1
|
Pengo M, Squitieri F. Beyond CAG Repeats: The Multifaceted Role of Genetics in Huntington Disease. Genes (Basel) 2024; 15:807. [PMID: 38927742 PMCID: PMC11203031 DOI: 10.3390/genes15060807] [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: 05/01/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG expansion on the huntingtin (HTT) gene and is characterized by progressive motor, cognitive, and neuropsychiatric decline. Recently, new genetic factors besides CAG repeats have been implicated in the disease pathogenesis. Most genetic modifiers are involved in DNA repair pathways and, as the cause of the loss of CAA interruption in the HTT gene, they exert their main influence through somatic expansion. However, this mechanism might not be the only driver of HD pathogenesis, and future studies are warranted in this field. The aim of the present review is to dissect the many faces of genetics in HD pathogenesis, from cis- and trans-acting genetic modifiers to RNA toxicity, mitochondrial DNA mutations, and epigenetics factors. Exploring genetic modifiers of HD onset and progression appears crucial to elucidate not only disease pathogenesis, but also to improve disease prediction and prevention, develop biomarkers of disease progression and response to therapies, and recognize new therapeutic opportunities. Since the same genetic mechanisms are also described in other repeat expansion diseases, their implications might encompass the whole spectrum of these disorders.
Collapse
Affiliation(s)
- Marta Pengo
- Department of Molecular and Translational Medicine, University of Brescia, 25121 Brescia, Italy;
| | - Ferdinando Squitieri
- Centre for Neurological Rare Diseases (CMNR), Fondazione Lega Italiana Ricerca Huntington (LIRH), 00161 Rome, Italy
- Huntington and Rare Diseases Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| |
Collapse
|
2
|
Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024; 32:1791-1804. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [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: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
Collapse
Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
| |
Collapse
|
3
|
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
4
|
Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
Collapse
Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
5
|
Khan A, Inkster AM, Peñaherrera MS, King S, Kildea S, Oberlander TF, Olson DM, Vaillancourt C, Brain U, Beraldo EO, Beristain AG, Clifton VL, Del Gobbo GF, Lam WL, Metz GAS, Ng JWY, Price EM, Schuetz JM, Yuan V, Portales-Casamar É, Robinson WP. The application of epiphenotyping approaches to DNA methylation array studies of the human placenta. Epigenetics Chromatin 2023; 16:37. [PMID: 37794499 PMCID: PMC10548571 DOI: 10.1186/s13072-023-00507-5] [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: 06/15/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential to ensure meaningful and replicable data analysis. Recently, "epiphenotyping" approaches have been developed whereby DNAme data can be used to impute information about phenotypic variables such as gestational age, sex, cell composition, and ancestry. These epiphenotypes offer avenues to compare phenotypic data across cohorts, and to understand how phenotypic variables relate to DNAme variability. However, the relationships between placental epiphenotyping variables and other technical and biological variables, and their application to downstream epigenome analyses, have not been well studied. RESULTS Using DNAme data from 204 placentas across three cohorts, we applied the PlaNET R package to estimate epiphenotypes gestational age, ancestry, and cell composition in these samples. PlaNET ancestry estimates were highly correlated with independent polymorphic ancestry-informative markers, and epigenetic gestational age, on average, was estimated within 4 days of reported gestational age, underscoring the accuracy of these tools. Cell composition estimates varied both within and between cohorts, as well as over very long placental processing times. Interestingly, the ratio of cytotrophoblast to syncytiotrophoblast proportion decreased with increasing gestational age, and differed slightly by both maternal ethnicity (lower in white vs. non-white) and genetic ancestry (lower in higher probability European ancestry). The cohort of origin and cytotrophoblast proportion were the largest drivers of DNAme variation in this dataset, based on their associations with the first principal component. CONCLUSIONS This work confirms that cohort, array (technical) batch, cell type proportion, self-reported ethnicity, genetic ancestry, and biological sex are important variables to consider in any analyses of Illumina DNAme data. We further demonstrate the specific utility of epiphenotyping tools developed for use with placental DNAme data, and show that these variables (i) provide an independent check of clinically obtained data and (ii) provide a robust approach to compare variables across different datasets. Finally, we present a general framework for the processing and analysis of placental DNAme data, integrating the epiphenotype variables discussed here.
Collapse
Affiliation(s)
- A Khan
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Center, Toronto, ON, M5G 2C4, Canada
| | - A M Inkster
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - M S Peñaherrera
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - S King
- Department of Psychiatry, McGill University, Montreal, QC, H3A 1A1, Canada
- Psychosocial Research Division, Douglas Hospital Research Centre, Montreal, QC, H4H 1R3, Canada
| | - S Kildea
- Mater Research Institute, University of Queensland, Brisbane, QLD, 4101, Australia
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, 4000, Australia
| | - T F Oberlander
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - D M Olson
- Department of Obstetrics and Gynecology, University of Alberta, 220 HMRC, Edmonton, AB, T6G 2S2, Canada
| | - C Vaillancourt
- Centre Armand Frappier Santé Biotechnologie - INRS and University of Quebec Intersectorial Health Research Network, Laval, QC, H7V 1B7, Canada
| | - U Brain
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - E O Beraldo
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - A G Beristain
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Obstetrics & Gynecology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - V L Clifton
- Mater Research Institute, University of Queensland, Brisbane, QLD, 4101, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia
| | - G F Del Gobbo
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, K1H 5B2, Canada
| | - W L Lam
- British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - G A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - J W Y Ng
- Faculty of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - E M Price
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, K1H 5B2, Canada
| | - J M Schuetz
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - V Yuan
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - É Portales-Casamar
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
- Centre de Recherche du CHU Sainte-Justine, 3175 Côte-Sainte-Catherine Road, Montréal, QC, H3T 1C5, Canada.
| | - W P Robinson
- BC Children's Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.
| |
Collapse
|
6
|
Fodder K, de Silva R, Warner TT, Bettencourt C. The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration. Acta Neuropathol Commun 2023; 11:106. [PMID: 37386505 PMCID: PMC10311741 DOI: 10.1186/s40478-023-01607-9] [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: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative diseases encompass a heterogeneous group of conditions characterised by the progressive degeneration of the structure and function of the central or peripheral nervous systems. The pathogenic mechanisms underlying these diseases are not fully understood. However, a central feature consists of regional aggregation of proteins in the brain, such as the accumulation of β-amyloid plaques in Alzheimer's disease (AD), inclusions of hyperphosphorylated microtubule-binding tau in AD and other tauopathies, or inclusions containing α-synuclein in Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Various pathogenic mechanisms are thought to contribute to disease, and an increasing number of studies implicate dysfunction of oligodendrocytes (the myelin producing cells of the central nervous system) and myelin loss. Aberrant DNA methylation, the most widely studied epigenetic modification, has been associated with many neurodegenerative diseases, including AD, PD, DLB and MSA, and recent findings highlight aberrant DNA methylation in oligodendrocyte/myelin-related genes. Here we briefly review the evidence showing that changes to oligodendrocytes and myelin are key in neurodegeneration, and explore the relevance of DNA methylation in oligodendrocyte (dys)function. As DNA methylation is reversible, elucidating its involvement in pathogenic mechanisms of neurodegenerative diseases and in dysfunction of specific cell-types such as oligodendrocytes may bring opportunities for therapeutic interventions for these diseases.
Collapse
Affiliation(s)
- Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Rohan de Silva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
| |
Collapse
|
7
|
Zhang Z, Wiencke JK, Kelsey KT, Koestler DC, Molinaro AM, Pike SC, Karra P, Christensen BC, Salas LA. Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. Front Neurosci 2023; 17:1198243. [PMID: 37404460 PMCID: PMC10315586 DOI: 10.3389/fnins.2023.1198243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction The human brain comprises heterogeneous cell types whose composition can be altered with physiological and pathological conditions. New approaches to discern the diversity and distribution of brain cells associated with neurological conditions would significantly advance the study of brain-related pathophysiology and neuroscience. Unlike single-nuclei approaches, DNA methylation-based deconvolution does not require special sample handling or processing, is cost-effective, and easily scales to large study designs. Existing DNA methylation-based methods for brain cell deconvolution are limited in the number of cell types deconvolved. Methods Using DNA methylation profiles of the top cell-type-specific differentially methylated CpGs, we employed a hierarchical modeling approach to deconvolve GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells. Results We demonstrate the utility of our method by applying it to data on normal tissues from various brain regions and in aging and diseased tissues, including Alzheimer's disease, autism, Huntington's disease, epilepsy, and schizophrenia. Discussion We expect that the ability to determine the cellular composition in the brain using only DNA from bulk samples will accelerate understanding brain cell type composition and cell-type-specific epigenetic states in normal and diseased brain tissues.
Collapse
Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - John K. Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl T. Kelsey
- Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI, United States
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Annette M. Molinaro
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States
| | - Steven C. Pike
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
- Department of Neurology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Prasoona Karra
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| |
Collapse
|
8
|
Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
Collapse
|
9
|
Mishra S, Raval M, Kachhawaha AS, Tiwari BS, Tiwari AK. Aging: Epigenetic modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:171-209. [PMID: 37019592 DOI: 10.1016/bs.pmbts.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Aging is one of the most complex and irreversible health conditions characterized by continuous decline in physical/mental activities that eventually poses an increased risk of several diseases and ultimately death. These conditions cannot be ignored by anyone but there are evidences that suggest that exercise, healthy diet and good routines may delay the Aging process significantly. Several studies have demonstrated that Epigenetics plays a key role in Aging and Aging-associated diseases through methylation of DNA, histone modification and non-coding RNA (ncRNA). Comprehension and relevant alterations in these epigenetic modifications can lead to new therapeutic avenues of age-delaying contrivances. These processes affect gene transcription, DNA replication and DNA repair, comprehending epigenetics as a key factor in understanding Aging and developing new avenues for delaying Aging, clinical advancements in ameliorating aging-related diseases and rejuvenating health. In the present article, we have described and advocated the epigenetic role in Aging and associated diseases.
Collapse
|
10
|
Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
Collapse
|
11
|
Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Ebrahimzadeh K, Noroozi R. The emerging role of long non-coding RNAs, microRNAs, and an accelerated epigenetic age in Huntington’s disease. Front Aging Neurosci 2022; 14:987174. [PMID: 36185471 PMCID: PMC9520620 DOI: 10.3389/fnagi.2022.987174] [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: 07/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disease with variable clinical manifestations. Recent studies highlighted the contribution of epigenetic alterations to HD progress and onset. The potential crosstalk between different epigenetic layers and players such as aberrant expression of non-coding RNAs and methylation alterations has been found to affect the pathogenesis of HD or mediate the effects of trinucleotide expansion in its pathophysiology. Also, microRNAs have been assessed for their roles in the modulation of HD manifestations, among them are miR-124, miR-128a, hsa-miR-323b-3p, miR-432, miR-146a, miR-19a, miR-27a, miR-101, miR-9*, miR-22, miR-132, and miR-214. Moreover, long non-coding RNAs such as DNM3OS, NEAT1, Meg3, and Abhd11os are suggested to be involved in the pathogenesis of HD. An accelerated DNA methylation age is another epigenetic signature reported recently for HD. The current literature search collected recent findings of dysregulation of miRNAs or lncRNAs as well as methylation changes and epigenetic age in HD.
Collapse
Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Kaveh Ebrahimzadeh,
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Rezvan Noroozi,
| |
Collapse
|
12
|
Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
Collapse
Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
| |
Collapse
|
13
|
Alfonso Perez G, Caballero Villarraso J. Neural Network Aided Detection of Huntington Disease. J Clin Med 2022; 11:jcm11082110. [PMID: 35456203 PMCID: PMC9032851 DOI: 10.3390/jcm11082110] [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: 03/02/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
Huntington Disease (HD) is a degenerative neurological disease that causes a significant impact on the quality of life of the patient and eventually death. In this paper we present an approach to create a biomarker using as an input DNA CpG methylation data to identify HD patients. DNA CpG methylation is a well-known epigenetic marker for disease state. Technological advances have made it possible to quickly analyze hundreds of thousands of CpGs. This large amount of information might introduce noise as potentially not all DNA CpG methylation levels will be related to the presence of the illness. In this paper, we were able to reduce the number of CpGs considered from hundreds of thousands to 237 using a non-linear approach. It will be shown that using only these 237 CpGs and non-linear techniques such as artificial neural networks makes it possible to accurately differentiate between control and HD patients. An underlying assumption in this paper is that there are no indications suggesting that the process is linear and therefore non-linear techniques, such as artificial neural networks, are a valid tool to analyze this complex disease. The proposed approach is able to accurately distinguish between control and HD patients using DNA CpG methylation data as an input and non-linear forecasting techniques. It should be noted that the dataset analyzed is relatively small. However, the results seem relatively consistent and the analysis can be repeated with larger data-sets as they become available.
Collapse
Affiliation(s)
- Gerardo Alfonso Perez
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Correspondence:
| | - Javier Caballero Villarraso
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Biochemical Laboratory, Reina Sofia University Hospital, 14004 Cordoba, Spain
| |
Collapse
|
14
|
Environmental stimulation in Huntington disease patients and animal models. Neurobiol Dis 2022; 171:105725. [DOI: 10.1016/j.nbd.2022.105725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
|
15
|
DNA Methylation in Huntington's Disease. Int J Mol Sci 2021; 22:ijms222312736. [PMID: 34884540 PMCID: PMC8657460 DOI: 10.3390/ijms222312736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides is the major DNA modification in mammalian cells that is a key component of stable epigenetic marks. This modification, which on the one hand is reversible, while on the other hand, can be maintained through successive rounds of replication plays roles in gene regulation, genome maintenance, transgenerational epigenetic inheritance, and imprinting. Disturbed DNA methylation contributes to a wide array of human diseases from single-gene disorders to sporadic metabolic diseases or cancer. DNA methylation was also shown to affect several neurodegenerative disorders, including Huntington's disease (HD), a fatal, monogenic inherited disease. HD is caused by a polyglutamine repeat expansion in the Huntingtin protein that brings about a multifaceted pathogenesis affecting several cellular processes. Research of the last decade found complex, genome-wide DNA methylation changes in HD pathogenesis that modulate transcriptional activity and genome stability. This article reviews current evidence that sheds light on the role of DNA methylation in HD.
Collapse
|
16
|
Bottero V, Alrafati F, Santiago JA, Potashkin JA. Transcriptomic and Network Meta-Analysis of Frontotemporal Dementias. Front Mol Neurosci 2021; 14:747798. [PMID: 34720873 PMCID: PMC8554122 DOI: 10.3389/fnmol.2021.747798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD), also known as frontotemporal dementia (FTD), results in a progressive decline in executive function, leading to behavioral changes, speech problems, and movement disorders. FTD is the second most common cause of young-onset dementia affecting approximately 50–60,000 Americans. FTD exists in familial and sporadic forms, with GRN progranulin and C9orf72 mutations being the most common causes. In this study, we compared the sporadic and familial transcriptome within the cerebellum, frontal cortex, hippocampus, and Brodmann’s area 8 of patients with FTD to determine genes and pathways involved in the disease process. Most dysregulated genes expression occurred in the frontal cortex and Brodmann’s area 8 for genetic and sporadic forms of FTD, respectively. A meta-analysis revealed 50 genes and 95 genes are dysregulated in at least three brain regions in patients with familial mutations and sporadic FTD patients, respectively. Familial FTD genes centered on the Wnt signaling pathway, whereas genes associated with the sporadic form of FTD centered on MAPK signaling. The results reveal the similarities and differences between sporadic and familial FTD. In addition, valproic acid and additional therapeutic agents may be beneficial in treating patients with FTD.
Collapse
Affiliation(s)
- Virginie Bottero
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Fahed Alrafati
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | | | - Judith A Potashkin
- Center for Neurodegenerative Diseases and Therapeutics, Chicago Medical School, Discipline of Cellular and Molecular Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| |
Collapse
|
17
|
Malla B, Guo X, Senger G, Chasapopoulou Z, Yildirim F. A Systematic Review of Transcriptional Dysregulation in Huntington's Disease Studied by RNA Sequencing. Front Genet 2021; 12:751033. [PMID: 34721539 PMCID: PMC8554124 DOI: 10.3389/fgene.2021.751033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder caused by an expansion of polyglutamine repeats in exon 1 of the Huntingtin gene. Transcriptional dysregulation accompanied by epigenetic alterations is an early and central disease mechanism in HD yet, the exact mechanisms and regulators, and their associated gene expression programs remain incompletely understood. This systematic review investigates genome-wide transcriptional studies that were conducted using RNA sequencing (RNA-seq) technology in HD patients and models. The review protocol was registered at the Open Science Framework (OSF). The biomedical literature and gene expression databases, PubMed and NCBI BioProject, Array Express, European Nucleotide Archive (ENA), European Genome-Phenome Archive (EGA), respectively, were searched using the defined terms specified in the protocol following the PRISMA guidelines. We conducted a complete literature and database search to retrieve all RNA-seq-based gene expression studies in HD published until August 2020, retrieving 288 articles and 237 datasets from PubMed and the databases, respectively. A total of 27 studies meeting the eligibility criteria were included in this review. Collectively, comparative analysis of the datasets revealed frequent genes that are consistently dysregulated in HD. In postmortem brains from HD patients, DNAJB1, HSPA1B and HSPB1 genes were commonly upregulated across all brain regions and cell types except for medium spiny neurons (MSNs) at symptomatic disease stage, and HSPH1 and SAT1 genes were altered in expression in all symptomatic brain datasets, indicating early and sustained changes in the expression of genes related to heat shock response as well as response to misfolded proteins. Specifically in indirect pathway medium spiny neurons (iMSNs), mitochondria related genes were among the top uniquely dysregulated genes. Interestingly, blood from HD patients showed commonly differentially expressed genes with a number of brain regions and cells, with the highest number of overlapping genes with MSNs and BA9 region at symptomatic stage. We also found the differential expression and predicted altered activity of a set of transcription factors and epigenetic regulators, including BCL6, EGR1, FOSL2 and CREBBP, HDAC1, KDM4C, respectively, which may underlie the observed transcriptional changes in HD. Altogether, our work provides a complete overview of the transcriptional studies in HD, and by data synthesis, reveals a number of common and unique gene expression and regulatory changes across different cell and tissue types in HD. These changes could elucidate new insights into molecular mechanisms of differential vulnerability in HD. Systematic Review Registration: https://osf.io/pm3wq.
Collapse
Affiliation(s)
- Bimala Malla
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xuanzong Guo
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gökçe Senger
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Zoi Chasapopoulou
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
18
|
Murthy M, Cheng YY, Holton JL, Bettencourt C. Neurodegenerative movement disorders: An epigenetics perspective and promise for the future. Neuropathol Appl Neurobiol 2021; 47:897-909. [PMID: 34318515 PMCID: PMC9291277 DOI: 10.1111/nan.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 02/02/2023]
Abstract
Neurodegenerative movement disorders (NMDs) are age‐dependent disorders that are characterised by the degeneration and loss of neurons, typically accompanied by pathological accumulation of different protein aggregates in the brain, which lead to motor symptoms. NMDs include Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, and Huntington's disease, among others. Epigenetic modifications are responsible for functional gene regulation during development, adult life and ageing and have progressively been implicated in complex diseases such as cancer and more recently in neurodegenerative diseases, such as NMDs. DNA methylation is by far the most widely studied epigenetic modification and consists of the reversible addition of a methyl group to the DNA without changing the DNA sequence. Although this research field is still in its infancy in relation to NMDs, an increasing number of studies point towards a role for DNA methylation in disease processes. This review addresses recent advances in epigenetic and epigenomic research in NMDs, with a focus on human brain DNA methylation studies. We discuss the current understanding of the DNA methylation changes underlying these disorders, the potential for use of these DNA modifications in peripheral tissues as biomarkers in early disease detection, classification and progression as well as a promising role in future disease management and therapy.
Collapse
Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Yun Yung Cheng
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| |
Collapse
|
19
|
Kwak JH, Lee K. Forebrain glutamatergic neuron-specific Ctcf deletion induces reactive microgliosis and astrogliosis with neuronal loss in adult mouse hippocampus. BMB Rep 2021. [PMID: 33612151 PMCID: PMC8249879 DOI: 10.5483/bmbrep.2021.54.6.265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
CCCTC-binding factor (CTCF), a zinc finger protein, is a transcription factor and regulator of chromatin structure. Forebrain excitatory neuron-specific CTCF deficiency contributes to inflammation via enhanced transcription of inflammation-related genes in the cortex and hippocampus. However, little is known about the long-term effect of CTCF deficiency on postnatal neurons, astrocytes, or microglia in the hippocampus of adult mice. To address this, we knocked out the Ctcf gene in forebrain glutamatergic neurons (Ctcf cKO) by crossing Ctcf-floxed mice with Camk2a-Cre mice and examined the hippocampi of 7.5-10-month-old male mice using immunofluorescence microscopy. We found obvious neuronal cell death and reactive gliosis in the hippocampal cornu ammonis (CA)1 in 7.5-10-month-old cKO mice. Prominent rod-shaped microglia that participate in immune surveillance were observed in the stratum pyramidale and radiatum layer, indicating a potential increase in inflammatory mediators released by hippocampal neurons. Although neuronal loss was not observed in CA3, and dentate gyrus (DG) CTCF depletion induced a significant increase in the number of microglia in the stratum oriens of CA3 and reactive microgliosis and astrogliosis in the molecular layer and hilus of the DG in 7.5-10-month-old cKO mice. These results suggest that long-term Ctcf deletion from forebrain excitatory neurons may contribute to reactive gliosis induced by neuronal damage and consequent neuronal loss in the hippocampal CA1, DG, and CA3 in sequence over 7 months of age.
Collapse
Affiliation(s)
- Ji-Hye Kwak
- Laboratory for Behavioral Neural Circuitry and Physiology, Department of Anatomy, Brain Science & Engineering Institute, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Kyungmin Lee
- Laboratory for Behavioral Neural Circuitry and Physiology, Department of Anatomy, Brain Science & Engineering Institute, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| |
Collapse
|
20
|
Baltayeva J, Konwar C, Castellana B, Mara DL, Christians JK, Beristain AG. Obesogenic diet exposure alters uterine natural killer cell biology and impairs vasculature remodeling in mice†. Biol Reprod 2021; 102:63-75. [PMID: 31436293 DOI: 10.1093/biolre/ioz163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/16/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Prepregnancy obesity associates with adverse reproductive outcomes that impact maternal and fetal health. While obesity-driven mechanisms underlying adverse pregnancy outcomes remain unclear, local uterine immune cells are strong but poorly studied candidates. Uterine immune cells, particularly uterine natural killer cells (uNKs), play central roles in orchestrating developmental events in pregnancy. However, the effect of obesity on uNK biology is poorly understood. Using an obesogenic high-fat/high-sugar diet (HFD) mouse model, we set out to examine the effects of maternal obesity on uNK composition and establishment of the maternal-fetal interface. HFD exposure resulted in weight gain-dependent increases in systemic inflammation and rates of fetal resorption. While HFD did not affect total uNK frequencies, HFD exposure did lead to an increase in natural cytotoxicity receptor-1 expressing uNKs as well as overall uNK activity. Importantly, HFD-associated changes in uNK coincided with impairments in uterine artery remodeling in mid but not late pregnancy. Comparison of uNK mRNA transcripts from control and HFD mice identified HFD-directed changes in genes that play roles in promoting activity/cytotoxicity and vascular biology. Together, this work provides new insight into how obesity may impact uNK processes central to the establishment of the maternal-fetal interface in early and mid pregnancy. Moreover, these findings shed light on the cellular processes affected by maternal obesity that may relate to overall pregnancy health.
Collapse
Affiliation(s)
- Jennet Baltayeva
- British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, Canada
| | - Chaini Konwar
- British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Barbara Castellana
- British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, Canada
| | - Danielle L Mara
- British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - Julian K Christians
- British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Alexander G Beristain
- British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Obstetrics & Gynecology, The University of British Columbia, Vancouver, Canada
| |
Collapse
|
21
|
Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
Collapse
Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
22
|
DNA methylation study of Huntington's disease and motor progression in patients and in animal models. Nat Commun 2020; 11:4529. [PMID: 32913184 PMCID: PMC7484780 DOI: 10.1038/s41467-020-18255-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Although Huntington's disease (HD) is a well studied Mendelian genetic disorder, less is known about its associated epigenetic changes. Here, we characterize DNA methylation levels in six different tissues from 3 species: a mouse huntingtin (Htt) gene knock-in model, a transgenic HTT sheep model, and humans. Our epigenome-wide association study (EWAS) of human blood reveals that HD mutation status is significantly (p < 10-7) associated with 33 CpG sites, including the HTT gene (p = 6.5 × 10-26). These Htt/HTT associations were replicated in the Q175 Htt knock-in mouse model (p = 6.0 × 10-8) and in the transgenic sheep model (p = 2.4 × 10-88). We define a measure of HD motor score progression among manifest HD cases based on multiple clinical assessments. EWAS of motor progression in manifest HD cases exhibits significant (p < 10-7) associations with methylation levels at three loci: near PEX14 (p = 9.3 × 10-9), GRIK4 (p = 3.0 × 10-8), and COX4I2 (p = 6.5 × 10-8). We conclude that HD is accompanied by profound changes of DNA methylation levels in three mammalian species.
Collapse
|
23
|
Abstract
DNA methylation at CpG sites is an essential epigenetic mark that regulates gene expression during mammalian development and diseases. Methylome refers to the entire set of methylation modifications present in the whole genome. Over the last several years, an increasing number of reports on brain DNA methylome reported the association between aberrant methylation and the abnormalities in the expression of critical genes known to have critical roles during aging and neurodegenerative diseases. Consequently, the role of methylation in understanding neurodegenerative diseases has been under focus. This review outlines the current knowledge of the human brain DNA methylomes during aging and neurodegenerative diseases. We describe the differentially methylated genes from fetal stage to old age and their biological functions. Additionally, we summarize the key aspects and methylated genes identified from brain methylome studies on neurodegenerative diseases. The brain methylome studies could provide a basis for studying the functional aspects of neurodegenerative diseases.
Collapse
Affiliation(s)
- Renuka Prasad
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Eek-Hoon Jho
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| |
Collapse
|
24
|
Bertogliat MJ, Morris-Blanco KC, Vemuganti R. Epigenetic mechanisms of neurodegenerative diseases and acute brain injury. Neurochem Int 2020; 133:104642. [PMID: 31838024 PMCID: PMC8074401 DOI: 10.1016/j.neuint.2019.104642] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 12/09/2019] [Indexed: 12/22/2022]
Abstract
Epigenetic modifications are emerging as major players in the pathogenesis of neurodegenerative disorders and susceptibility to acute brain injury. DNA and histone modifications act together with non-coding RNAs to form a complex gene expression machinery that adapts the brain to environmental stressors and injury response. These modifications influence cell-level operations like neurogenesis and DNA repair to large, intricate processes such as brain patterning, memory formation, motor function and cognition. Thus, epigenetic imbalance has been shown to influence the progression of many neurological disorders independent of aberrations in the genetic code. This review aims to highlight ways in which epigenetics applies to several commonly researched neurodegenerative diseases and forms of acute brain injury as well as shed light on the benefits of epigenetics-based treatments.
Collapse
Affiliation(s)
- Mario J Bertogliat
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Kahlilia C Morris-Blanco
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; William S. Middleton VA Hospital, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; William S. Middleton VA Hospital, Madison, WI, USA.
| |
Collapse
|
25
|
Abstract
Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG trinucleotide expansion in the HTT gene, which encodes for an abnormal polyglutamine tract in the huntingtin protein (HTT). This review examines the known mechanisms of HTT gene regulation. We discuss HTT expression patterns, features of the HTT promoter, regulatory regions of the HTT promoter with functional significance, and HTT regulators located outside of the proximal promoter region. The factors that influence HTT expression in the brain and the mechanisms of HTT transcriptional regulation are currently poorly understood, despite continuing research. Expanding knowledge of HTT regulation will inform future studies investigating HTT function. Improving understanding of HTT expression and control may also uncover novel therapeutic approaches for HD through the development of methods to modulate mHTT levels.
Collapse
Affiliation(s)
- Sarah B Thomson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, and BC Children's Hospital, Vancouver, BC, Canada
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, and BC Children's Hospital, Vancouver, BC, Canada.,Department of Medicine, Centre for Brain Health, and Division of Neurology, University of British Columbia Hospital, Vancouver, BC, Canada
| |
Collapse
|
26
|
Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. Semin Cell Dev Biol 2019; 90:114-127. [PMID: 30096365 PMCID: PMC6642822 DOI: 10.1016/j.semcdb.2018.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome, constituting several billion base pairs, must be contracted to fit within the volume of a nucleus where the diameter is on the scale of μm. The 3D structure and packing of such a long sequence cannot be left to pure chance, as DNA must be efficiently used for its primary roles as a matrix for transcription and replication. In recent years, methods like chromatin conformation capture (including 3C, 4C, Hi-C, ChIA-PET and Multi-ChIA) and optical microscopy have advanced substantially and have shed new light on how eukaryotic genomes are hierarchically organized; first into 10-nm fiber, next into DNA loops, topologically associated domains and finally into interphase or mitotic chromosomes. This knowledge has allowed us to revise our understanding regarding the mechanisms governing the process of DNA organization. Mounting experimental evidence suggests that the key element in the formation of loops is the binding of the CCCTC-binding factor (CTCF) to DNA; a protein that can be referred to as the chief organizer of the genome. However, CTCF does not work alone but in cooperation with other proteins, such as cohesin or Yin Yang 1 (YY1). In this short review, we briefly describe our current understanding of the structure of eukaryotic genomes, how they are established and how the formation of DNA loops can influence gene expression. We discuss the recent discoveries describing the 3D structure of the CTCF-DNA complex and the role of CTCF in establishing genome structure. Finally, we briefly explain how various genetic disorders might arise as a consequence of mutations in the CTCF target sequence or alteration of genomic imprinting.
Collapse
Affiliation(s)
- Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Wayne K Dawson
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 103-8657, Japan
| | - Anna Maria Rusek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Clinical Molecular Biology Department, Medical University of Bialystok, Bialystok, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Centre for Innovative Research, Medical University of Bialystok, Bialystok, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
| |
Collapse
|
27
|
Rustad SR, Papale LA, Alisch RS. DNA Methylation and Hydroxymethylation and Behavior. Curr Top Behav Neurosci 2019; 42:51-82. [PMID: 31392630 DOI: 10.1007/7854_2019_104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Environmentally sensitive molecular mechanisms in the brain, such as DNA methylation, have become a significant focus of neuroscience research because of mounting evidence indicating that they are critical in response to social situations, stress, threats, and behavior. The recent identification of 5-hydroxymethylcytosine (5hmC), which is enriched in the brain (tenfold over peripheral tissues), raises new questions as to the role of this base in mediating epigenetic effects in the brain. The development of genome-wide methods capable of distinguishing 5-methylcytosine (5mC) from 5hmC has revealed that a growing number of behaviors are linked to independent disruptions of 5mC and 5hmC levels, further emphasizing the unique importance of both of these modifications in the brain. Here, we review the recent links that indicate DNA methylation (both 5mC and 5hmC) is highly dynamic and that perturbations in this modification may contribute to behaviors related to psychiatric disorders and hold clinical relevance.
Collapse
Affiliation(s)
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA. .,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| |
Collapse
|
28
|
De Souza RAG, Kosior N, Thomson SB, Mathelier A, Zhang AW, Bečanović K, Wasserman WW, Leavitt BR. Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus. J Huntingtons Dis 2018; 7:223-237. [PMID: 30103339 DOI: 10.3233/jhd-170272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Huntington's disease is a late onset neurological disorder caused by a trinucleotide CAG repeat expansion mutation in the HTT gene encoding for the protein huntingtin. Despite considerable ongoing research, the wild-type function of huntingtin is not yet fully understood. OBJECTIVE To improve knowledge of HTT gene regulation at the transcriptional level and inform future studies aimed at uncovering the HTT gene's normal function. METHODS The HTT gene region was functionally characterized through an in silico analysis using publicly available data sets. ChIP-seq data sets and the online STRING database were used to identify putative transcription factor binding sites (TFBSs) and protein-protein interactions within the HTT promoter region. siRNA-mediated knockdown and ChIP-qPCR of STAT1, a TF identified from the in silico analysis, were used to validate the bioinformatics screen. RESULTS 16 regions containing potential regulatory genomic markers were identified. TFBSs for 59 transcription factors (TFs) were detected in one or more of the 16 candidate regions. Using these TFs, 15 clusters of protein-protein interactions were identified using STRING. siRNA-mediated knockdown of STAT1 resulted in an increase in HTT expression, and ChIP-qPCR detected enrichment of STAT1 binding at one of the predicted regions. These assays confirmed the utility of the bioinformatic analysis. CONCLUSIONS Putative regulatory regions outside of the immediate HTT promoter region have been identified with specific protein-protein interactions. Future work will focus on in vitro and in vivo studies to examine the effect of modulating identified TFBSs and altering the levels of specific TFs of interest in regulating HTT gene expression.
Collapse
Affiliation(s)
- Rebecca A G De Souza
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Natalia Kosior
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Sarah B Thomson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Allen W Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Kristina Bečanović
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
29
|
Zadel M, Maver A, Kovanda A, Peterlin B. DNA Methylation Profiles in Whole Blood of Huntington's Disease Patients. Front Neurol 2018; 9:655. [PMID: 30158895 PMCID: PMC6104454 DOI: 10.3389/fneur.2018.00655] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms, especially DNA methylation, are suggested to play a role in the age-of-onset in Huntington's disease (HD) based on studies on patient brains, and cellular and animal models. Methylation is tissue-specific and it is not clear how HD specific methylation in the brain correlates with the blood compartment, which represents a much more clinically accessible sample. Therefore, we explored the presence of HD specific DNA methylation patterns in whole blood on a cohort of HDM and healthy controls from Slovenia. We compared CpG site-specific DNA methylation in whole blood of 11 symptomatic and 9 pre-symptomatic HDM (HDM), and 15 healthy controls, by using bisulfite converted DNA on the Infinium® Human Methylation27 BeadChip microarray (Illumina) covering 27,578 CpG sites and 14,495 genes. Of the examined 14,495 genes, 437 were differentially methylated (p < 0.01) in pre-symptomatic HDM compared to controls, with three genes (CLDN16, DDC, NXT2) retaining statistical significance after the correction for multiple testing (false discovery rate, FDR < 0.05). Comparisons between symptomatic HDM and controls, and the comparison of symptomatic and pre-symptomatic HDM further identified 260 and 198 differentially methylated genes (p < 0.01), respectively, whereas the comparison of all HDM (symptomatic and pre-symptomatic) and healthy controls identified 326 differentially methylated genes (p < 0.01), however, none of these changes retained significance (FDR < 0.05) after the correction for multiple testing. The results of our study suggest that methylation signatures in the blood compartment are not robust enough to prove as valuable biomarkers for predicting HD progression, but recognizable changes in methylation deserve further research.
Collapse
Affiliation(s)
- Maja Zadel
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
30
|
Early alteration of epigenetic-related transcription in Huntington's disease mouse models. Sci Rep 2018; 8:9925. [PMID: 29967375 PMCID: PMC6028428 DOI: 10.1038/s41598-018-28185-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022] Open
Abstract
Transcriptional dysregulation in Huntington’s disease (HD) affects the expression of genes involved in survival and neuronal functions throughout the progression of the pathology. In recent years, extensive research has focused on epigenetic and chromatin-modifying factors as a causative explanation for such dysregulation, offering attractive targets for pharmacological therapies. In this work, we extensively examined the gene expression profiles in the cortex, striatum, hippocampus and cerebellum of juvenile R6/1 and N171-82Q mice, models of rapidly progressive HD, to retrieve the early transcriptional signatures associated with this pathology. These profiles were largely consistent across HD datasets, contained tissular and neuronal-specific genes and showed significant correspondence with the transcriptional changes in mouse strains deficient for epigenetic regulatory genes. The most prominent cases were the conditional knockout of the lysine acetyltransferase CBP in post-mitotic forebrain neurons, the double knockout of the histone methyltransferases Ezh1 and Ezh2, components of the polycomb repressor complex 2 (PRC2), and the conditional mutants of the histone methyltransferases G9a (Ehmt2) and GLP (Ehmt1). Based on these observations, we propose that the neuronal epigenetic status is compromised in the prodromal stages of HD, leading to an altered transcriptional programme that is prominently involved in neuronal identity.
Collapse
|
31
|
Epigenetic modulation by small molecule compounds for neurodegenerative disorders. Pharmacol Res 2018; 132:135-148. [PMID: 29684672 DOI: 10.1016/j.phrs.2018.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The accumulation of somatic and genetic mutations which altered the structure and coding information of the DNA are the major cause of neurological disorders. However, our recent understanding of molecular mechanisms of 'epigenetic' phenomenon reveals that the modifications of chromatin play a significant role in the development and severity of neurological disorders. These epigenetic processes are dynamic and reversible as compared to genetic ablations which are stable and irreversible. Therefore, targeting these epigenetic processes through small molecule modulators are of great therapeutic potential. To date, large number of small molecule modulators have been discovered which are capable of altering the brain pathology by targeting epigenetic enzymes. In this review, we shall put forward the key studies supporting the role of altered epigenetic processes in neurological disorders with especial emphasis on neurodegenerative disorders. A few small molecule modulators which have been shown to possess promising results in the animal model system of neurological disorders will also be discussed with future perspectives.
Collapse
|
32
|
Davis L, Onn I, Elliott E. The emerging roles for the chromatin structure regulators CTCF and cohesin in neurodevelopment and behavior. Cell Mol Life Sci 2018; 75:1205-1214. [PMID: 29110030 PMCID: PMC11105208 DOI: 10.1007/s00018-017-2706-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/09/2017] [Accepted: 10/31/2017] [Indexed: 12/19/2022]
Abstract
Recent genetic and technological advances have determined a role for chromatin structure in neurodevelopment. In particular, compounding evidence has established roles for CTCF and cohesin, two elements that are central in the establishment of chromatin structure, in proper neurodevelopment and in regulation of behavior. Genetic aberrations in CTCF, and in subunits of the cohesin complex, have been associated with neurodevelopmental disorders in human genetic studies, and subsequent animal studies have established definitive, although sometime opposing roles, for these factors in neurodevelopment and behavior. Considering the centrality of these factors in cellular processes in general, the mechanisms through which dysregulation of CTCF and cohesin leads specifically to neurological phenotypes is intriguing, although poorly understood. The connection between CTCF, cohesin, chromatin structure, and behavior is likely to be one of the next frontiers in our understanding of the development of behavior in general, and neurodevelopmental disorders in particular.
Collapse
Affiliation(s)
- Liron Davis
- Molecular and Behavioral Neurosciences Laboratory, Faculty of Medicine in the Galilee, Bar-Ilan University, Hanrietta Sold 8, 1311502, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Laboratory, Faculty of Medicine in the Galilee, Bar-Ilan University, 1311502, Safed, Israel
| | - Evan Elliott
- Molecular and Behavioral Neurosciences Laboratory, Faculty of Medicine in the Galilee, Bar-Ilan University, Hanrietta Sold 8, 1311502, Safed, Israel.
| |
Collapse
|
33
|
Arzate-Mejía RG, Recillas-Targa F, Corces VG. Developing in 3D: the role of CTCF in cell differentiation. Development 2018; 145:dev137729. [PMID: 29567640 PMCID: PMC5897592 DOI: 10.1242/dev.137729] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
CTCF is a highly conserved zinc-finger DNA-binding protein that mediates interactions between distant sequences in the genome. As a consequence, CTCF regulates enhancer-promoter interactions and contributes to the three-dimensional organization of the genome. Recent studies indicate that CTCF is developmentally regulated, suggesting that it plays a role in cell type-specific genome organization. Here, we review these studies and discuss how CTCF functions during the development of various cell and tissue types, ranging from embryonic stem cells and gametes, to neural, muscle and cardiac cells. We propose that the lineage-specific control of CTCF levels, and its partnership with lineage-specific transcription factors, allows for the control of cell type-specific gene expression via chromatin looping.
Collapse
Affiliation(s)
- Rodrigo G Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
34
|
Abstract
The dominant polyglutamine (polyQ) disorders are a group of progressive and incurable neurodegenerative disorders, which are caused by unstable expanded CAG trinucleotide repeats in the coding regions of their respective causative genes. The most prevalent polyQ disorders worldwide are Huntington’s disease and spinocerebellar ataxia type 3. Epigenetic mechanisms, such as DNA methylation, histone modifications and chromatin remodeling and noncoding RNA regulation, regulate gene expression or genome function. Epigenetic dysregulation has been suggested to play a pivotal role in the pathogenesis of polyQ disorders. Here, we summarize the current knowledge of epigenetic changes present in several representative polyQ disorders and discuss the potentiality of miRNAs as therapeutic targets for the clinic therapy of these disorders.
Collapse
Affiliation(s)
- Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
35
|
Sjöholm LK, Ransome Y, Ekström TJ, Karlsson O. Evaluation of Post-Mortem Effects on Global Brain DNA Methylation and Hydroxymethylation. Basic Clin Pharmacol Toxicol 2017; 122:208-213. [PMID: 28834189 DOI: 10.1111/bcpt.12875] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 12/17/2022]
Abstract
The number of epigenetic studies on brain functions and diseases are dramatically increasing, but little is known about the impact of post-mortem intervals and post-sampling effects on DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we examined post-mortem-induced changes in global brain 5mC and 5hmC levels at post-mortem intervals up to 540 min., and studied effects of tissue heat stabilization, using LUMA and ELISA. The global 5mC and 5hmC levels were generally higher in the cerebellum of adult rats than neonates. When measured by ELISA, the global 5mC content in adults, but not neonates, decreased with the post-mortem interval reaching a significantly lower level in cerebellum tissue at the post-mortem interval 540 min. (2.9 ± 0.7%; mean ± S.E.M.) compared to control (3.7 ± 0.6%). The global 5hmC levels increased with post-mortem interval reaching a significantly higher level at 540 min. (0.29 ± 0.06%) compared to control (0.19 ± 0.03%). This suggests that the post-mortem interval may confound 5mC and 5hmC analysis in human brain tissues as the post-mortem handling could vary substantially. The reactive oxygen species (ROS) level in cerebellum also increased over time, in particular in adults, and may be part of the mechanism that causes the observed post-mortem changes in 5mC and 5hmC. The global 5mC and 5hmC states were unaffected by heat stabilization, allowing analysis of tissues that are stabilized to preserve more labile analytes. Further studies in human samples are needed to confirm post-mortem effects on DNA methylation/hydroxymethylation and elucidate details of the underlying mechanisms.
Collapse
Affiliation(s)
- Louise K Sjöholm
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Yusuf Ransome
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tomas J Ekström
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Oskar Karlsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| |
Collapse
|
36
|
Abstract
This paper provides a brief introductory review of the most recent advances in our knowledge about the structural and functional aspects of two transcriptional regulators: MeCP2, a protein whose mutated forms are involved in Rett syndrome; and CTCF, a constitutive transcriptional insulator. This is followed by a description of the PTMs affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins, focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate. An overview is provided for some of the currently known genes that are dually regulated by these two proteins. Finally, a model is put forward to account for their possible involvement in their regulation of gene expression.
Collapse
Affiliation(s)
- Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,b Center for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Philippe T Georgel
- c Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,d Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
| |
Collapse
|
37
|
Bastaki F, Nair P, Mohamed M, Malik EM, Helmi M, Al-Ali MT, Hamzeh AR. Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report. BMC MEDICAL GENETICS 2017; 18:68. [PMID: 28619046 PMCID: PMC5472882 DOI: 10.1186/s12881-017-0429-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/28/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autosomal dominant mental retardation 21 (MRD21) is a very rare condition, characterized by short stature, microcephaly, mild facial dysmorphisms and intellectual disability that ranged from mild to severe. MRD21 is caused by mutations in CCCTC-binding factor (CTCF) and this was established through only four unrelated cases, two of which had frameshift mutations. CTCF is a master transcriptional regulator that controls chromatin structure and may serve as insulator and transcriptional activator and repressor. CASE PRESENTATION This study presents, clinically and molecularly, an Emirati patient with de novo frameshift mutation in CTCF. This novel mutation was uncovered using whole exome sequencing and was confirmed by Sanger sequencing in the trio. In silico analysis, using SIFT Indel, indicates that this frameshift; p.Lys206Profs*13 is functionally damaging with the likely involvement of nonsense-mediated mRNA decay. CONCLUSIONS Upon comparing the clinical picture of the herewith-reported individual with previously reported cases of MRD21, there seems to be many common symptoms, and few new ones that were not observed before. This helps to further define this rare condition and its molecular underpinnings.
Collapse
Affiliation(s)
- Fatma Bastaki
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Pratibha Nair
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, United Arab Emirates
| | - Madiha Mohamed
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Ethar Mustafa Malik
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Mustafa Helmi
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | | | - Abdul Rezzak Hamzeh
- Centre for Arab Genomic Studies, P.O. Box 22252, Dubai, United Arab Emirates.
| |
Collapse
|
38
|
CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function. Genes (Basel) 2017; 8:genes8060148. [PMID: 28545252 PMCID: PMC5485512 DOI: 10.3390/genes8060148] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/18/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.
Collapse
|
39
|
Francelle L, Lotz C, Outeiro T, Brouillet E, Merienne K. Contribution of Neuroepigenetics to Huntington's Disease. Front Hum Neurosci 2017; 11:17. [PMID: 28194101 PMCID: PMC5276857 DOI: 10.3389/fnhum.2017.00017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 12/29/2022] Open
Abstract
Unbalanced epigenetic regulation is thought to contribute to the progression of several neurodegenerative diseases, including Huntington’s disease (HD), a genetic disorder considered as a paradigm of epigenetic dysregulation. In this review, we attempt to address open questions regarding the role of epigenetic changes in HD, in the light of recent advances in neuroepigenetics. We particularly discuss studies using genome-wide scale approaches that provide insights into the relationship between epigenetic regulations, gene expression and neuronal activity in normal and diseased neurons, including HD neurons. We propose that cell-type specific techniques and 3D-based methods will advance knowledge of epigenome in the context of brain region vulnerability in neurodegenerative diseases. A better understanding of the mechanisms underlying epigenetic changes and of their consequences in neurodegenerative diseases is required to design therapeutic strategies more effective than current strategies based on histone deacetylase (HDAC) inhibitors. Researches in HD may play a driving role in this process.
Collapse
Affiliation(s)
- Laetitia Francelle
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Caroline Lotz
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
| | - Tiago Outeiro
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Emmanuel Brouillet
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de Recherche Fondamentale, Institut d'Imagerie Biomédicale, Molecular Imaging Center, Neurodegenerative diseases Laboratory, UMR 9199, CNRS Université Paris-Sud, Université Paris-Saclay Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
| |
Collapse
|
40
|
Kim-Ha J, Kim YJ. Age-related epigenetic regulation in the brain and its role in neuronal diseases. BMB Rep 2017; 49:671-680. [PMID: 27866512 PMCID: PMC5346312 DOI: 10.5483/bmbrep.2016.49.12.184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 11/20/2022] Open
Abstract
Accumulating evidence indicates many brain functions are mediated by epigenetic regulation of neural genes, and their dysregulations result in neuronal disorders. Experiences such as learning and recall, as well as physical exercise, induce neuronal activation through epigenetic modifications and by changing the noncoding RNA profiles. Animal models, brain samples from patients, and the development of diverse analytical methods have broadened our understanding of epigenetic regulation in the brain. Diverse and specific epigenetic changes are suggested to correlate with neuronal development, learning and memory, aging and age-related neuronal diseases. Although the results show some discrepancies, a careful comparison of the data (including methods, regions and conditions examined) would clarify the problems confronted in understanding epigenetic regulation in the brain.
Collapse
Affiliation(s)
- Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Korea
| | - Young-Joon Kim
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, and Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
41
|
Horvath S, Langfelder P, Kwak S, Aaronson J, Rosinski J, Vogt TF, Eszes M, Faull RL, Curtis MA, Waldvogel HJ, Choi OW, Tung S, Vinters HV, Coppola G, Yang XW. Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels. Aging (Albany NY) 2016; 8:1485-512. [PMID: 27479945 PMCID: PMC4993344 DOI: 10.18632/aging.101005] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023]
Abstract
Age of Huntington's disease (HD) motoric onset is strongly related to the number of CAG trinucleotide repeats in the huntingtin gene, suggesting that biological tissue age plays an important role in disease etiology. Recently, a DNA methylation based biomarker of tissue age has been advanced as an epigenetic aging clock. We sought to inquire if HD is associated with an accelerated epigenetic age. DNA methylation data was generated for 475 brain samples from various brain regions of 26 HD cases and 39 controls. Overall, brain regions from HD cases exhibit a significant epigenetic age acceleration effect (p=0.0012). A multivariate model analysis suggests that HD status increases biological age by 3.2 years. Accelerated epigenetic age can be observed in specific brain regions (frontal lobe, parietal lobe, and cingulate gyrus). After excluding controls, we observe a negative correlation (r=-0.41, p=5.5×10-8) between HD gene CAG repeat length and the epigenetic age of HD brain samples. Using correlation network analysis, we identify 11 co-methylation modules with a significant association with HD status across 3 broad cortical regions. In conclusion, HD is associated with an accelerated epigenetic age of specific brain regions and more broadly with substantial changes in brain methylation levels.
Collapse
Affiliation(s)
- Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Peter Langfelder
- Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Seung Kwak
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Jeff Aaronson
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Jim Rosinski
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Thomas F. Vogt
- CHDI Management/CHDI Foundation, Princeton, NJ 08540, USA
| | - Marika Eszes
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
- Centre for Brain Research, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
| | - Richard L.M. Faull
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
- Centre for Brain Research, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
| | - Maurice A. Curtis
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
- Centre for Brain Research, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
| | - Henry J. Waldvogel
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
- Centre for Brain Research, Faculty of Medical and Health Science (FMHS), University of Auckland, Auckland, New Zealand
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Spencer Tung
- Pathology and Laboratory Medicine, and Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Harry V. Vinters
- Pathology and Laboratory Medicine, and Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA Brain Research Institute, Los Angeles, CA 90095, USA
| | - X. William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- UCLA Brain Research Institute, Los Angeles, CA 90095, USA
| |
Collapse
|