | - Gabrielle Aldykiewicz
- 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
| | - Lisa Paul
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Laurie Ozelius
- 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
| | - 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
| | - Bridget Perry
- Department of Communication Sciences and Disorders, MGH Institute of Health Professions, Charlestown, MA 02129, USA
| | - Jordan R Green
- Department of Communication Sciences and Disorders, MGH Institute of Health Professions, Charlestown, MA 02129, USA
| | - Jeffrey W Miller
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nutan Sharma
- 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
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26
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Nadler MJS, Chang W, Ozkaynak E, Huo Y, Nong Y, Boillot M, Johnson M, Moreno A, Matthew P Anderson. Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation. Commun Biol 2023; 6:347. [PMID: 36997626 PMCID: PMC10063665 DOI: 10.1038/s42003-023-04683-8] [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: 06/09/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons arose and expanded in the genome of hominoid primates concurrent with the slowing of brain maturation. We report genes with intronic SVA transposons are enriched for neurodevelopmental disease and transcribed into long non-coding SVA-lncRNAs. Human-specific SVAs in microcephaly CDK5RAP2 and epilepsy SCN8A gene introns repress their expression via transcription factor ZNF91 to delay neuronal maturation. Deleting the SVA in CDK5RAP2 initiates multi-dimensional and in SCN8A selective sodium current neuronal maturation by upregulating these genes. SVA-lncRNA AK057321 forms RNA:DNA heteroduplexes with the genomic SVAs and upregulates these genes to initiate neuronal maturation. SVA-lncRNA AK057321 also promotes species-specific cortex and cerebellum-enriched expression upregulating human genes with intronic SVAs (e.g., HTT, CHAF1B and KCNJ6) but not mouse orthologs. The diversity of neuronal genes with intronic SVAs suggest this hominoid-specific SVA transposon-based gene regulatory mechanism may act at multiple steps to specialize and achieve neoteny of the human brain.
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Affiliation(s)
- Monica J S Nadler
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Weipang Chang
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Ekim Ozkaynak
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Yuda Huo
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Yi Nong
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Morgane Boillot
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Mark Johnson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Antonio Moreno
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA
| | - Matthew P Anderson
- Department of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA.
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02115, USA.
- Boston Children's Hospital Intellectual and Developmental Disabilities Research Center, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Program in Neuroscience, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Neuroscience Therapeutic Focus Area, Regeneron, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA.
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27
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X-linked dystonia parkinsonism: epidemiology, genetics, clinical features, diagnosis, and treatment. Acta Neurol Belg 2023; 123:45-55. [PMID: 36418540 DOI: 10.1007/s13760-022-02144-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
X-linked dystonia parkinsonism (XDP) is a rare X-linked recessive degenerative movement disorder that only affects Filipino descent, predominantly males. Its underlying cause is associated with the genetic alterations in the TAF1/DYT3 multiple transcription system. SINE-VNTR-Alu (SVA) retrotransposon insertion was suggested to be the responsible genetic mutation. Clinically, it initially presents as focal dystonia and generalizes within years. Parkinsonism arises years later and coexists with dystonia. Nonmotor symptoms like cognitive impairment and mood disorders are also common among XDP patients. XDP diagnosis relies on clinical history and physical examination. On imaging, abnormalities of the striatum, such as atrophy, are widely seen and can explain the clinical presentations with a three-model pathway of the striatum. Treatments aim for symptomatic relief of dystonia and parkinsonism and to prevent complications. Oral medications, chemo-denervation, and surgery are used in XDP patients. This review summarizes the currently important information regarding XDP, providing a synoptic overview and understanding of XDP for future studies.
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28
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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29
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Reyes CJ, Asano K, Todd PK, Klein C, Rakovic A. Repeat-Associated Non-AUG Translation of AGAGGG Repeats that Cause X-Linked Dystonia-Parkinsonism. Mov Disord 2022; 37:2284-2289. [PMID: 35971992 DOI: 10.1002/mds.29183] [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: 05/01/2022] [Revised: 07/05/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disorder caused by the intronic insertion of a SINE-VNTR-Alu (SVA) retrotransposon carrying an (AGAGGG)n repeat expansion in the TAF1 gene. The molecular mechanisms by which this mutation causes neurodegeneration remain elusive. OBJECTIVES We investigated whether (AGAGGG)n repeats undergo repeat-associated non-AUG (RAN) translation, a pathogenic mechanism common among repeat expansion diseases. METHODS XDP-specific RAN translation reporter plasmids were generated, transfected in HEK293 cells, and putative dipeptide repeat proteins (DPRs) were detected by Western blotting. Immunocytochemistry was performed in COS-7 cells to determine the subcellular localization of one DPR. RESULTS We detected putative DPRs from two reading frames, supporting the translation of poly-(Glu-Gly) and poly-(Arg-Glu) species. XDP RAN translation initiates within the (AGAGGG)n sequence and poly-(Glu-Gly) DPRs formed nuclear inclusions in transfected cells. CONCLUSIONS In summary, our work provides the first in-vitro proof of principle that the XDP-linked (AGAGGG)n repeat expansions can undergo RAN translation. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Katsura Asano
- Molecular Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
- Laboratory of Translational Control Study, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Hiroshima Research Center for Healthy Aging, Hiroshima University, Hiroshima, Japan
| | - Peter K Todd
- Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
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Kõks S, Pfaff AL, Singleton LM, Bubb VJ, Quinn JP. Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson's disease. Exp Biol Med (Maywood) 2022; 247:1680-1690. [PMID: 36000172 PMCID: PMC9597212 DOI: 10.1177/15353702221117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The pathophysiology of Parkinson's disease (PD) is a complex process of the interaction between genetic and environmental factors. Studies on the genetic component of PD have predominantly focused on single nucleotide polymorphisms (SNPs) using a cross-sectional case-control design in large genome-wide association studies. This approach while giving insight into a significant portion of the genetics of PD does not fully account for all the genetic components resulting in missing heritability. In this study, we approached this problem by focusing on the non-reference genome transposable elements (TEs) and their impact on the progression of PD using a longitudinal study design within the Parkinson's progression markers initiative (PPMI) cohort. We analyzed 2886 Alu repeats, 360 LINE1 and 128 SINE-VNTR-Alus (SVAs) that were called from the whole-genome sequence data which are not within the reference genome. The presence or absence of these non-reference TE variants is known as a retrotransposon insertion polymorphism, and measuring this polymorphism describes the impact of TEs on the traits. The variations for the presence or absence of the non-reference TE elements were modeled to align with the changes in the 114 outcome measures during the five-year follow-up period of the PPMI cohort. Linear mixed-effects models were used, and many TEs were found to have a highly significant effect on the longitudinal changes in the clinically important PD outcomes such as UPDRS subscale II, UPDRS total scores, and modified Schwab and England ADL scale. In addition, the progression of several imaging and functional measures, including the Caudate/Putamen ratio and levodopa equivalent daily dose (LEDD) were also significantly affected by the TEs. In conclusion, this study identified the overwhelming effect of the non-reference TEs on the progression of PD and is a good example of the impact the variations in the "junk DNA" have on complex diseases.
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Affiliation(s)
- Sulev Kõks
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia,Sulev Kõks.
| | - Abigail L Pfaff
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
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31
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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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32
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di Biase L, Di Santo A, Caminiti ML, Pecoraro PM, Carbone SP, Di Lazzaro V. Dystonia Diagnosis: Clinical Neurophysiology and Genetics. J Clin Med 2022; 11:jcm11144184. [PMID: 35887948 PMCID: PMC9320296 DOI: 10.3390/jcm11144184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/16/2022] [Indexed: 12/12/2022] Open
Abstract
Dystonia diagnosis is based on clinical examination performed by a neurologist with expertise in movement disorders. Clues that indicate the diagnosis of a movement disorder such as dystonia are dystonic movements, dystonic postures, and three additional physical signs (mirror dystonia, overflow dystonia, and geste antagonists/sensory tricks). Despite advances in research, there is no diagnostic test with a high level of accuracy for the dystonia diagnosis. Clinical neurophysiology and genetics might support the clinician in the diagnostic process. Neurophysiology played a role in untangling dystonia pathophysiology, demonstrating characteristic reduction in inhibition of central motor circuits and alterations in the somatosensory system. The neurophysiologic measure with the greatest evidence in identifying patients affected by dystonia is the somatosensory temporal discrimination threshold (STDT). Other parameters need further confirmations and more solid evidence to be considered as support for the dystonia diagnosis. Genetic testing should be guided by characteristics such as age at onset, body distribution, associated features, and coexistence of other movement disorders (parkinsonism, myoclonus, and other hyperkinesia). The aim of the present review is to summarize the state of the art regarding dystonia diagnosis focusing on the role of neurophysiology and genetic testing.
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Affiliation(s)
- Lazzaro di Biase
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
- Brain Innovations Lab., Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
- Correspondence: or ; Tel.: +39-062-2541-1220
| | - Alessandro Di Santo
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
| | - Maria Letizia Caminiti
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
| | - Pasquale Maria Pecoraro
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
| | - Simona Paola Carbone
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
| | - Vincenzo Di Lazzaro
- Neurology Unit, Campus Bio-Medico University Hospital Foundation, Via Álvaro del Portillo 200, 00128 Rome, Italy; (A.D.S.); (M.L.C.); (P.M.P.); (S.P.C.); (V.D.L.)
- Unit of Neurology, Neurophysiology, Neurobiology, Department of Medicine, Campus Bio-Medico University of Rome, Via Álvaro del Portillo 21, 00128 Rome, Italy
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33
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Genetic screening in patients of Meige syndrome and blepharospasm. Neurol Sci 2022; 43:3683-3694. [PMID: 35044558 DOI: 10.1007/s10072-022-05900-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Meige syndrome (MS) is cranial dystonia, including bilateral eyelid spasms (blepharospasm; BSP) and involuntary movements of the jaw muscles (oromandibular dystonia; OMD). Up to now, the pathogenic genes of MS and BSP are still unclear. METHODS We performed Sanger sequencing of GNAL, TOR1A, TOR2A, THAP1, and REEP4 exons on 78 patients, including 53 BSP and 25 MS and 96 healthy controls. RESULTS c.845G > C[R282P] of TOR1A, c.629delC[p.Gly210AlafsTer60] of TOR2A, c.1322A > G[N441S] of GNAL, c.446G > A[R149Q], and c.649C > T[R217C] of REEP4 were identified and predicated as deleterious probably damaging variants. Three potential alterations of splicing variants of TOR1A and TOR2A were identified in patients. The frequencies of TOR1A rs1435566780 and THAP1 rs545930392 were higher in patients than in controls. CONCLUSIONS TOR1A rs1435566780 (c.*16G > C(G > A)) and THAP1 rs545930392 (c.192G > A[K64K]) may contribute to the etiology of MS and BSP. Other identified rare mutations predicted as deleterious probably damaging need further confirmation. Larger MS and BSP cohorts and functional studies will need to be performed further to elucidate the association between these genes and the diseases.
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Pozojevic J, von Holt BH, Westenberger A. Factors influencing reduced penetrance and variable expressivity in X-linked dystonia-parkinsonism. MED GENET-BERLIN 2022; 34:97-102. [PMID: 38835911 PMCID: PMC11007627 DOI: 10.1515/medgen-2022-2135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
X-linked dystonia-parkinsonism (XDP) is a neurodegenerative movement disorder that primarily affects adult Filipino men. It is caused by a founder retrotransposon insertion in TAF1 that contains a hexanucleotide repeat, the number of which differs among the patients and correlates with the age at disease onset (AAO) and other clinical parameters. A recent work has identified additional genetic modifiers of age-associated penetrance in XDP, bringing to light the DNA mismatch repair genes MSH3 and PMS2. Despite X-linked recessive inheritance, a minor subset of patients are female, manifesting the disease via various mechanisms such as homozygosity, imbalanced X-chromosome inactivation, or aneuploidy. Here, we summarize and discuss clinical and genetic aspects of XDP, with a focus on variable disease expressivity as a consequence of subtle genetic differences within a seemingly homogenous population of patients.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Björn-Hergen von Holt
- Institute of Medical Biometry and Statistics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
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35
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Rangwala AM, Mingione VR, Georghiou G, Seeliger MA. Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome. Biomolecules 2022; 12:biom12050685. [PMID: 35625613 PMCID: PMC9138534 DOI: 10.3390/biom12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.
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36
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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37
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El-Saafin F, Bergamasco MI, Chen Y, May RE, Esakky P, Hediyeh-Zadeh S, Dixon M, Wilcox S, Davis MJ, Strasser A, Smyth GK, Thomas T, Voss AK. Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death. Cell Death Differ 2022; 29:1013-1027. [PMID: 35361962 PMCID: PMC9091217 DOI: 10.1038/s41418-022-00982-5] [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: 03/26/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/08/2022] Open
Abstract
Mutations in genes encoding general transcription factors cause neurological disorders. Despite clinical prominence, the consequences of defects in the basal transcription machinery during brain development are unclear. We found that loss of the TATA-box binding protein-associated factor TAF8, a component of the general transcription factor TFIID, in the developing central nervous system affected the expression of many, but notably not all genes. Taf8 deletion caused apoptosis, unexpectedly restricted to forebrain regions. Nuclear levels of the transcription factor p53 were elevated in the absence of TAF8, as were the mRNAs of the pro-apoptotic p53 target genes Noxa, Puma and Bax. The cell death in Taf8 forebrain regions was completely rescued by additional loss of p53, but Taf8 and p53 brains failed to initiate a neuronal expression program. Taf8 deletion caused aberrant transcription of promoter regions and splicing anomalies. We propose that TAF8 supports the directionality of transcription and co-transcriptional splicing, and that failure of these processes causes p53-induced apoptosis of neuronal cells in the developing mouse embryo.
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Affiliation(s)
- Farrah El-Saafin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Maria I Bergamasco
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Yunshun Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rose E May
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Prabagaran Esakky
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mathew Dixon
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
- The University of Queensland Diamantina Institute, Woolloongabba, QLD, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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38
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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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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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40
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van Bree EJ, Guimarães RLFP, Lundberg M, Blujdea ER, Rosenkrantz JL, White FTG, Poppinga J, Ferrer-Raventós P, Schneider AFE, Clayton I, Haussler D, Reinders MJT, Holstege H, Ewing AD, Moses C, Jacobs FMJ. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res 2022; 32:656-670. [PMID: 35332097 PMCID: PMC8997352 DOI: 10.1101/gr.275515.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease-associated risk loci and in the BCKDK Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.
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Affiliation(s)
- Elisabeth J van Bree
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Mischa Lundberg
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Elena R Blujdea
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jimi L Rosenkrantz
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Fred T G White
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Josse Poppinga
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Paula Ferrer-Raventós
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Anne-Fleur E Schneider
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Isabella Clayton
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - David Haussler
- UC Santa Cruz Genomics Institute, and Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
| | - Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Colette Moses
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
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41
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A New Pathologic KMT2B Variant Associated with Childhood Onset Dystonia Presenting as Variable Phenotypes among Family Members. Tremor Other Hyperkinet Mov (N Y) 2022; 12:7. [PMID: 35415007 PMCID: PMC8932353 DOI: 10.5334/tohm.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/10/2022] [Indexed: 11/20/2022] Open
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Fröhlich A, Pfaff AL, Bubb VJ, Koks S, Quinn JP. Characterisation of the Function of a SINE-VNTR-Alu Retrotransposon to Modulate Isoform Expression at the MAPT Locus. Front Mol Neurosci 2022; 15:815695. [PMID: 35370538 PMCID: PMC8965460 DOI: 10.3389/fnmol.2022.815695] [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: 11/15/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
SINE-VNTR-Alu retrotransposons represent one class of transposable elements which contribute to the regulation and evolution of the primate genome and have the potential to be involved in genetic instability and disease progression. However, these polymorphic elements have not been extensively analysed when addressing the missing heritability of neurodegenerative diseases, including Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). SVA_67, a retrotransposon insertion polymorphism, is located in a 1.8 Mb region of high linkage disequilibrium, called the MAPT locus, which is known to contribute to increased risk of developing PD, frontotemporal dementia and other tauopathies. To investigate the role of SVA_67 in directing differential gene expression at this locus, we characterised the impact of SVA_67 allele dosage on isoform expression of several genes in the MAPT locus using the datasets from both the Parkinson’s Progression Markers Initiative and New York Genome Center Consortium Target ALS cohort. The Parkinson’s data was from gene expression in the blood and the ALS data from a variety of CNS regions and allowed us to demonstrate that SVA_67 presence or absence correlated with both isoform- and tissue-specific expression of multiple genes at this locus. This study highlights the importance of addressing SVA polymorphism in disease genetics to gain insight into a better understanding of the role of these regulatory domains to a variety of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Alexander Fröhlich,
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Pozojevic J, Algodon SM, Cruz JN, Trinh J, Brüggemann N, Laß J, Grütz K, Schaake S, Tse R, Yumiceba V, Kruse N, Schulz K, Sreenivasan VKA, Rosales RL, Jamora RDG, Diesta CCE, Matschke J, Glatzel M, Seibler P, Händler K, Rakovic A, Kirchner H, Spielmann M, Kaiser FJ, Klein C, Westenberger A. Transcriptional Alterations in X-Linked Dystonia–Parkinsonism Caused by the SVA Retrotransposon. Int J Mol Sci 2022; 23:ijms23042231. [PMID: 35216353 PMCID: PMC8875906 DOI: 10.3390/ijms23042231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
X-linked dystonia–parkinsonism (XDP) is a severe neurodegenerative disorder that manifests as adult-onset dystonia combined with parkinsonism. A SINE-VNTR-Alu (SVA) retrotransposon inserted in an intron of the TAF1 gene reduces its expression and alters splicing in XDP patient-derived cells. As a consequence, increased levels of the TAF1 intron retention transcript TAF1-32i can be found in XDP cells as compared to healthy controls. Here, we investigate the sequence of the deep intronic region included in this transcript and show that it is also present in cells from healthy individuals, albeit in lower amounts than in XDP cells, and that it undergoes degradation by nonsense-mediated mRNA decay. Furthermore, we investigate epigenetic marks (e.g., DNA methylation and histone modifications) present in this intronic region and the spanning sequence. Finally, we show that the SVA evinces regulatory potential, as demonstrated by its ability to repress the TAF1 promoter in vitro. Our results enable a better understanding of the disease mechanisms underlying XDP and transcriptional alterations caused by SVA retrotransposons.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Shela Marie Algodon
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joseph Neos Cruz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Department of Neurology, University Hospital Schleswig Holstein, 23538 Lübeck, Germany
| | - Joshua Laß
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Susen Schaake
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Ronnie Tse
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Veronica Yumiceba
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Nathalie Kruse
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Kristin Schulz
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Varun K. A. Sreenivasan
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Raymond L. Rosales
- The Hospital Neuroscience Institute, Department of Neurology and Psychiatry and The FMS-Research Center for Health Sciences, University of Santo Tomas, Manila 1008, Philippines;
| | - Roland Dominic G. Jamora
- Department of Neurosciences, College of Medicine-Philippine General Hospital, University of the Philippines Manila, Manila 1000, Philippines;
| | - Cid Czarina E. Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati City 1229, Philippines;
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.M.); (M.G.)
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Kristian Händler
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
| | - Henriette Kirchner
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, 23538 Lübeck, Germany; (V.Y.); (N.K.); (K.S.); (V.K.A.S.); (K.H.); (H.K.); (M.S.)
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, 23538 Lübeck, Germany
| | - Frank J. Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45147 Essen, Germany;
- Essener Zentrum für Seltene Erkrankungen, Universitätsmedizin Essen, 45147 Essen, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany; (J.P.); (S.M.A.); (J.N.C.); (J.T.); (N.B.); (J.L.); (K.G.); (S.S.); (R.T.); (P.S.); (A.R.)
- Correspondence: (C.K.); (A.W.)
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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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Cirnaru MD, Creus-Muncunill J, Nelson S, Lewis TB, Watson J, Ellerby LM, Gonzalez-Alegre P, Ehrlich ME. Striatal Cholinergic Dysregulation after Neonatal Decrease in X-Linked Dystonia Parkinsonism-Related TAF1 Isoforms. Mov Disord 2021; 36:2780-2794. [PMID: 34403156 DOI: 10.1002/mds.28750] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND X-linked dystonia parkinsonism is a generalized, progressive dystonia followed by parkinsonism with onset in adulthood and accompanied by striatal neurodegeneration. Causative mutations are located in a noncoding region of the TATA-box binding protein-associated factor 1 (TAF1) gene and result in aberrant splicing. There are 2 major TAF1 isoforms that may be decreased in symptomatic patients, including the ubiquitously expressed canonical cTAF1 and the neuronal-specific nTAF1. OBJECTIVE The objective of this study was to determine the behavioral and transcriptomic effects of decreased cTAF1 and/or nTAF1 in vivo. METHODS We generated adeno-associated viral (AAV) vectors encoding microRNAs targeting Taf1 in a splice-isoform selective manner. We performed intracerebroventricular viral injections in newborn mice and rats and intrastriatal infusions in 3-week-old rats. The effects of Taf1 knockdown were assayed at 4 months of age with evaluation of motor function, histology, and RNA sequencing of the striatum, followed by its validation. RESULTS We report motor deficits in all cohorts, more pronounced in animals injected at P0, in which we also identified transcriptomic alterations in multiple neuronal pathways, including the cholinergic synapse. In both species, we show a reduced number of striatal cholinergic interneurons and their marker mRNAs after Taf1 knockdown in the newborn. CONCLUSION This study provides novel information regarding the requirement for TAF1 in the postnatal maintenance of striatal cholinergic neurons, the dysfunction of which is involved in other inherited forms of dystonia. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Maria-Daniela Cirnaru
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shareen Nelson
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Travis B Lewis
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jaime Watson
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, Novato, California, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Bhadresha K, Patel M, Brahmbhatt J, Jain N, Rawal R. Targeting Bone Metastases Signaling Pathway Using Moringa oleifera Seed Nutri-miRs: A Cross Kingdom Approach. Nutr Cancer 2021; 74:2522-2539. [PMID: 34751606 DOI: 10.1080/01635581.2021.2001547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Moringa oleifera is a medicinally important plant that has various medical and nutritional uses. Plant miRNAs are a class of non-coding endogenous small RNAs that regulate human-specific mRNA but the mechanistic actions are largely unknown. Here, in this study, we aim to explore the mechanistic action and influence of M. oleifera seed miRNAs on vital human target genes using computer based approaches. The M. oleifera seed miRNAs sequence was taken from published data and identified its human gene targets using a psRNA target analysis server. We identified 94 miRNAs that are able to significantly regulate 47 human target genes, which has enormous biological and functional importance. Out of 47 human targeted genes, 23 genes were found to be associated with PI3K-AKT, RUNX, and MAPK1/MAPK3 signaling pathway which has shown to play key roles in bone metastases during cancer progression. The M. oleifera seed miRNAs hold a strong potential for future research that might uncover the possibility of miRNA-facilitated cross-kingdom regulation and therapeutic targets for bone metastases.
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Affiliation(s)
- Kinjal Bhadresha
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jpan Brahmbhatt
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Nayan Jain
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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Capponi S, Stöffler N, Penney EB, Grütz K, Nizamuddin S, Vermunt MW, Castelijns B, Fernandez-Cerado C, Legarda GP, Velasco-Andrada MS, Muñoz EL, Ang MA, Diesta CCE, Creyghton MP, Klein C, Bragg DC, De Rijk P, Timmers HTM. Dissection of TAF1 neuronal splicing and implications for neurodegeneration in X-linked dystonia-parkinsonism. Brain Commun 2021; 3:fcab253. [PMID: 34746789 PMCID: PMC8567410 DOI: 10.1093/braincomms/fcab253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a monogenic neurodegenerative disorder of the basal ganglia, which presents as a combination of hyperkinetic movements and parkinsonian features. The underlying genetic mechanism involves the insertion of a SINE-VNTR-Alu retrotransposon within the TAF1 gene. Interestingly, alterations of TAF1 have been involved in multiple neurological diseases. In XDP, the SINE-VNTR-Alu insertion in TAF1 has been proposed to result in alternative splicing defects, including the decreased incorporation of a neuron-specific microexon annotated as 34′. This mechanism has become controversial as recent studies failed to provide support. In order to resolve this conundrum, we examined the alternative splicing patterns of TAF1 mRNAs in XDP and control brains. The impact of the disease-associated SINE-VNTR-Alu on alternative splicing of microexon 34′ was further investigated in cellular assays. Subsequently, microexon 34′ incorporation was explored by RT-PCR and Nanopore long-read sequencing of TAF1 mRNAs from XDP and control brains tissues. Using cell-based splicing assays, we demonstrate that presence of the disease-associated SINE-VNTR-Alu does not affect the inclusion of microexon 34′. In addition, we show that (1) microexon 34′-containing TAF1 mRNAs are detected at similar levels in XDP as in controls and that (2) the architecture of TAF1 transcripts is remarkably similar between XDP and controls brains. These results indicate that microexon 34′ incorporation into TAF1 mRNA is not affected in XDP brains. Our findings shift the current paradigm of XDP by discounting alternative splicing of TAF1 microexon 34′ as the molecular basis for this disease.
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Affiliation(s)
- Simona Capponi
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Nadja Stöffler
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Ellen B Penney
- The Collaborative Center for X-Linked Dystonia Parkinsonism (CCXDP), Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Karen Grütz
- Institute of Neurogenetics, University of Lübeck, Lübeck 23538, Germany
| | - Sheikh Nizamuddin
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Marit W Vermunt
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | - Bas Castelijns
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | | | - G Paul Legarda
- Sunshine Care Foundation, Roxas City, 5800 Capiz, Philippines
| | | | - Edwin L Muñoz
- Department of Pathology, College of Medicine, University of the Philippines, 1000 Manila, Philippines
| | - Mark A Ang
- Department of Pathology, College of Medicine, University of the Philippines, 1000 Manila, Philippines
| | - Cid Czarina E Diesta
- Department of Neurosciences, Makati Medical Center, 1229 Makati City, Philippines
| | - Menno P Creyghton
- Erasmus University Medical Center, Department of Developmental Biology, Rotterdam 3015 GD, The Netherlands
| | - Christine Klein
- Institute of Neurogenetics and Department of Neurology, University of Lübeck, 23538 Lübeck, Germany
| | - D Cristopher Bragg
- The Collaborative Center for X-Linked Dystonia Parkinsonism (CCXDP), Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB - University of Antwerp, B-2610 Antwerp, Belgium
| | - H T Marc Timmers
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, Germany
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Sabatella M, Mantere T, Waanders E, Neveling K, Mensenkamp AR, van Dijk F, Hehir‐Kwa JY, Derks R, Kwint M, O'Gorman L, Tropa Martins M, Gidding CEM, Lequin MH, Küsters B, Wesseling P, Nelen M, Biegel JA, Hoischen A, Jongmans MC, Kuiper RP. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol 2021; 255:202-211. [PMID: 34231212 PMCID: PMC8519051 DOI: 10.1002/path.5755] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat‐rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long‐range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE‐VNTR‐Alu, subfamily E (SVA‐E) retrotransposon element, which was present in a mosaic state in the mother. This SVA‐E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long‐read sequencing to identify genomic variations in high‐risk cancer‐predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Tuomo Mantere
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter OuluUniversity of OuluOuluFinland
| | - Esmé Waanders
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Kornelia Neveling
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Arjen R Mensenkamp
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Freerk van Dijk
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
| | | | - Ronnie Derks
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Michael Kwint
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Luke O'Gorman
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | | | - Maarten H Lequin
- Department of RadiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Benno Küsters
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Pieter Wesseling
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of PathologyAmsterdam University Medical Centers, Location VUmc and Brain Tumor Center AmsterdamAmsterdamThe Netherlands
| | - Marcel Nelen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Jacklyn A Biegel
- Department of Pathology and Laboratory MedicineChildren's Hospital, Los AngelesLos AngelesCAUSA
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI)Radboud University Medical CenterNijmegenThe Netherlands
| | - Marjolijn C Jongmans
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Roland P Kuiper
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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Diez-Fairen M, Alvarez Jerez P, Berghausen J, Bandres-Ciga S. The Genetic Landscape of Parkinsonism-Related Dystonias and Atypical Parkinsonism-Related Syndromes. Int J Mol Sci 2021; 22:ijms22158100. [PMID: 34360863 PMCID: PMC8347917 DOI: 10.3390/ijms22158100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022] Open
Abstract
In recent decades, genetic research has nominated promising pathways and biological insights contributing to the etiological landscape of parkinsonism-related dystonias and atypical parkinsonism-related syndromes. Several disease-causing mutations and genetic risk factors have been unraveled, providing a deeper molecular understanding of the complex genetic architecture underlying these conditions. These disorders are difficult to accurately diagnose and categorize, thus making genetics research challenging. On one hand, dystonia is an umbrella term linked to clinically heterogeneous forms of disease including dopa-responsive dystonia, myoclonus-dystonia, rapid-onset dystonia-parkinsonism and dystonia-parkinsonism, often viewed as a precursor to Parkinson’s disease. On the other hand, atypical parkinsonism disorders, such as progressive supranuclear palsy, multiple system atrophy and corticobasal degeneration, are rare in nature and represent a wide range of diverse and overlapping phenotypic variabilities, with genetic research limited by sample size availability. The current review summarizes the plethora of available genetic information for these diseases, outlining limits and future directions.
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