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Jasoliya M, Gu J, AlOlaby RR, Durbin-Johnson B, Chedin F, Tassone F. Profiling Genome-Wide DNA Methylation in Children with Autism Spectrum Disorder and in Children with Fragile X Syndrome. Genes (Basel) 2022; 13:genes13101795. [PMID: 36292679 PMCID: PMC9602177 DOI: 10.3390/genes13101795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is an early onset, developmental disorder whose genetic cause is heterogeneous and complex. In total, 70% of ASD cases are due to an unknown etiology. Among the monogenic causes of ASD, fragile X syndrome (FXS) accounts for 2–4% of ASD cases, and 60% of individuals with FXS present with ASD. Epigenetic changes, specifically DNA methylation, which modulates gene expression levels, play a significant role in the pathogenesis of both disorders. Thus, in this study, using the Human Methylation EPIC Bead Chip, we examined the global DNA methylation profiles of biological samples derived from 57 age-matched male participants (2–6 years old), including 23 subjects with ASD, 23 subjects with FXS with ASD (FXSA) and 11 typical developing (TD) children. After controlling for technical variation and white blood cell composition, using the conservatory threshold of the false discovery rate (FDR ≤ 0.05), in the three comparison groups, TD vs. AD, TD vs. FXSA and ASD vs. FXSA, we identified 156, 79 and 3100 differentially methylated sites (DMS), and 14, 13 and 263 differential methylation regions (DMRs). Interestingly, several genes differentially methylated among the three groups were among those listed in the SFARI Gene database, including the PAK2, GTF2I and FOXP1 genes important for brain development. Further, enrichment analyses identified pathways involved in several functions, including synaptic plasticity. Our preliminary study identified a significant role of altered DNA methylation in the pathology of ASD and FXS, suggesting that the characterization of a DNA methylation signature may help to unravel the pathogenicity of FXS and ASD and may help the development of an improved diagnostic classification of children with ASD and FXSA. In addition, it may pave the way for developing therapeutic interventions that could reverse the altered methylome profile in children with neurodevelopmental disorders.
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Affiliation(s)
- Mittal Jasoliya
- Biochemistry and Molecular Medicine, University of California, Sacramento, CA 95817, USA
| | - Jianlei Gu
- School of Public Health: Biostatistics, Yale University, New Haven, CT 06510, USA
| | - Reem R. AlOlaby
- College of Health Sciences, California Northstate University, Sacramento, CA 95757, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, Division of Biostatistics, University of California, Davis, CA 95616, USA
| | - Frederic Chedin
- Davis, Genome Center, University of California, Davis, CA 95616, USA
- Davis, Molecular & Cellular Biology, University of California, Davis, CA 95616, USA
| | - Flora Tassone
- Biochemistry and Molecular Medicine, University of California, Sacramento, CA 95817, USA
- MIND Institute, UC Davis, Sacramento, CA 95817, USA
- Correspondence: ; Tel.: +1-916-703-0463
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Abeti R, Jasoliya M, Al-Mahdawi S, Pook M, Gonzalez-Robles C, Hui CK, Cortopassi G, Giunti P. A Drug Combination Rescues Frataxin-Dependent Neural and Cardiac Pathophysiology in FA Models. Front Mol Biosci 2022; 9:830650. [PMID: 35664670 PMCID: PMC9160322 DOI: 10.3389/fmolb.2022.830650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Friedreich’s ataxia (FA) is an inherited multisystemic neuro- and cardio-degenerative disorder. Seventy-four clinical trials are listed for FA (including past and present), but none are considered FDA/EMA-approved therapy. To date, FA therapeutic strategies have focused along two main lines using a single-drug approach: a) increasing frataxin and b) enhancing downstream pathways, including antioxidant levels and mitochondrial function. Our novel strategy employed a combinatorial approach to screen approved compounds to determine if a combination of molecules provided an additive or synergistic benefit to FA cells and/or animal models. Eight single drug molecules were administered to FA fibroblast patient cells: nicotinamide riboside, hemin, betamethasone, resveratrol, epicatechin, histone deacetylase inhibitor 109, methylene blue, and dimethyl fumarate. We measured their individual ability to induce FXN transcription and mitochondrial biogenesis in patient cells. Single-drug testing highlighted that dimethyl fumarate and resveratrol increased these two parameters. In addition, the simultaneous administration of these two drugs was the most effective in terms of FXN mRNA and mitobiogenesis increase. Interestingly, this combination also improved mitochondrial functions and reduced reactive oxygen species in neurons and cardiomyocytes. Behavioral tests in an FA mouse model treated with dimethyl fumarate and resveratrol demonstrated improved rotarod performance. Our data suggest that dimethyl fumarate is effective as a single agent, and the addition of resveratrol provides further benefit in some assays without showing toxicity. Therefore, they could be a valuable combination to counteract FA pathophysiology. Further studies will help fully understand the potential of a combined therapeutic strategy in FA pathophysiology.
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Affiliation(s)
- Rosella Abeti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL, Institute of Neurology, London, United Kingdom
- *Correspondence: Rosella Abeti, ; Paola Giunti,
| | - Mittal Jasoliya
- Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, CA, United States
| | - Sahar Al-Mahdawi
- Department of Life Sciences, Institute of Environment, Health, and Societies, College of Health and Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Pook
- Department of Life Sciences, Institute of Environment, Health, and Societies, College of Health and Life Sciences, Division of Biosciences, Brunel University London, Uxbridge, United Kingdom
| | - Cristina Gonzalez-Robles
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL, Institute of Neurology, London, United Kingdom
| | - Chun Kiu Hui
- Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, CA, United States
| | - Gino Cortopassi
- Department of Molecular Biosciences, School of Veterinary Medicine, UC Davis, Davis, CA, United States
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL, Institute of Neurology, London, United Kingdom
- *Correspondence: Rosella Abeti, ; Paola Giunti,
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Zhou Z, Hagopian K, López-Domínguez JA, Kim K, Jasoliya M, Roberts MN, Cortopassi GA, Showalter MR, Roberts BS, González-Reyes JA, Baar K, Rutkowsky J, Ramsey JJ. A ketogenic diet impacts markers of mitochondrial mass in a tissue specific manner in aged mice. Aging (Albany NY) 2021; 13:7914-7930. [PMID: 33735837 PMCID: PMC8034930 DOI: 10.18632/aging.202834] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Declines in mitochondrial mass are thought to be a hallmark of mammalian aging, and a ketogenic diet (KD) may prevent the age-related decreases in mitochondrial content. The objective of this study was to investigate the impact of a KD on markers of mitochondrial mass. Mice were fed an isocaloric control diet (CD) or KD from 12 months of age. Tissues were collected after 1 month and 14 months of intervention, and a panel of commonly used markers of mitochondrial mass (mitochondrial enzyme activities and levels, mitochondrial to nuclear DNA ratio, and cardiolipin content) were measured. Our results showed that a KD stimulated activities of marker mitochondrial enzymes including citrate synthase, Complex I, and Complex IV in hindlimb muscle in aged mice. KD also increased the activity of citrate synthase and prevented an age-related decrease in Complex IV activity in aged brain. No other markers were increased in these tissues. Furthermore, the impacts of a KD on liver and kidney were mixed with no pattern indicative of a change in mitochondrial mass. In conclusion, results of the present study suggest that a KD induces tissue-specific changes in mitochondrial enzyme activities, or structure, rather than global changes in mitochondrial mass across tissues.
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Affiliation(s)
- Zeyu Zhou
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Kevork Hagopian
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - José A López-Domínguez
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Kyoungmi Kim
- Department of Public Health Sciences, School of Medicine, University of California, Davis, CA 95617, USA
| | - Mittal Jasoliya
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Megan N Roberts
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Gino A Cortopassi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Megan R Showalter
- NIH-West Coast Metabolomics Center, University of California, Davis, CA 95616, USA
| | - Bryan S Roberts
- NIH-West Coast Metabolomics Center, University of California, Davis, CA 95616, USA
| | - José A González-Reyes
- Department of Cell Biology, Physiology and Immunology, Campus de Excelencia Internacional Agroalimentario, ceiA3, University of Córdoba, Córdoba, Spain
| | - Keith Baar
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, CA 95616, USA
| | - Jennifer Rutkowsky
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Jon J Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Alolaby RR, Jiraanont P, Durbin-Johnson B, Jasoliya M, Tang HT, Hagerman R, Tassone F. Molecular Biomarkers Predictive of Sertraline Treatment Response in Young Children With Autism Spectrum Disorder. Front Genet 2020; 11:308. [PMID: 32346385 PMCID: PMC7174723 DOI: 10.3389/fgene.2020.00308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/16/2020] [Indexed: 11/29/2022] Open
Abstract
Sertraline is one among several selective serotonin reuptake inhibitors (SSRIs) that exhibited improvement of language development in Autism Spectrum Disorder (ASD); however, the molecular mechanism has not been elucidated. A double blind, randomized, 6-month, placebo-controlled, clinical trial of low-dose sertraline in children ages (3–6 years) with ASD was conducted at the UC Davis MIND Institute. It aimed at evaluating the efficacy and benefit with respect to early expressive language development and global clinical improvement. This study aimed to identify molecular biomarkers that might be key players in the serotonin pathway and might be predictive of a clinical response to sertraline. Fifty eight subjects with the diagnosis of ASD were randomized to sertraline or placebo. Eight subjects from the sertraline arm and five from the placebo arm discontinued from the study. Furthermore, four subjects did not have a successful blood draw. Hence, genotypes for 41 subjects (20 on placebo and 21 on sertraline) were determined for several genes involved in the serotonin pathway including the serotonin transporter-linked polymorphic region (5-HTTLPR), the tryptophan hydroxylase 2 (TPH2), and the Brain-Derived Neurotrophic Factor (BDNF). In addition, plasma levels of BDNF, Matrix metallopeptidase 9 (MMP-9) and a selected panel of cytokines were determined at baseline and post-treatment. Intent-to-treat analysis revealed several primary significant correlations between molecular changes and the Mullen Scales of Early Learning (MSEL) and Clinical Global Impression Scale – Improvement (CGI-I) of treatment and control groups but they were not significant after adjustment for multiple testing. Thus, sertraline showed no benefit for treatment of young children with ASD in language development or changes in molecular markers in this study. These results indicate that sertraline may not be beneficial for the treatment of children with ASD; however, further investigation of larger groups as well as longer term follow-up studies are warranted.
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Affiliation(s)
- Reem Rafik Alolaby
- College of Health Sciences, California Northstate University, Rancho Cordova, CA, United States
| | - Poonnada Jiraanont
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Blythe Durbin-Johnson
- Division of Biostatistics, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Mittal Jasoliya
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Randi Hagerman
- MIND Institute, University of California Davis Medical Center, Davis, Davis, CA, United States.,Department of Pediatrics, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California Davis Medical Center, Davis, Davis, CA, United States
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Jasoliya M, Sacca F, Sahdeo S, Chedin F, Pane C, Brescia Morra V, Filla A, Pook M, Cortopassi G. Dimethyl fumarate dosing in humans increases frataxin expression: A potential therapy for Friedreich's Ataxia. PLoS One 2019; 14:e0217776. [PMID: 31158268 PMCID: PMC6546270 DOI: 10.1371/journal.pone.0217776] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/18/2019] [Indexed: 11/19/2022] Open
Abstract
Friedreich's Ataxia (FA) is an inherited neurodegenerative disorder resulting from decreased expression of the mitochondrial protein frataxin, for which there is no approved therapy. High throughput screening of clinically used drugs identified Dimethyl fumarate (DMF) as protective in FA patient cells. Here we demonstrate that DMF significantly increases frataxin gene (FXN) expression in FA cell model, FA mouse model and in DMF treated humans. DMF also rescues mitochondrial biogenesis deficiency in FA-patient derived cell model. We further examined the mechanism of DMF's frataxin induction in FA patient cells. It has been shown that transcription-inhibitory R-loops form at GAA expansion mutations, thus decreasing FXN expression. In FA patient cells, we demonstrate that DMF significantly increases transcription initiation. As a potential consequence, we observe significant reduction in both R-loop formation and transcriptional pausing thereby significantly increasing FXN expression. Lastly, DMF dosed Multiple Sclerosis (MS) patients showed significant increase in FXN expression by ~85%. Since inherited deficiency in FXN is the primary cause of FA, and DMF is demonstrated to increase FXN expression in humans, DMF could be considered for Friedreich's therapy.
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Affiliation(s)
- Mittal Jasoliya
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Francesco Sacca
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Sunil Sahdeo
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California, United States of America
| | - Chiara Pane
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Vincenzo Brescia Morra
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Alessandro Filla
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Mark Pook
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Gino Cortopassi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Hayashi G, Jasoliya M, Sahdeo S, Saccà F, Pane C, Filla A, Marsili A, Puorro G, Lanzillo R, Brescia Morra V, Cortopassi G. Dimethyl fumarate mediates Nrf2-dependent mitochondrial biogenesis in mice and humans. Hum Mol Genet 2017; 26:2864-2873. [PMID: 28460056 PMCID: PMC6251607 DOI: 10.1093/hmg/ddx167] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/21/2017] [Accepted: 04/25/2017] [Indexed: 12/15/2022] Open
Abstract
The induction of mitochondrial biogenesis could potentially alleviate mitochondrial and muscle disease. We show here that dimethyl fumarate (DMF) dose-dependently induces mitochondrial biogenesis and function dosed to cells in vitro, and also dosed in vivo to mice and humans. The induction of mitochondrial gene expression is more dependent on DMF's target Nrf2 than hydroxycarboxylic acid receptor 2 (HCAR2). Thus, DMF induces mitochondrial biogenesis primarily through its action on Nrf2, and is the first drug demonstrated to increase mitochondrial biogenesis with in vivo human dosing. This is the first demonstration that mitochondrial biogenesis is deficient in Multiple Sclerosis patients, which could have implications for MS pathophysiology and therapy. The observation that DMF stimulates mitochondrial biogenesis, gene expression and function suggests that it could be considered for mitochondrial disease therapy and/or therapy in muscle disease in which mitochondrial function is important.
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Affiliation(s)
- Genki Hayashi
- Department of Molecular Biosciences, University of California, Davis, 95616 CA, USA
| | - Mittal Jasoliya
- Department of Molecular Biosciences, University of California, Davis, 95616 CA, USA
| | - Sunil Sahdeo
- Janssen Pharmaceuticals, 3210 Merryfield Row, San Diego, 92121 CA, USA
| | - Francesco Saccà
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Chiara Pane
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Alessandro Filla
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Angela Marsili
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Giorgia Puorro
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Roberta Lanzillo
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Vincenzo Brescia Morra
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples 80131, Italy
| | - Gino Cortopassi
- Department of Molecular Biosciences, University of California, Davis, 95616 CA, USA
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Sahdeo S, Scott BD, McMackin MZ, Jasoliya M, Brown B, Wulff H, Perlman SL, Pook MA, Cortopassi GA. Dyclonine rescues frataxin deficiency in animal models and buccal cells of patients with Friedreich's ataxia. Hum Mol Genet 2014; 23:6848-62. [PMID: 25113747 PMCID: PMC4245046 DOI: 10.1093/hmg/ddu408] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/02/2014] [Accepted: 08/04/2014] [Indexed: 12/18/2022] Open
Abstract
Inherited deficiency in the mitochondrial protein frataxin (FXN) causes the rare disease Friedreich's ataxia (FA), for which there is no successful treatment. We identified a redox deficiency in FA cells and used this to model the disease. We screened a 1600-compound library to identify existing drugs, which could be of therapeutic benefit. We identified the topical anesthetic dyclonine as protective. Dyclonine increased FXN transcript and FXN protein dose-dependently in FA cells and brains of animal models. Dyclonine also rescued FXN-dependent enzyme deficiencies in the iron-sulfur enzymes, aconitase and succinate dehydrogenase. Dyclonine induces the Nrf2 [nuclear factor (erythroid-derived 2)-like 2] transcription factor, which we show binds an upstream response element in the FXN locus. Additionally, dyclonine also inhibited the activity of histone methyltransferase G9a, known to methylate histone H3K9 to silence FA chromatin. Chronic dosing in a FA mouse model prevented a performance decline in balance beam studies. A human clinical proof-of-concept study was completed in eight FA patients dosed twice daily using a 1% dyclonine rinse for 1 week. Six of the eight patients showed an increase in buccal cell FXN levels, and fold induction was significantly correlated with disease severity. Dyclonine represents a novel therapeutic strategy that can potentially be repurposed for the treatment of FA.
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Affiliation(s)
- Sunil Sahdeo
- Department of Molecular Biosciences, School of Veterinary Medicine
| | - Brian D Scott
- Department of Molecular Biosciences, School of Veterinary Medicine
| | | | - Mittal Jasoliya
- Department of Molecular Biosciences, School of Veterinary Medicine
| | - Brandon Brown
- Department of Pharmacology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Heike Wulff
- Department of Pharmacology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Susan L Perlman
- Department of Neurology, University of California School of Medicine, Los Angeles, CA 90095, USA and
| | - Mark A Pook
- School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, UK
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