1
|
Estevez-Fraga C, Altmann A, Parker CS, Scahill RI, Costa B, Chen Z, Manzoni C, Zarkali A, Durr A, Roos RAC, Landwehrmeyer B, Leavitt BR, Rees G, Tabrizi SJ, McColgan P. Genetic topography and cortical cell loss in Huntington's disease link development and neurodegeneration. Brain 2023; 146:4532-4546. [PMID: 37587097 PMCID: PMC10629790 DOI: 10.1093/brain/awad275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/12/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023] Open
Abstract
Cortical cell loss is a core feature of Huntington's disease (HD), beginning many years before clinical motor diagnosis, during the premanifest stage. However, it is unclear how genetic topography relates to cortical cell loss. Here, we explore the biological processes and cell types underlying this relationship and validate these using cell-specific post-mortem data. Eighty premanifest participants on average 15 years from disease onset and 71 controls were included. Using volumetric and diffusion MRI we extracted HD-specific whole brain maps where lower grey matter volume and higher grey matter mean diffusivity, relative to controls, were used as proxies of cortical cell loss. These maps were combined with gene expression data from the Allen Human Brain Atlas (AHBA) to investigate the biological processes relating genetic topography and cortical cell loss. Cortical cell loss was positively correlated with the expression of developmental genes (i.e. higher expression correlated with greater atrophy and increased diffusivity) and negatively correlated with the expression of synaptic and metabolic genes that have been implicated in neurodegeneration. These findings were consistent for diffusion MRI and volumetric HD-specific brain maps. As wild-type huntingtin is known to play a role in neurodevelopment, we explored the association between wild-type huntingtin (HTT) expression and developmental gene expression across the AHBA. Co-expression network analyses in 134 human brains free of neurodegenerative disorders were also performed. HTT expression was correlated with the expression of genes involved in neurodevelopment while co-expression network analyses also revealed that HTT expression was associated with developmental biological processes. Expression weighted cell-type enrichment (EWCE) analyses were used to explore which specific cell types were associated with HD cortical cell loss and these associations were validated using cell specific single nucleus RNAseq (snRNAseq) data from post-mortem HD brains. The developmental transcriptomic profile of cortical cell loss in preHD was enriched in astrocytes and endothelial cells, while the neurodegenerative transcriptomic profile was enriched for neuronal and microglial cells. Astrocyte-specific genes differentially expressed in HD post-mortem brains relative to controls using snRNAseq were enriched in the developmental transcriptomic profile, while neuronal and microglial-specific genes were enriched in the neurodegenerative transcriptomic profile. Our findings suggest that cortical cell loss in preHD may arise from dual pathological processes, emerging as a consequence of neurodevelopmental changes, at the beginning of life, followed by neurodegeneration in adulthood, targeting areas with reduced expression of synaptic and metabolic genes. These events result in age-related cell death across multiple brain cell types.
Collapse
Affiliation(s)
- Carlos Estevez-Fraga
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Andre Altmann
- Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Christopher S Parker
- Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Rachael I Scahill
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Beatrice Costa
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zhongbo Chen
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Claudia Manzoni
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Angeliki Zarkali
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute (ICM), AP-HP, Inserm, CNRS, Paris 75013, France
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden 2333, The Netherlands
| | | | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver BC V5Z 4H4Canada
- Division of Neurology, Department of Medicine, University of British Columbia Hospital, Vancouver BC V6T 2B5, Canada
| | - Geraint Rees
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London WC1N 3AR, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Peter McColgan
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| |
Collapse
|
2
|
Jiang A, Handley RR, Lehnert K, Snell RG. From Pathogenesis to Therapeutics: A Review of 150 Years of Huntington's Disease Research. Int J Mol Sci 2023; 24:13021. [PMID: 37629202 PMCID: PMC10455900 DOI: 10.3390/ijms241613021] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Huntington's disease (HD) is a debilitating neurodegenerative genetic disorder caused by an expanded polyglutamine-coding (CAG) trinucleotide repeat in the huntingtin (HTT) gene. HD behaves as a highly penetrant dominant disorder likely acting through a toxic gain of function by the mutant huntingtin protein. Widespread cellular degeneration of the medium spiny neurons of the caudate nucleus and putamen are responsible for the onset of symptomology that encompasses motor, cognitive, and behavioural abnormalities. Over the past 150 years of HD research since George Huntington published his description, a plethora of pathogenic mechanisms have been proposed with key themes including excitotoxicity, dopaminergic imbalance, mitochondrial dysfunction, metabolic defects, disruption of proteostasis, transcriptional dysregulation, and neuroinflammation. Despite the identification and characterisation of the causative gene and mutation and significant advances in our understanding of the cellular pathology in recent years, a disease-modifying intervention has not yet been clinically approved. This review includes an overview of Huntington's disease, from its genetic aetiology to clinical presentation and its pathogenic manifestation. An updated view of molecular mechanisms and the latest therapeutic developments will also be discussed.
Collapse
Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand; (R.R.H.); (K.L.); (R.G.S.)
| | | | | | | |
Collapse
|
3
|
D’Egidio F, Castelli V, Cimini A, d’Angelo M. Cell Rearrangement and Oxidant/Antioxidant Imbalance in Huntington's Disease. Antioxidants (Basel) 2023; 12:571. [PMID: 36978821 PMCID: PMC10045781 DOI: 10.3390/antiox12030571] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Huntington's Disease (HD) is a hereditary neurodegenerative disorder caused by the expansion of a CAG triplet repeat in the HTT gene, resulting in the production of an aberrant huntingtin (Htt) protein. The mutant protein accumulation is responsible for neuronal dysfunction and cell death. This is due to the involvement of oxidative damage, excitotoxicity, inflammation, and mitochondrial impairment. Neurons naturally adapt to bioenergetic alteration and oxidative stress in physiological conditions. However, this dynamic system is compromised when a neurodegenerative disorder occurs, resulting in changes in metabolism, alteration in calcium signaling, and impaired substrates transport. Thus, the aim of this review is to provide an overview of the cell's answer to the stress induced by HD, focusing on the role of oxidative stress and its balance with the antioxidant system.
Collapse
Affiliation(s)
| | | | | | - Michele d’Angelo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| |
Collapse
|
4
|
Integrative Meta-Analysis of Huntington's Disease Transcriptome Landscape. Genes (Basel) 2022; 13:genes13122385. [PMID: 36553652 PMCID: PMC9777612 DOI: 10.3390/genes13122385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder with autosomal dominant inheritance caused by glutamine expansion in the Huntingtin gene (HTT). Striatal projection neurons (SPNs) in HD are more vulnerable to cell death. The executive striatal population is directly connected with the Brodmann Area (BA9), which is mainly involved in motor functions. Analyzing the disease samples from BA9 from the SRA database provides insights related to neuron degeneration, which helps to identify a promising therapeutic strategy. Most gene expression studies examine the changes in expression and associated biological functions. In this study, we elucidate the relationship between variants and their effect on gene/downstream transcript expression. We computed gene and transcript abundance and identified variants from RNA-seq data using various pipelines. We predicted the effect of genome-wide association studies (GWAS)/novel variants on regulatory functions. We found that many variants affect the histone acetylation pattern in HD, thereby perturbing the transcription factor networks. Interestingly, some variants affect miRNA binding as well as their downstream gene expression. Tissue-specific network analysis showed that mitochondrial, neuroinflammation, vasculature, and angiogenesis-related genes are disrupted in HD. From this integrative omics analysis, we propose that abnormal neuroinflammation acts as a two-edged sword that indirectly affects the vasculature and associated energy metabolism. Rehabilitation of blood-brain barrier functionality and energy metabolism may secure the neuron from cell death.
Collapse
|
5
|
Faragó A, Zsindely N, Farkas A, Neller A, Siági F, Szabó MR, Csont T, Bodai L. Acetylation State of Lysine 14 of Histone H3.3 Affects Mutant Huntingtin Induced Pathogenesis. Int J Mol Sci 2022; 23:15173. [PMID: 36499499 PMCID: PMC9738228 DOI: 10.3390/ijms232315173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a polyglutamine-coding CAG repeat in the Huntingtin gene. One of the main causes of neurodegeneration in HD is transcriptional dysregulation that, in part, is caused by the inhibition of histone acetyltransferase (HAT) enzymes. HD pathology can be alleviated by increasing the activity of specific HATs or by inhibiting histone deacetylase (HDAC) enzymes. To determine which histone's post-translational modifications (PTMs) might play crucial roles in HD pathology, we investigated the phenotype-modifying effects of PTM mimetic mutations of variant histone H3.3 in a Drosophila model of HD. Specifically, we studied the mutations (K→Q: acetylated; K→R: non-modified; and K→M: methylated) of lysine residues K9, K14, and K27 of transgenic H3.3. In the case of H3.3K14Q modification, we observed the amelioration of all tested phenotypes (viability, longevity, neurodegeneration, motor activity, and circadian rhythm defects), while H3.3K14R had the opposite effect. H3.3K14Q expression prevented the negative effects of reduced Gcn5 (a HAT acting on H3K14) on HD pathology, while it only partially hindered the positive effects of heterozygous Sirt1 (an HDAC acting on H3K14). Thus, we conclude that the Gcn5-dependent acetylation of H3.3K14 might be an important epigenetic contributor to HD pathology.
Collapse
Affiliation(s)
- Anikó Faragó
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Anita Farkas
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Alexandra Neller
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Fruzsina Siági
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Márton Richárd Szabó
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - Tamás Csont
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| |
Collapse
|
6
|
McColgan P, Gregory S, Zeun P, Zarkali A, Johnson EB, Parker C, Fayer K, Lowe J, Nair A, Estevez-Fraga C, Papoutsi M, Zhang H, Scahill RI, Tabrizi SJ, Rees G. Neurofilament light-associated connectivity in young-adult Huntington's disease is related to neuronal genes. Brain 2022; 145:3953-3967. [PMID: 35758263 PMCID: PMC9679168 DOI: 10.1093/brain/awac227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 05/27/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Upregulation of functional network connectivity in the presence of structural degeneration is seen in the premanifest stages of Huntington's disease (preHD) 10-15 years from clinical diagnosis. However, whether widespread network connectivity changes are seen in gene carriers much further from onset has yet to be explored. We characterized functional network connectivity throughout the brain and related it to a measure of disease pathology burden (CSF neurofilament light, NfL) and measures of structural connectivity in asymptomatic gene carriers, on average 24 years from onset. We related these measurements to estimates of cortical and subcortical gene expression. We found no overall differences in functional (or structural) connectivity anywhere in the brain comparing control and preHD participants. However, increased functional connectivity, particularly between posterior cortical areas, correlated with increasing CSF NfL level in preHD participants. Using the Allen Human Brain Atlas and expression-weighted cell-type enrichment analysis, we demonstrated that this functional connectivity upregulation occurred in cortical regions associated with regional expression of genes specific to neuronal cells. This relationship was validated using single-nucleus RNAseq data from post-mortem Huntington's disease and control brains showing enrichment of neuronal-specific genes that are differentially expressed in Huntington's disease. Functional brain networks in asymptomatic preHD gene carriers very far from disease onset show evidence of upregulated connectivity correlating with increased disease burden. These changes occur among brain areas that show regional expression of genes specific to neuronal GABAergic and glutamatergic cells.
Collapse
Affiliation(s)
- Peter McColgan
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Sarah Gregory
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Paul Zeun
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Angeliki Zarkali
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Eileanoir B Johnson
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Christopher Parker
- Department of Computer Science and Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Kate Fayer
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Jessica Lowe
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Akshay Nair
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Carlos Estevez-Fraga
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Marina Papoutsi
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Hui Zhang
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Rachael I Scahill
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Sarah J Tabrizi
- Huntington’s Disease Centre, Department of Neurodegenerative disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Geraint Rees
- University College London Institute of Cognitive Neuroscience, University College London, London WC1N 3AZ, UK
| |
Collapse
|
7
|
Modelling the Human Blood-Brain Barrier in Huntington Disease. Int J Mol Sci 2022; 23:ijms23147813. [PMID: 35887162 PMCID: PMC9321930 DOI: 10.3390/ijms23147813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/05/2023] Open
Abstract
While blood–brain barrier (BBB) dysfunction has been described in neurological disorders, including Huntington’s disease (HD), it is not known if endothelial cells themselves are functionally compromised when promoting BBB dysfunction. Furthermore, the underlying mechanisms of BBB dysfunction remain elusive given the limitations with mouse models and post mortem tissue to identify primary deficits. We established models of BBB and undertook a transcriptome and functional analysis of human induced pluripotent stem cell (iPSC)-derived brain-like microvascular endothelial cells (iBMEC) from HD patients or unaffected controls. We demonstrated that HD-iBMECs have abnormalities in barrier properties, as well as in specific BBB functions such as receptor-mediated transcytosis.
Collapse
|
8
|
Paul BD. Cysteine metabolism and hydrogen sulfide signaling in Huntington's disease. Free Radic Biol Med 2022; 186:93-98. [PMID: 35550919 PMCID: PMC10066926 DOI: 10.1016/j.freeradbiomed.2022.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/17/2022] [Accepted: 05/05/2022] [Indexed: 02/06/2023]
Abstract
The semi-essential amino acid, cysteine, plays important roles in both essential cellular processes as well as in modulation of signaling cascades. Cysteine is obtained both from the diet as well as generated endogenously via the transsulfuration pathway. Cysteine is further utilized in protein synthesis and biosynthesis of various sulfur containing molecules. One of the products of cysteine catabolism, hydrogen sulfide (H2S), is a gaseous signaling molecule, which regulates a multitude of cellular processes. Cysteine metabolism is dysregulated in several neurodegenerative diseases and during aging. This minireview focuses on aberrant cysteine and H2S metabolism in Huntington's disease, a neurodegenerative disease caused by expansion of polyglutamine encoding repeats in the gene huntingtin, which leads to motor and cognitive deficits.
Collapse
Affiliation(s)
- Bindu D Paul
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
9
|
Martí-Martínez S, Valor LM. A Glimpse of Molecular Biomarkers in Huntington's Disease. Int J Mol Sci 2022; 23:ijms23105411. [PMID: 35628221 PMCID: PMC9142992 DOI: 10.3390/ijms23105411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder that is caused by an abnormal expansion of CAG repeats in the Huntingtin (HTT) gene. Although the main symptomatology is explained by alterations at the level of the central nervous system, predominantly affecting the basal ganglia, a peripheral component of the disease is being increasingly acknowledged. Therefore, the manifestation of the disease is complex and variable among CAG expansion carriers, introducing uncertainty in the appearance of specific signs, age of onset and severity of disease. The monogenic nature of the disorder allows a precise diagnosis, but the use of biomarkers with prognostic value is still needed to achieve clinical management of the patients in an individual manner. In addition, we need tools to evaluate the patient's response to potential therapeutic approaches. In this review, we provide a succinct summary of the most interesting molecular biomarkers that have been assessed in patients, mostly obtained from body fluids such as cerebrospinal fluid, peripheral blood and saliva.
Collapse
Affiliation(s)
- Silvia Martí-Martínez
- Servicio de Neurología, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain;
| | - Luis M. Valor
- Laboratorio de Apoyo a la Investigación, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-913-988
| |
Collapse
|
10
|
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
|
11
|
Srinivasan E, Ram V, Rajasekaran R. A review on Huntington protein Insight into protein aggregation and therapeutic interventions. Curr Drug Metab 2022; 23:260-282. [PMID: 35319359 DOI: 10.2174/1389200223666220321103942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 01/15/2022] [Indexed: 11/22/2022]
Abstract
Huntington disease (HD) is a distressing, innate neurodegenerative disease that descends from CAG repeat expansion in the huntingtin gene causing behavioral changes, motor dysfunction, and dementia in children and adults. Mutation in huntingtin (HTT) protein has been suggested to cause neuron loss in the cortex and striatum through various mechanisms including abnormal regulation of transcription, proteasomal dysfunction, post-translational modification, and other events, regulating toxicity. Pathogenesis of HD involves cleavage of the huntingtin protein followed by the neuronal accumulation of its aggregated form. Several research groups made possible efforts to reduce huntingtin gene expression, protein accumulation, and protein aggregation using inhibitors and molecular chaperones as developing drugs against HD. Herein, we review the mechanism proposed towards the formation of HTT protein aggregation and the impact of therapeutic strategies for the treatment of HD.
Collapse
Affiliation(s)
- E Srinivasan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai - 602105, Tamil Nadu, India
| | - Vavish Ram
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore - 632014, Tamil Nadu, India
| |
Collapse
|
12
|
Senousy MA, Hanafy ME, Shehata N, Rizk SM. Erythropoietin and Bacillus Calmette-Guérin Vaccination Mitigate 3-Nitropropionic Acid-Induced Huntington-like Disease in Rats by Modulating the PI3K/Akt/mTOR/P70S6K Pathway and Enhancing the Autophagy. ACS Chem Neurosci 2022; 13:721-732. [PMID: 35226456 DOI: 10.1021/acschemneuro.1c00523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Oxidative stress and mitochondrial dysfunction are among the mechanisms expected to explain the pathogenesis of Huntington's disease. Erythropoietin (EPO) and the Bacillus Calmette-Guérin (BCG) vaccine have neuroprotective effects against neurodegenerative diseases; however, the full mechanisms of their action are currently unclear. Here, for the first time, we investigated the neuroprotective effect of BCG vaccination in Huntington-like disease induced by 3-nitropropionic acid (3-NP) and its combination with EPO. Male Wistar rats were randomized into five groups: saline-treated control; 3-NP group (20 mg/kg/day, i.p.) for 7 days; EPO-treated group (5000 IU/kg/day, i.p.) for 14 days after 3-NP administration; live BCG vaccine prophylactic group (5000 cfu/g, i.p.) 10 days prior to 3-NP administration; and live BCG vaccine (5000 cfu/g, i.p.) 10 days before 3-NP administration, followed by EPO treatment (5000 IU/kg/day, i.p.) for 14 days. In a histopathological examination, striatum neurodegeneration was evidenced in the 3-NP injected rats. Administration of 3-NP elevated the levels of p-PI3K, p-Akt, p-mTOR, p-P70S6K, BAX, malondialdehyde, nitric oxide, and cytochrome oxidase while reduced the levels of BCL-2, superoxide dismutase, reduced glutathione, and the autophagy marker microtubule-associated protein light chain 3 in the striatum. EPO and BCG ameliorated the biochemical, histopathological, and behavioral derangements induced by 3-NP, with prominent neuroprotection observed in rats administered the BCG prophylactic combined with EPO treatment. These results highlight the role played by EPO and BCG in the management of 3-NP-induced Huntington-like disease by inhibiting the PI3K/Akt/mTOR/P70S6K pathway and enhancing the autophagy.
Collapse
Affiliation(s)
- Mahmoud A. Senousy
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mona Essam Hanafy
- Central Administration of Biological and Innovative Products and Clinical Studies, Egyptian Drug Authority, Giza 00202, Egypt
| | - Nahla Shehata
- Central Administration of Biological and Innovative Products and Clinical Studies, Egyptian Drug Authority, Giza 00202, Egypt
| | - Sherine M. Rizk
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| |
Collapse
|
13
|
Callahan JW, Wokosin DL, Bevan MD. Dysregulation of the Basal Ganglia Indirect Pathway in Early Symptomatic Q175 Huntington's Disease Mice. J Neurosci 2022; 42:2080-2102. [PMID: 35058372 PMCID: PMC8916764 DOI: 10.1523/jneurosci.0782-21.2022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 11/21/2022] Open
Abstract
The debilitating psychomotor symptoms of Huntington's disease (HD) are linked partly to degeneration of the basal ganglia indirect pathway. At early symptomatic stages, before major cell loss, indirect pathway neurons exhibit numerous cellular and synaptic changes in HD and its models. However, the impact of these alterations on circuit activity remains poorly understood. To address this gap, optogenetic- and reporter-guided electrophysiological interrogation was used in early symptomatic male and female Q175 HD mice. D2 dopamine receptor-expressing striatal projection neurons (D2-SPNs) were hypoactive during synchronous cortical slow-wave activity, consistent with known reductions in dendritic excitability and cortical input strength. Downstream prototypic parvalbumin-expressing external globus pallidus (PV+ GPe) neurons discharged at 2-3 times their normal rate, even during periods of D2-SPN inactivity, arguing that defective striatopallidal inhibition was not the only cause of their hyperactivity. Indeed, PV+ GPe neurons also exhibited abnormally elevated autonomous firing ex vivo Optogenetic inhibition of PV+ GPe neurons in vivo partially and fully ameliorated the abnormal hypoactivity of postsynaptic subthalamic nucleus (STN) and putative PV- GPe neurons, respectively. In contrast to STN neurons whose autonomous firing is impaired in HD mice, putative PV- GPe neuron activity was unaffected ex vivo, implying that excessive inhibition was responsible for their hypoactivity in vivo Together with previous studies, these data demonstrate that (1) indirect pathway nuclei are dysregulated in Q175 mice through changes in presynaptic activity and/or intrinsic cellular and synaptic properties; and (2) prototypic PV+ GPe neuron hyperactivity and excessive target inhibition are prominent features of early HD pathophysiology.SIGNIFICANCE STATEMENT The early symptoms of Huntington's disease (HD) are linked to degenerative changes in the action-suppressing indirect pathway of the basal ganglia. Consistent with this linkage, the intrinsic properties of cells in this pathway exhibit complex alterations in HD and its models. However, the impact of these changes on activity is poorly understood. Using electrophysiological and optogenetic approaches, we demonstrate that the indirect pathway is highly dysregulated in early symptomatic HD mice through changes in upstream activity and/or intrinsic properties. Furthermore, we reveal that hyperactivity of external globus pallidus neurons and excessive inhibition of their targets are key features of early HD pathophysiology. Together, these findings could help to inform the development and targeting of viral-based, gene therapeutic approaches for HD.
Collapse
Affiliation(s)
- Joshua W Callahan
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - David L Wokosin
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Mark D Bevan
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| |
Collapse
|
14
|
Floreani L, Ansaloni F, Mangoni D, Agostoni E, Sanges R, Persichetti F, Gustincich S. Analysis of LINE1 Retrotransposons in Huntington’s Disease. Front Cell Neurosci 2022; 15:743797. [PMID: 35095420 PMCID: PMC8795916 DOI: 10.3389/fncel.2021.743797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that made up about half the human genome. Among them, the autonomous non-LTR retrotransposon long interspersed nuclear element-1 (L1) is the only currently active TE in mammals and covers about 17% of the mammalian genome. L1s exert their function as structural elements in the genome, as transcribed RNAs to influence chromatin structure and as retrotransposed elements to shape genomic variation in somatic cells. L1s activity has been shown altered in several diseases of the nervous system. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by an expansion of a CAG repeat in the HTT gene which leads to a gradual loss of neurons most prominently in the striatum and, to a lesser extent, in cortical brain regions. The length of the expanded CAG tract is related to age at disease onset, with longer repeats leading to earlier onset. Here we carried out bioinformatic analysis of public RNA-seq data of a panel of HD mouse models showing that a decrease of L1 RNA expression recapitulates two hallmarks of the disease: it correlates to CAG repeat length and it occurs in the striatum, the site of neurodegeneration. Results were then experimentally validated in HttQ111 knock-in mice. The expression of L1-encoded proteins was independent from L1 RNA levels and differentially regulated in time and tissues. The pattern of expression L1 RNAs in human HD post-mortem brains showed similarity to mouse models of the disease. This work suggests the need for further study of L1s in HD and adds support to the current hypothesis that dysregulation of TEs may be involved in neurodegenerative diseases.
Collapse
Affiliation(s)
- Lavinia Floreani
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Elena Agostoni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- *Correspondence: Remo Sanges,
| | - Francesca Persichetti
- Department of Health Sciences, University of Piemonte Orientale “ A. Avogadro,”Novara, Italy
- Francesca Persichetti,
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- Stefano Gustincich,
| |
Collapse
|
15
|
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
|
16
|
Jiang X, Chen M, Song W, Lin GN. Label propagation-based semi-supervised feature selection on decoding clinical phenotypes with RNA-seq data. BMC Med Genomics 2021; 14:141. [PMID: 34465339 PMCID: PMC8406783 DOI: 10.1186/s12920-021-00985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Clinically, behavior, cognitive, and mental functions are affected during the neurodegenerative disease progression. To date, the molecular pathogenesis of these complex disease is still unclear. With the rapid development of sequencing technologies, it is possible to delicately decode the molecular mechanisms corresponding to different clinical phenotypes at the genome-wide transcriptomic level using computational methods. Our previous studies have shown that it is difficult to distinguish disease genes from non-disease genes. Therefore, to precisely explore the molecular pathogenesis under complex clinical phenotypes, it is better to identify biomarkers corresponding to different disease stages or clinical phenotypes. So, in this study, we designed a label propagation-based semi-supervised feature selection approach (LPFS) to prioritize disease-associated genes corresponding to different disease stages or clinical phenotypes. METHODS In this study, we pioneering put label propagation clustering and feature selection into one framework and proposed label propagation-based semi-supervised feature selection approach. LPFS prioritizes disease genes related to different disease stages or phenotypes through the alternative iteration of label propagation clustering based on sample network and feature selection with gene expression profiles. Then the GO and KEGG pathway enrichment analysis were carried as well as the gene functional analysis to explore molecular mechanisms of specific disease phenotypes, thus to decode the changes in individual behavioral and mental characteristics during neurodegenerative disease progression. RESULTS Large amounts of experiments were conducted to verify the performance of LPFS with Huntington's gene expression data. Experimental results shown that LPFS performs better in comparison with the-state-of-art methods. GO and KEGG enrichment analysis of key gene sets shown that TGF-beta signaling pathway, cytokine-cytokine receptor interaction, immune response, and inflammatory response were gradually affected during the Huntington's disease progression. In addition, we found that the expression of SLC4A11, ZFP474, AMBP, TOP2A, PBK, CCDC33, APSL, DLGAP5, and Al662270 changed seriously by the development of the disease. CONCLUSIONS In this study, we designed a label propagation-based semi-supervised feature selection model to precisely selected key genes of different disease phenotypes. We conducted experiments using the model with Huntington's disease mice gene expression data to decode the mechanisms of it. We found many cell types, including astrocyte, microglia, and GABAergic neuron, could be involved in the pathological process.
Collapse
Affiliation(s)
- Xue Jiang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Miao Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, 200030 China
| |
Collapse
|
17
|
Jiang X, Pan W, Chen M, Wang W, Song W, Lin GN. Integrative enrichment analysis of gene expression based on an artificial neuron. BMC Med Genomics 2021; 14:173. [PMID: 34433483 PMCID: PMC8386081 DOI: 10.1186/s12920-021-00988-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/18/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Huntington's disease is a kind of chronic progressive neurodegenerative disease with complex pathogenic mechanisms. To data, the pathogenesis of Huntington's disease is still not fully understood, and there has been no effective treatment. The rapid development of high-throughput sequencing technologies makes it possible to explore the molecular mechanisms at the transcriptome level. Our previous studies on Huntington's disease have shown that it is difficult to distinguish disease-associated genes from non-disease genes. Meanwhile, recent progress in bio-medicine shows that the molecular origin of chronic complex diseases may not exist in the diseased tissue, and differentially expressed genes between different tissues may be helpful to reveal the molecular origin of chronic diseases. Therefore, developing integrative analysis computational methods for the multi-tissues gene expression data, exploring the relationship between differentially expressed genes in different tissues and the disease, can greatly accelerate the molecular discovery process. METHODS For analysis of the intra- and inter- tissues' differentially expressed genes, we designed an integrative enrichment analysis method based on an artificial neuron (IEAAN). Firstly, we calculated the differential expression scores of genes which are seen as features of the corresponding gene, using fold-change approach with intra- and inter- tissues' gene expression data. Then, we weighted sum all the differential expression scores through a sigmoid function to get differential expression enrichment score. Finally, we ranked the genes according to the enrichment score. Top ranking genes are supposed to be the potential disease-associated genes. RESULTS In this study, we conducted large amounts of experiments to analyze the differentially expressed genes of intra- and inter- tissues. Experimental results showed that genes differentially expressed between different tissues are more likely to be Huntington's disease-associated genes. Five disease-associated genes were selected out in this study, two of which have been reported to be implicated in Huntington's disease. CONCLUSIONS We proposed a novel integrative enrichment analysis method based on artificial neuron (IEAAN), which displays better prediction precision of disease-associated genes in comparison with the state-of-the-art statistical-based methods. Our comprehensive evaluation suggests that genes differentially expressed between striatum and liver tissues of health individuals are more likely to be Huntington's disease-associated genes.
Collapse
Affiliation(s)
- Xue Jiang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Weihao Pan
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Miao Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Weidi Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030 China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, 200030 China
| |
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
|
Malaiya S, Cortes-Gutierrez M, Herb BR, Coffey SR, Legg SRW, Cantle JP, Colantuoni C, Carroll JB, Ament SA. Single-Nucleus RNA-Seq Reveals Dysregulation of Striatal Cell Identity Due to Huntington's Disease Mutations. J Neurosci 2021; 41:5534-5552. [PMID: 34011527 PMCID: PMC8221598 DOI: 10.1523/jneurosci.2074-20.2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 03/25/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Cell death in HD occurs primarily in striatal medium spiny neurons (MSNs), but the involvement of specific MSN subtypes and of other striatal cell types remains poorly understood. To gain insight into cell type-specific disease processes, we studied the nuclear transcriptomes of 4524 cells from the striatum of a genetically precise knock-in mouse model of the HD mutation, HttQ175/+, and from wild-type controls. We used 14- to 15-month-old male mice, a time point at which multiple behavioral, neuroanatomical, and neurophysiological changes are present but at which there is no known cell death. Thousands of differentially expressed genes (DEGs) were distributed across most striatal cell types, including transcriptional changes in glial populations that are not apparent from RNA-seq of bulk tissue. Reconstruction of cell type-specific transcriptional networks revealed a striking pattern of bidirectional dysregulation for many cell type-specific genes. Typically, these genes were repressed in their primary cell type, yet de-repressed in other striatal cell types. Integration with existing epigenomic and transcriptomic data suggest that partial loss-of-function of the polycomb repressive complex 2 (PRC2) may underlie many of these transcriptional changes, leading to deficits in the maintenance of cell identity across virtually all cell types in the adult striatum.SIGNIFICANCE STATEMENT Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder characterized by specific loss of medium spiny neurons (MSNs) in the striatum, accompanied by more subtle changes in many other cell types. It is thought that changes in transcriptional regulation are an important underlying mechanism, but cell type-specific gene expression changes are not well understood, particularly at time points relevant to the onset of disease-related symptoms. Single-nucleus (sn)RNA-seq in a genetically precise mouse model enabled us to identify novel patterns of transcriptional dysregulation because of HD mutations, including bidirectional dysregulation of many cell type identity genes that may be driven by partial loss-of-function of the polycomb repressive complex (PRC). Identifying these regulators of transcriptional dysregulation in HD can be leveraged to design novel disease-modifying therapeutics.
Collapse
Affiliation(s)
- Sonia Malaiya
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Marcia Cortes-Gutierrez
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Brian R Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Sydney R Coffey
- Department of Psychology, Western Washington University, Bellingham, Washington 98225
| | - Samuel R W Legg
- Department of Psychology, Western Washington University, Bellingham, Washington 98225
| | - Jeffrey P Cantle
- Department of Psychology, Western Washington University, Bellingham, Washington 98225
| | - Carlo Colantuoni
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Jeffrey B Carroll
- Department of Psychology, Western Washington University, Bellingham, Washington 98225
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland 21201
| |
Collapse
|
20
|
Pogoda A, Chmielewska N, Maciejak P, Szyndler J. Transcriptional Dysregulation in Huntington's Disease: The Role in Pathogenesis and Potency for Pharmacological Targeting. Curr Med Chem 2021; 28:2783-2806. [PMID: 32628586 DOI: 10.2174/0929867327666200705225821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/15/2020] [Accepted: 06/19/2020] [Indexed: 11/22/2022]
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a mutation in the gene that encodes a critical cell regulatory protein, huntingtin (Htt). The expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats causes improper folding of functional proteins and is an initial trigger of pathological changes in the brain. Recent research has indicated that the functional dysregulation of many transcription factors underlies the neurodegenerative processes that accompany HD. These disturbances are caused not only by the loss of wild-type Htt (WT Htt) function but also by the occurrence of abnormalities that result from the action of mutant Htt (mHtt). In this review, we aim to describe the role of transcription factors that are currently thought to be strongly associated with HD pathogenesis, namely, RE1-silencing transcription factor, also known as neuron-restrictive silencer factor (REST/NRSF), forkhead box proteins (FOXPs), peroxisome proliferator-activated receptor gamma coactivator-1a (PGC1α), heat shock transcription factor 1 (HSF1), and nuclear factor κ light-chain-enhancer of activated B cells (NF- κB). We also take into account the role of these factors in the phenotype of HD as well as potential pharmacological interventions targeting the analyzed proteins. Furthermore, we considered whether molecular manipulation resulting in changes in transcription factor function may have clinical potency for treating HD.
Collapse
Affiliation(s)
- Aleksandra Pogoda
- Faculty of Medicine, Medical University of Warsaw, Zwirki i Wigury Street 61, 02-097 Warsaw, Poland
| | - Natalia Chmielewska
- Department of Neurochemistry, Institute of Psychiatry and Neurology, Sobieskiego Street 9, 02-957 Warsaw, Poland
| | - Piotr Maciejak
- Department of Neurochemistry, Institute of Psychiatry and Neurology, Sobieskiego Street 9, 02-957 Warsaw, Poland
| | - Janusz Szyndler
- Department of Experimental and Clinical Pharmacology, Centre for Preclinical Research and Technology CePT, Medical University of Warsaw, Banacha Street 1B, 02-097 Warsaw, Poland
| |
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
|
Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:2020293118. [PMID: 33952696 DOI: 10.1073/pnas.2020293118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Transcriptional dysregulation in Huntington's disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-sequencing (Patch-seq) in an in vitro HD model to investigate the effects of mutant Huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased the synaptic output of striatal neurons in a cell autonomous fashion and identified a number of genes whose dysregulation was correlated with physiological deficiencies in mutant Htt neurons. In support of a pivotal role for epigenetic mechanisms in HD pathophysiology, we found that inhibiting histone deacetylase 1/3 activities rectified several functional and morphological deficits and alleviated the aberrant transcriptional profiles in mutant Htt neurons. With this study, we demonstrate that Patch-seq technology can be applied both to better understand molecular mechanisms underlying a complex neurological disease at the single-cell level and to provide a platform for screening for therapeutics for the disease.
Collapse
|
23
|
Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi MA, Ellerby LM, Zhang F, Levin JZ, Meshorer E. Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity. Genome Biol 2021; 22:73. [PMID: 33663567 PMCID: PMC7934477 DOI: 10.1186/s13059-021-02301-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Many neurodegenerative diseases develop only later in life, when cells in the nervous system lose their structure or function. In many forms of neurodegenerative diseases, this late-onset phenomenon remains largely unexplained. RESULTS Analyzing single-cell RNA sequencing from Alzheimer's disease (AD) and Huntington's disease (HD) patients, we find increased transcriptional heterogeneity in disease-state neurons. We hypothesize that transcriptional heterogeneity precedes neurodegenerative disease pathologies. To test this idea experimentally, we use juvenile forms (72Q; 180Q) of HD iPSCs, differentiate them into committed neuronal progenitors, and obtain single-cell expression profiles. We show a global increase in gene expression variability in HD. Autophagy genes become more stable, while energy and actin-related genes become more variable in the mutant cells. Knocking down several differentially variable genes results in increased aggregate formation, a pathology associated with HD. We further validate the increased transcriptional heterogeneity in CHD8+/- cells, a model for autism spectrum disorder. CONCLUSIONS Overall, our results suggest that although neurodegenerative diseases develop over time, transcriptional regulation imbalance is present already at very early developmental stages. Therefore, an intervention aimed at this early phenotype may be of high diagnostic value.
Collapse
Affiliation(s)
- Matan Sorek
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- The Edmond and Lily Center for Brain Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Walaa Oweis
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Moria Maman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Shahar Simon
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Cynthia C Hession
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neville E Sanjana
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- New York Genome Center and Department of Biology, New York University, New York, NY, USA
| | - Xi Shi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Congyi Lu
- New York Genome Center and Department of Biology, New York University, New York, NY, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaohong Xu
- Department of Neurology and Stroke Center, The First Affiliated Hospital, Jinan University, 613 Huangpu Avenue West, Guangzhou, 510632, Guangdong, China
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Department of Physiology, National University of Singapore, Singapore, 117597, Singapore
- British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Center for Brain Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| |
Collapse
|
24
|
Hecklau K, Mueller S, Koch SP, Mehkary MH, Kilic B, Harms C, Boehm-Sturm P, Yildirim F. The Effects of Selective Inhibition of Histone Deacetylase 1 and 3 in Huntington's Disease Mice. Front Mol Neurosci 2021; 14:616886. [PMID: 33679321 PMCID: PMC7925995 DOI: 10.3389/fnmol.2021.616886] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/27/2021] [Indexed: 01/15/2023] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease characterized by a late clinical onset of psychiatric, cognitive, and motor symptoms. Transcriptional dysregulation is an early and central disease mechanism which is accompanied by epigenetic alterations in HD. Previous studies demonstrated that targeting transcriptional changes by inhibition of histone deacetylases (HDACs), especially the class I HDACs, provides therapeutic effects. Yet, their exact mechanisms of action and the features of HD pathology, on which these inhibitors act remain to be elucidated. Here, using transcriptional profiling, we found that selective inhibition of HDAC1 and HDAC3 by RGFP109 alleviated transcriptional dysregulation of a number of genes, including the transcription factor genes Neurod2 and Nr4a2, and gene sets and programs, especially those that are associated to insulin-like growth factor pathway, in the striatum of R6/1 mice. RGFP109 treatment led to a modest improvement of the motor skill learning and coordination deficit on the RotaRod test, while it did not alter the locomotor and anxiety-like phenotypes in R6/1 animals. We also found, by volumetric MRI, a widespread brain atrophy in the R6/1 mice at the symptomatic disease stage, on which RGFP109 showed no significant effects. Collectively, our combined work suggests that specific HDAC1 and HDAC3 inhibition may offer benefits for alleviating the motor phenotypic deficits and transcriptional dysregulation in HD.
Collapse
Affiliation(s)
- Katharina Hecklau
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Mueller
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Paul Koch
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mustafa Hussain Mehkary
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Busra Kilic
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Harms
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Boehm-Sturm
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité – Universitätsmedizin Berlin, Berlin, Germany
- Charité Core Facility 7T Experimental MRIs, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité – Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
25
|
Bergonzoni G, Döring J, Biagioli M. D1R- and D2R-Medium-Sized Spiny Neurons Diversity: Insights Into Striatal Vulnerability to Huntington's Disease Mutation. Front Cell Neurosci 2021; 15:628010. [PMID: 33642998 PMCID: PMC7902492 DOI: 10.3389/fncel.2021.628010] [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: 11/10/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder caused by an aberrant expansion of the CAG tract within the exon 1 of the HD gene, HTT. HD progressively impairs motor and cognitive capabilities, leading to a total loss of autonomy and ultimate death. Currently, no cure or effective treatment is available to halt the disease. Although the HTT gene is ubiquitously expressed, the striatum appears to be the most susceptible district to the HD mutation with Medium-sized Spiny Neurons (MSNs) (D1R and D2R) representing 95% of the striatal neuronal population. Why are striatal MSNs so vulnerable to the HD mutation? Particularly, why do D1R- and D2R-MSNs display different susceptibility to HD? Here, we highlight significant differences between D1R- and D2R-MSNs subpopulations, such as morphology, electrophysiology, transcriptomic, functionality, and localization in the striatum. We discuss possible reasons for their selective degeneration in the context of HD. Our review suggests that a better understanding of cell type-specific gene expression dysregulation within the striatum might reveal new paths to therapeutic intervention or prevention to ameliorate HD patients' life expectancy.
Collapse
Affiliation(s)
| | | | - Marta Biagioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| |
Collapse
|
26
|
Alcalà-Vida R, Awada A, Boutillier AL, Merienne K. Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration. Neurobiol Dis 2020; 147:105155. [PMID: 33127472 DOI: 10.1016/j.nbd.2020.105155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), are progressive conditions characterized by selective, disease-dependent loss of neuronal regions and/or subpopulations. Neuronal loss is preceded by a long period of neuronal dysfunction, during which glial cells also undergo major changes, including neuroinflammatory response. Those dramatic changes affecting both neuronal and glial cells associate with epigenetic and transcriptional dysregulations, characterized by defined cell-type-specific signatures. Notably, increasing studies support the view that altered regulation of transcriptional enhancers, which are distal regulatory regions of the genome capable of modulating the activity of promoters through chromatin looping, play a critical role in transcriptional dysregulation in HD and AD. We review current knowledge on enhancers in HD and AD, and highlight challenging issues to better decipher the epigenetic code of neurodegenerative diseases.
Collapse
Affiliation(s)
- Rafael Alcalà-Vida
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | - Ali Awada
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France
| | | | - Karine Merienne
- LNCA, University of Strasbourg, France; CNRS UMR 7364, Strasbourg, France.
| |
Collapse
|
27
|
Mitchell CT, Krier I, Arjomand J, Borowsky B, Tabrizi SJ, Leavitt BR, Luthi-Carter R. Longitudinal expression changes are weak correlates of disease progression in Huntington's disease. Brain Commun 2020; 2:fcaa172. [PMID: 33305259 PMCID: PMC7713990 DOI: 10.1093/braincomms/fcaa172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/31/2020] [Accepted: 09/16/2020] [Indexed: 11/15/2022] Open
Abstract
Huntington's disease is a severe but slowly progressive hereditary illness for which only symptomatic treatments are presently available. Clinical measures of disease progression are somewhat subjective and may require years to detect significant change. There is a clear need to identify more sensitive, objective and consistent measures to detect disease progression in Huntington's disease clinical trials. Whereas Huntington's disease demonstrates a robust and consistent gene expression signature in the brain, previous studies of blood cell RNAs have lacked concordance with clinical disease stage. Here we utilized longitudinally collected samples from a well-characterized cohort of control, Huntington's disease-at-risk and Huntington's disease subjects to evaluate the possible correlation of gene expression and disease status within individuals. We interrogated these data in both cross-sectional and longitudinal analyses. A number of changes in gene expression showed consistency within this study and as compared to previous reports in the literature. The magnitude of the mean disease effect over 2 years' time was small, however, and did not track closely with motor symptom progression over the same time period. We therefore conclude that while blood-derived gene expression indicators can be of value in understanding Huntington's disease pathogenesis, they are insufficiently sensitive to be of use as state biomarkers.
Collapse
Affiliation(s)
- Christopher T Mitchell
- University of Leicester, University Road, Leicester LE1 7RH, UK
- School of Medicine, King's College London, London, UK
| | - Irina Krier
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | | | - Sarah J Tabrizi
- UCL Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Dementia Research Institute at UCL, Huntington's Disease Centre, London WC1N 3BG, UK
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada 75Z 4H4
| | - Ruth Luthi-Carter
- University of Leicester, University Road, Leicester LE1 7RH, UK
- School of Medicine, King's College London, London, UK
| |
Collapse
|
28
|
Reactive Species in Huntington Disease: Are They Really the Radicals You Want to Catch? Antioxidants (Basel) 2020; 9:antiox9070577. [PMID: 32630706 PMCID: PMC7401865 DOI: 10.3390/antiox9070577] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023] Open
Abstract
Huntington disease (HD) is a neurodegenerative condition and one of the so-called rare or minority diseases, due to its low prevalence (affecting 1–10 of every 100,000 people in western countries). The causative gene, HTT, encodes huntingtin, a protein with a yet unknown function. Mutant huntingtin causes a range of phenotypes, including oxidative stress and the activation of microglia and astrocytes, which leads to chronic inflammation of the brain. Although substantial efforts have been made to find a cure for HD, there is currently no medical intervention able to stop or even delay progression of the disease. Among the many targets of therapeutic intervention, oxidative stress and inflammation have been extensively studied and some clinical trials have been promoted to target them. In the present work, we review the basic research on oxidative stress in HD and the strategies used to fight it. Many of the strategies to reduce the phenotypes associated with oxidative stress have produced positive results, yet no substantial functional recovery has been observed in animal models or patients with the disease. We discuss possible explanations for this and suggest potential ways to overcome it.
Collapse
|
29
|
Miyazaki H, Yamanaka T, Oyama F, Kino Y, Kurosawa M, Yamada-Kurosawa M, Yamano R, Shimogori T, Hattori N, Nukina N. FACS-array-based cell purification yields a specific transcriptome of striatal medium spiny neurons in a murine Huntington disease model. J Biol Chem 2020; 295:9768-9785. [PMID: 32499373 DOI: 10.1074/jbc.ra120.012983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/21/2020] [Indexed: 12/27/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by expanded CAG repeats in the Huntingtin gene. Results from previous studies have suggested that transcriptional dysregulation is one of the key mechanisms underlying striatal medium spiny neuron (MSN) degeneration in HD. However, some of the critical genes involved in HD etiology or pathology could be masked in a common expression profiling assay because of contamination with non-MSN cells. To gain insight into the MSN-specific gene expression changes in presymptomatic R6/2 mice, a common HD mouse model, here we used a transgenic fluorescent protein marker of MSNs for purification via FACS before profiling gene expression with gene microarrays and compared the results of this "FACS-array" with those obtained with homogenized striatal samples (STR-array). We identified hundreds of differentially expressed genes (DEGs) and enhanced detection of MSN-specific DEGs by comparing the results of the FACS-array with those of the STR-array. The gene sets obtained included genes ubiquitously expressed in both MSNs and non-MSN cells of the brain and associated with transcriptional regulation and DNA damage responses. We proposed that the comparative gene expression approach using the FACS-array may be useful for uncovering the gene cascades affected in MSNs during HD pathogenesis.
Collapse
Affiliation(s)
- Haruko Miyazaki
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan.,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fumitaka Oyama
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Chemistry and Life Science, Kogakuin University, Tokyo, Japan
| | - Yoshihiro Kino
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Masaru Kurosawa
- Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Institute for Environmental and Gender-specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | | | - Risa Yamano
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan .,Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Saitama, Japan.,Laboratory for Molecular Mechanisms of Brain Development, RIKEN Center for Brain Science, Saitama, Japan.,Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|
30
|
Merienne N, Meunier C, Schneider A, Seguin J, Nair SS, Rocher AB, Le Gras S, Keime C, Faull R, Pellerin L, Chatton JY, Neri C, Merienne K, Déglon N. Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures. Cell Rep 2020; 26:2477-2493.e9. [PMID: 30811995 DOI: 10.1016/j.celrep.2019.02.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/21/2018] [Accepted: 02/01/2019] [Indexed: 12/21/2022] Open
Abstract
The role of brain cell-type-specific functions and profiles in pathological and non-pathological contexts is still poorly defined. Such cell-type-specific gene expression profiles in solid, adult tissues would benefit from approaches that avoid cellular stress during isolation. Here, we developed such an approach and identified highly selective transcriptomic signatures in adult mouse striatal direct and indirect spiny projection neurons, astrocytes, and microglia. Integrating transcriptomic and epigenetic data, we obtained a comprehensive model for cell-type-specific regulation of gene expression in the mouse striatum. A cross-analysis with transcriptomic and epigenomic data generated from mouse and human Huntington's disease (HD) brains shows that opposite epigenetic mechanisms govern the transcriptional regulation of striatal neurons and glial cells and may contribute to pathogenic and compensatory mechanisms. Overall, these data validate this less stressful method for the investigation of cellular specificity in the adult mouse brain and demonstrate the potential of integrative studies using multiple databases.
Collapse
Affiliation(s)
- Nicolas Merienne
- Department of Clinical Neurosciences, Laboratory of Neurotherapies and Neuromodulation (LNTM), Lausanne University Hospital, 1011 Lausanne, Switzerland; Neuroscience Research Center, LNTM, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Cécile Meunier
- Department of Physiology, Laboratory of Neuroenergetics, University of Lausanne, 1005 Lausanne, Switzerland
| | - Anne Schneider
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Jonathan Seguin
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Satish S Nair
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging, Team Compensation in Neurodegenerative Diseases and Aging, 75252 Paris, France
| | - Anne B Rocher
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Stéphanie Le Gras
- University of Strasbourg, CNRS, INSERM, UMR 7104, Microarray and Sequencing Platform, Institute of Genetic and Molecular and Cellular Biology, 67404 Illkirch, France
| | - Céline Keime
- University of Strasbourg, CNRS, INSERM, UMR 7104, Microarray and Sequencing Platform, Institute of Genetic and Molecular and Cellular Biology, 67404 Illkirch, France
| | - Richard Faull
- Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, Auckland 1023, New Zealand
| | - Luc Pellerin
- Department of Physiology, Laboratory of Neuroenergetics, University of Lausanne, 1005 Lausanne, Switzerland; Centre de Résonance Magnétique des Systèmes Biologiques UMR 5536, CNRS-Université de Bordeaux, 146 rue Léo Saignat, Bordeaux, France
| | - Jean-Yves Chatton
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; Cellular Imaging Facility, University of Lausanne, 1005 Lausanne, Switzerland
| | - Christian Neri
- Sorbonnes Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging, Team Compensation in Neurodegenerative Diseases and Aging, 75252 Paris, France
| | - Karine Merienne
- University of Strasbourg, CNRS, UMR 7364, Laboratory of Cognitive and Adaptive Neuroscience, 67000 Strasbourg, France
| | - Nicole Déglon
- Department of Clinical Neurosciences, Laboratory of Neurotherapies and Neuromodulation (LNTM), Lausanne University Hospital, 1011 Lausanne, Switzerland; Neuroscience Research Center, LNTM, Lausanne University Hospital, 1011 Lausanne, Switzerland.
| |
Collapse
|
31
|
Zielonka D, Witkowski G, Puch EA, Lesniczak M, Mazur-Michalek I, Isalan M, Mielcarek M. Prevalence of Non-psychiatric Comorbidities in Pre-symptomatic and Symptomatic Huntington's Disease Gene Carriers in Poland. Front Med (Lausanne) 2020; 7:79. [PMID: 32219094 PMCID: PMC7078243 DOI: 10.3389/fmed.2020.00079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/25/2020] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is monogenic neurodegenerative disorder caused by CAG expansions within the Huntingtin gene (Htt); it has a prevalence of 1 in 10,000 worldwide and is invariably fatal. Typically, healthy individuals have fewer than 35 CAG repeats, while the CAG expansions range from 36 to ~200 in HD patients. The hallmark of HD is neurodegeneration, especially in the striatal nuclei, basal ganglia and cerebral cortex, leading to neurological symptoms that involve motor, cognitive, and psychiatric events. However, HD is a complex disorder that may also affect peripheral organs, so it is possible that HD patients could be affected by comorbidities. Hence, we investigated the prevalence of comorbid conditions in HD patients (pre-symptomatic and symptomatic groups) and compared the frequency of those conditions to a control group. Our groups represent 65% of HD gene carriers registered in Poland. We identified 8 clusters of comorbid conditions in both HD groups, namely: musculoskeletal, allergies, cardiovascular, neurological, gastrointestinal, thyroid, psychiatric, and ophthalmologic. We found that HD patients have a significantly higher percentage of co-existing conditions in comparison to the control group. Among the 8 clusters of diseases, musculoskeletal, psychiatric, and cardiovascular events were significantly more frequent in both pre- and symptomatic HD patients, while neurological and gastrointestinal clusters showed significantly higher occurrence in the HD symptomatic group. A greater recognition of comorbidity in HD might help to better understand health outcomes and improve clinical management.
Collapse
Affiliation(s)
- Daniel Zielonka
- Department of Public Health, Poznan University of Medical Sciences, Poznan, Poland
| | - Grzegorz Witkowski
- First Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Elzbieta A. Puch
- Department of Human Evolutionary Biology, Adam Mickiewicz University, Poznan, Poland
| | - Marta Lesniczak
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Iwona Mazur-Michalek
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| |
Collapse
|
32
|
Gallardo-Orihuela A, Hervás-Corpión I, Hierro-Bujalance C, Sanchez-Sotano D, Jiménez-Gómez G, Mora-López F, Campos-Caro A, Garcia-Alloza M, Valor LM. Transcriptional correlates of the pathological phenotype in a Huntington's disease mouse model. Sci Rep 2019; 9:18696. [PMID: 31822756 PMCID: PMC6904489 DOI: 10.1038/s41598-019-55177-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Huntington disease (HD) is a fatal neurodegenerative disorder without a cure that is caused by an aberrant expansion of CAG repeats in exon 1 of the huntingtin (HTT) gene. Although a negative correlation between the number of CAG repeats and the age of disease onset is established, additional factors may contribute to the high heterogeneity of the complex manifestation of symptoms among patients. This variability is also observed in mouse models, even under controlled genetic and environmental conditions. To better understand this phenomenon, we analysed the R6/1 strain in search of potential correlates between pathological motor/cognitive phenotypical traits and transcriptional alterations. HD-related genes (e.g., Penk, Plk5, Itpka), despite being downregulated across the examined brain areas (the prefrontal cortex, striatum, hippocampus and cerebellum), exhibited tissue-specific correlations with particular phenotypical traits that were attributable to the contribution of the brain region to that trait (e.g., striatum and rotarod performance, cerebellum and feet clasping). Focusing on the striatum, we determined that the transcriptional dysregulation associated with HD was partially exacerbated in mice that showed poor overall phenotypical scores, especially in genes with relevant roles in striatal functioning (e.g., Pde10a, Drd1, Drd2, Ppp1r1b). However, we also observed transcripts associated with relatively better outcomes, such as Nfya (CCAAT-binding transcription factor NF-Y subunit A) plus others related to neuronal development, apoptosis and differentiation. In this study, we demonstrated that altered brain transcription can be related to the manifestation of HD-like symptoms in mouse models and that this can be extrapolated to the highly heterogeneous population of HD patients.
Collapse
Affiliation(s)
- Andrea Gallardo-Orihuela
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Irati Hervás-Corpión
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Carmen Hierro-Bujalance
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Daniel Sanchez-Sotano
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Gema Jiménez-Gómez
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Francisco Mora-López
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Servicio de Inmunología, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Antonio Campos-Caro
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Monica Garcia-Alloza
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain.,Área de Fisiología, Facultad de Medicina, Universidad de Cádiz, Plaza Fragela, 11003, Cádiz, Spain
| | - Luis M Valor
- Instituto de Investigación e Innovación en Ciencias Biomédicas de la Provincia de Cádiz (INiBICA), Cádiz, Spain. .,Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain.
| |
Collapse
|
33
|
Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington's disease. Proc Natl Acad Sci U S A 2019; 116:24840-24851. [PMID: 31744868 DOI: 10.1073/pnas.1908113116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Huntington's disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.
Collapse
|
34
|
Goodnight AV, Kremsky I, Khampang S, Jung YH, Billingsley JM, Bosinger SE, Corces VG, Chan AWS. Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington's Disease Monkey pluripotent stem cells. Epigenetics Chromatin 2019; 12:67. [PMID: 31722751 PMCID: PMC6852955 DOI: 10.1186/s13072-019-0313-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion, resulting in a mutant huntingtin protein. While it is now clear that astrocytes are affected by HD and significantly contribute to neuronal dysfunction and pathogenesis, the alterations in the transcriptional and epigenetic profiles in HD astrocytes have yet to be characterized. Here, we examine global transcription and chromatin accessibility dynamics during in vitro astrocyte differentiation in a transgenic non-human primate model of HD. RESULTS We found global changes in accessibility and transcription across different stages of HD pluripotent stem cell differentiation, with distinct trends first observed in neural progenitor cells (NPCs), once cells have committed to a neural lineage. Transcription of p53 signaling and cell cycle pathway genes was highly impacted during differentiation, with depletion in HD NPCs and upregulation in HD astrocytes. E2F target genes also displayed this inverse expression pattern, and strong associations between E2F target gene expression and accessibility at nearby putative enhancers were observed. CONCLUSIONS The results suggest that chromatin accessibility and transcription are altered throughout in vitro HD astrocyte differentiation and provide evidence that E2F dysregulation contributes to aberrant cell-cycle re-entry and apoptosis throughout the progression from NPCs to astrocytes.
Collapse
Affiliation(s)
- Alexandra V Goodnight
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA
| | - Isaac Kremsky
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Sujittra Khampang
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
- Embryonic Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yoon Hee Jung
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - James M Billingsley
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA.
| | - Anthony W S Chan
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA.
| |
Collapse
|
35
|
Brouillet E, Merienne K. What is gained or 'lost in translation' in Huntington's disease. Brain 2019; 142:2900-2902. [PMID: 31560061 DOI: 10.1093/brain/awz274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This scientific commentary refers to ‘Increased translation as a novel pathogenic mechanism in Huntington’s disease’, by Jordi Creus-Muncunill et al. (doi:10.1093/brain/awz230).
Collapse
Affiliation(s)
- Emmanuel Brouillet
- CEA, DRF, Institut de Biology François Jacob, Molecular Imaging Research Center (MIRCen), F Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F, Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS/Strasbourg University UMR 7364, Laboratory of Adaptive and Cognitive Neuroscience (LNCA), Strasbourg F, France
| |
Collapse
|
36
|
Galvan L, Francelle L, Gaillard MC, de Longprez L, Carrillo-de Sauvage MA, Liot G, Cambon K, Stimmer L, Luccantoni S, Flament J, Valette J, de Chaldée M, Auregan G, Guillermier M, Joséphine C, Petit F, Jan C, Jarrige M, Dufour N, Bonvento G, Humbert S, Saudou F, Hantraye P, Merienne K, Bemelmans AP, Perrier AL, Déglon N, Brouillet E. The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin. Brain 2019. [PMID: 29534157 PMCID: PMC5917821 DOI: 10.1093/brain/awy057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The neurobiological functions of a number of kinases expressed in the brain are unknown. Here, we report new findings on DCLK3 (doublecortin like kinase 3), which is preferentially expressed in neurons in the striatum and dentate gyrus. Its function has never been investigated. DCLK3 expression is markedly reduced in Huntington's disease. Recent data obtained in studies related to cancer suggest DCLK3 could have an anti-apoptotic effect. Thus, we hypothesized that early loss of DCLK3 in Huntington's disease may render striatal neurons more susceptible to mutant huntingtin (mHtt). We discovered that DCLK3 silencing in the striatum of mice exacerbated the toxicity of an N-terminal fragment of mHtt. Conversely, overexpression of DCLK3 reduced neurodegeneration produced by mHtt. DCLK3 also produced beneficial effects on motor symptoms in a knock-in mouse model of Huntington's disease. Using different mutants of DCLK3, we found that the kinase activity of the protein plays a key role in neuroprotection. To investigate the potential mechanisms underlying DCLK3 effects, we studied the transcriptional changes produced by the kinase domain in human striatal neurons in culture. Results show that DCLK3 regulates in a kinase-dependent manner the expression of many genes involved in transcription regulation and nucleosome/chromatin remodelling. Consistent with this, histological evaluation showed DCLK3 is present in the nucleus of striatal neurons and, protein-protein interaction experiments suggested that the kinase domain interacts with zinc finger proteins, including the transcriptional activator adaptor TADA3, a core component of the Spt-ada-Gcn5 acetyltransferase (SAGA) complex which links histone acetylation to the transcription machinery. Our novel findings suggest that the presence of DCLK3 in striatal neurons may play a key role in transcription regulation and chromatin remodelling in these brain cells, and show that reduced expression of the kinase in Huntington's disease could render the striatum highly vulnerable to neurodegeneration.
Collapse
Affiliation(s)
- Laurie Galvan
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Laetitia Francelle
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Lucie de Longprez
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Maria-Angeles Carrillo-de Sauvage
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Géraldine Liot
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France.,Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F38000, Grenoble, France.,INSERM U1216, F38000, Grenoble, France.,CHU de Grenoble, F38000, Grenoble, France
| | - Karine Cambon
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Lev Stimmer
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,Inserm UMS27, F-92265 Fontenay-aux-Roses, France
| | - Sophie Luccantoni
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,Inserm UMS27, F-92265 Fontenay-aux-Roses, France
| | - Julien Flament
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,Inserm UMS27, F-92265 Fontenay-aux-Roses, France
| | - Julien Valette
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Michel de Chaldée
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Gwenaelle Auregan
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Martine Guillermier
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Charlène Joséphine
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Fanny Petit
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Caroline Jan
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Margot Jarrige
- Inserm U861, I-STEM, AFM, Evry 91030 Cedex France.,UEVE U861, I-STEM, AFM Evry 91030, France
| | - Noëlle Dufour
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Gilles Bonvento
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Sandrine Humbert
- Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F38000, Grenoble, France.,INSERM U1216, F38000, Grenoble, France.,CHU de Grenoble, F38000, Grenoble, France
| | - Frédéric Saudou
- Univ. Grenoble Alpes, Grenoble Institut des Neurosciences, GIN, F38000, Grenoble, France.,INSERM U1216, F38000, Grenoble, France.,CHU de Grenoble, F38000, Grenoble, France
| | - Philippe Hantraye
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS/Strasbourg University UMR 7364, Laboratory of Adaptive and Cognitive Neuroscience (LNCA), Strasbourg F-67000, France
| | - Alexis-Pierre Bemelmans
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| | - Anselme L Perrier
- Inserm U861, I-STEM, AFM, Evry 91030 Cedex France.,UEVE U861, I-STEM, AFM Evry 91030, France
| | - Nicole Déglon
- Lausanne University Medical School (CHUV), Department of Clinical Neurosciences (DNC), Laboratory of Cellular and Molecular Neurotherapies (LNCM), Lausanne, Switzerland.,Lausanne University Medical School (CHUV), Neuroscience Research Center (CRN), Laboratory of Cellular and Molecular Neurotherapies (LNCM), Lausanne, Switzerland
| | - Emmanuel Brouillet
- CEA, DRF, Institut François Jacob, Molecular Imaging Research Center (MIRCen), F-92265 Fontenay-aux-Roses, France.,CNRS, CEA, Paris-Sud Univ., Univ. Paris-Saclay, Neurodegenerative Diseases Laboratory (UMR9199), F-92265, Fontenay-aux-Roses, France
| |
Collapse
|
37
|
Harding RJ, Loppnau P, Ackloo S, Lemak A, Hutchinson A, Hunt B, Holehouse AS, Ho JC, Fan L, Toledo-Sherman L, Seitova A, Arrowsmith CH. Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems. J Biol Chem 2019; 294:6986-7001. [PMID: 30842263 PMCID: PMC6497952 DOI: 10.1074/jbc.ra118.007204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
The gene mutated in individuals with Huntington's disease (HD) encodes the 348-kDa huntingtin (HTT) protein. Pathogenic HD CAG-expansion mutations create a polyglutamine (polyQ) tract at the N terminus of HTT that expands above a critical threshold of ∼35 glutamine residues. The effect of these HD mutations on HTT is not well understood, in part because it is difficult to carry out biochemical, biophysical, and structural studies of this large protein. To facilitate such studies, here we have generated expression constructs for the scalable production of HTT in multiple eukaryotic expression systems. Our set of HTT expression clones comprised both N- and C-terminally FLAG-tagged HTT constructs with polyQ lengths representative of the general population, HD patients, and juvenile HD patients, as well as the more extreme polyQ expansions used in some HD tissue and animal models. Our expression system yielded milligram quantities of pure recombinant HTT protein, including many of the previously mapped post-translational modifications. We characterized both apo and HTT-HTT-associated protein 40 (HAP40) complex samples produced with this HD resource, demonstrating that this toolkit can be used to generate physiologically meaningful HTT complexes. We further demonstrate that these resources can produce sufficient material for protein-intensive experiments, such as small-angle X-ray scattering, providing biochemical insight into full-length HTT protein structure. The work outlined and the tools generated here lay a foundation for further biochemical and structural work on the HTT protein and for studying its functional interactions with other biomolecules.
Collapse
Affiliation(s)
- Rachel J Harding
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Suzanne Ackloo
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ashley Hutchinson
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Brittany Hunt
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alex S Holehouse
- the Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130
| | - Jolene C Ho
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Lixin Fan
- the Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core of NCI, National Institutes of Health, Frederick, Maryland 21701, and
| | | | - Alma Seitova
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
38
|
Rangel-Barajas C, Rebec GV. Overview of Huntington's Disease Models: Neuropathological, Molecular, and Behavioral Differences. ACTA ACUST UNITED AC 2019; 83:e47. [PMID: 30040221 DOI: 10.1002/cpns.47] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transgenic mouse models of Huntington's disease (HD), a neurodegenerative condition caused by a single gene mutation, have been transformative in their ability to reveal the molecular processes and pathophysiological mechanisms underlying the HD behavioral phenotype. Three model categories have been generated depending on the genetic context in which the mutation is expressed: truncated, full-length, and knock-in. No single model, however, broadly replicates the behavioral symptoms and massive neuronal loss that occur in human patients. The disparity between model and patient requires careful consideration of what each model has to offer when testing potential treatments. Although the translation of animal data to the clinic has been limited, each model can make unique contributions toward an improved understanding of the neurobehavioral underpinnings of HD. Thus, conclusions based on data obtained from more than one model are likely to have the most success in the search for new treatment targets. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Claudia Rangel-Barajas
- Program in Neuroscience, Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana
| | - George V Rebec
- Program in Neuroscience, Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana
| |
Collapse
|
39
|
Sassone J, Papadimitriou E, Thomaidou D. Regenerative Approaches in Huntington's Disease: From Mechanistic Insights to Therapeutic Protocols. Front Neurosci 2018; 12:800. [PMID: 30450032 PMCID: PMC6224350 DOI: 10.3389/fnins.2018.00800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Huntington’s Disease (HD) is a neurodegenerative disorder caused by a CAG expansion in the exon-1 of the IT15 gene encoding the protein Huntingtin. Expression of mutated Huntingtin in humans leads to dysfunction and ultimately degeneration of selected neuronal populations of the striatum and cerebral cortex. Current available HD therapy relies on drugs to treat chorea and control psychiatric symptoms, however, no therapy has been proven to slow down disease progression or prevent disease onset. Thus, although 24 years have passed since HD gene identification, HD remains a relentless progressive disease characterized by cognitive dysfunction and motor disability that leads to death of the majority of patients, on average 10–20 years after its onset. Up to now several molecular pathways have been implicated in the process of neurodegeneration involved in HD and have provided potential therapeutic targets. Based on these data, approaches currently under investigation for HD therapy aim on the one hand at getting insight into the mechanisms of disease progression in a human-based context and on the other hand at silencing mHTT expression by using antisense oligonucleotides. An innovative and still poorly investigated approach is to identify new factors that increase neurogenesis and/or induce reprogramming of endogenous neuroblasts and parenchymal astrocytes to generate new healthy neurons to replace lost ones and/or enforce neuroprotection of pre-existent striatal and cortical neurons. Here, we review studies that use human disease-in-a-dish models to recapitulate HD pathogenesis or are focused on promoting in vivo neurogenesis of endogenous striatal neuroblasts and direct neuronal reprogramming of parenchymal astrocytes, which combined with neuroprotective protocols bear the potential to re-establish brain homeostasis lost in HD.
Collapse
Affiliation(s)
- Jenny Sassone
- Vita-Salute University and San Raffaele Scientific Institute, Milan, Italy
| | | | - Dimitra Thomaidou
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| |
Collapse
|
40
|
Chanda K, Das S, Chakraborty J, Bucha S, Maitra A, Chatterjee R, Mukhopadhyay D, Bhattacharyya NP. Altered Levels of Long NcRNAs Meg3 and Neat1 in Cell And Animal Models Of Huntington's Disease. RNA Biol 2018; 15:1348-1363. [PMID: 30321100 PMCID: PMC6284602 DOI: 10.1080/15476286.2018.1534524] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington's disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays we observed perturbations in the levels of 12 ncRNAs in HD mouse brain, eight of which had human homologs. Of these, Meg3, Neat1, and Xist showed a consistent and significant increase in HD cell and animal models. Transient knock-down of Meg3 and Neat1 in cell models of HD led to a significant decrease of aggregates formed by mutant huntingtin and downregulation of the endogenous Tp53 expression. Understanding Meg3 and Neat1 functions in the context of HD pathogenesis is likely to open up new strategies to control the disease.
Collapse
Affiliation(s)
- Kaushik Chanda
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Srijit Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Joyeeta Chakraborty
- Human Genetics Unit, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Sudha Bucha
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, P.O. N.S.S., Kalyani, West Bengal, India
| | | | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Nitai P Bhattacharyya
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| |
Collapse
|
41
|
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: 30] [Impact Index Per Article: 5.0] [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
|
42
|
Pan Y, Zhu Y, Yang W, Tycksen E, Liu S, Palucki J, Zhu L, Sasaki Y, Sharma MK, Kim AH, Zhang B, Yano H. The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity. J Biol Chem 2018; 293:11850-11866. [PMID: 29891550 DOI: 10.1074/jbc.ra117.001211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/14/2018] [Indexed: 01/12/2023] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an abnormal expansion of polyglutamine repeats in the huntingtin protein (Htt). Transcriptional dysregulation is an early event in the course of HD progression and is thought to contribute to disease pathogenesis, but how mutant Htt causes transcriptional alterations and subsequent cell death in neurons is not well understood. RNA-Seq analysis revealed that expression of a mutant Htt fragment in primary cortical neurons leads to robust gene expression changes before neuronal death. Basic helix-loop-helix transcription factor Twist1, which is essential for embryogenesis and is normally expressed at low levels in mature neurons, was substantially up-regulated in mutant Htt-expressing neurons in culture and in the brains of HD mouse models. Knockdown of Twist1 by RNAi in mutant Htt-expressing primary cortical neurons reversed the altered expression of a subset of genes involved in neuronal function and, importantly, abrogated neurotoxicity. Using brain-derived neurotrophic factor (Bdnf), which is known to be involved in HD pathogenesis, as a model gene, we found that Twist1 knockdown could reverse mutant Htt-induced DNA hypermethylation at the Bdnf regulatory region and reactivate Bdnf expression. Together, these results suggest that Twist1 is an important upstream mediator of mutant Htt-induced neuronal death and may in part operate through epigenetic mechanisms.
Collapse
Affiliation(s)
| | - Ying Zhu
- From the Department of Neurological Surgery
| | - Wei Yang
- Genome Technology Access Center.,Department of Genetics
| | | | | | | | | | | | | | - Albert H Kim
- From the Department of Neurological Surgery.,Department of Genetics.,Department of Developmental Biology.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bo Zhang
- Department of Developmental Biology.,Center of Regenerative Medicine
| | - Hiroko Yano
- From the Department of Neurological Surgery, .,Department of Genetics.,Center of Regenerative Medicine.,Department of Neurology, and.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
43
|
Epigenetic Regulation in Neurodegenerative Diseases. Trends Neurosci 2018; 41:587-598. [PMID: 29885742 DOI: 10.1016/j.tins.2018.05.005] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022]
Abstract
Mechanisms of epigenetic regulation, including DNA methylation, chromatin remodeling, and histone post-translational modifications, are involved in multiple aspects of neuronal function and development. Recent discoveries have shed light on critical functions of chromatin in the aging brain, with an emerging realization that the maintenance of a healthy brain relies heavily on epigenetic mechanisms. Here, we present recent advances, with a focus on histone modifications and the implications for several neurodegenerative diseases including Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). We highlight common and unique epigenetic mechanisms among these situations and point to emerging therapeutic approaches.
Collapse
|
44
|
Harding RJ, Tong YF. Proteostasis in Huntington's disease: disease mechanisms and therapeutic opportunities. Acta Pharmacol Sin 2018; 39:754-769. [PMID: 29620053 DOI: 10.1038/aps.2018.11] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/18/2018] [Indexed: 02/08/2023] Open
Abstract
Many neurodegenerative diseases are characterized by impairment of protein quality control mechanisms in neuronal cells. Ineffective clearance of misfolded proteins by the proteasome, autophagy pathways and exocytosis leads to accumulation of toxic protein oligomers and aggregates in neurons. Toxic protein species affect various cellular functions resulting in the development of a spectrum of different neurodegenerative proteinopathies, including Huntington's disease (HD). Playing an integral role in proteostasis, dysfunction of the ubiquitylation system in HD is progressive and multi-faceted with numerous biochemical pathways affected, in particular, the ubiquitin-proteasome system and autophagy routes for protein aggregate degradation. Unravelling the molecular mechanisms involved in HD pathogenesis of proteostasis provides new insight in disease progression in HD as well as possible therapeutic avenues. Recent developments of potential therapeutics are discussed in this review.
Collapse
|
45
|
Ament SA, Pearl JR, Cantle JP, Bragg RM, Skene PJ, Coffey SR, Bergey DE, Wheeler VC, MacDonald ME, Baliga NS, Rosinski J, Hood LE, Carroll JB, Price ND. Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. Mol Syst Biol 2018; 14:e7435. [PMID: 29581148 PMCID: PMC5868199 DOI: 10.15252/msb.20167435] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/23/2018] [Accepted: 02/26/2018] [Indexed: 12/19/2022] Open
Abstract
Transcriptional changes occur presymptomatically and throughout Huntington's disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD We reconstructed a genome-scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and CAG repeat length-dependent gene expression changes in Htt CAG knock-in mouse striatum and replicated many of these associations in independent transcriptomic and proteomic datasets. Thirteen of 48 of these predicted TF-target gene modules were also differentially expressed in striatal tissue from human disease. We experimentally validated a specific model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found CAG repeat length-dependent changes in the genomic occupancy of SMAD3 and confirmed our model's prediction that many SMAD3 target genes are downregulated early in HD.
Collapse
Affiliation(s)
- Seth A Ament
- Institute for Systems Biology, Seattle, WA, USA
- Institute for Genome Sciences and Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jocelynn R Pearl
- Institute for Systems Biology, Seattle, WA, USA
- Molecular & Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Jeffrey P Cantle
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Robert M Bragg
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, USA
| | - Peter J Skene
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sydney R Coffey
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, USA
| | | | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jim Rosinski
- CHDI Management, CHDI Foundation, Princeton, NJ, USA
| | | | - Jeffrey B Carroll
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, USA
| | | |
Collapse
|
46
|
McColgan P, Gregory S, Seunarine KK, Razi A, Papoutsi M, Johnson E, Durr A, Roos RAC, Leavitt BR, Holmans P, Scahill RI, Clark CA, Rees G, Tabrizi SJ. Brain Regions Showing White Matter Loss in Huntington's Disease Are Enriched for Synaptic and Metabolic Genes. Biol Psychiatry 2018; 83:456-465. [PMID: 29174593 PMCID: PMC5803509 DOI: 10.1016/j.biopsych.2017.10.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND The earliest white matter changes in Huntington's disease are seen before disease onset in the premanifest stage around the striatum, within the corpus callosum, and in posterior white matter tracts. While experimental evidence suggests that these changes may be related to abnormal gene transcription, we lack an understanding of the biological processes driving this regional vulnerability. METHODS Here, we investigate the relationship between regional transcription in the healthy brain, using the Allen Institute for Brain Science transcriptome atlas, and regional white matter connectivity loss at three time points over 24 months in subjects with premanifest Huntington's disease relative to control participants. The baseline cohort included 72 premanifest Huntington's disease participants and 85 healthy control participants. RESULTS We show that loss of corticostriatal, interhemispheric, and intrahemispheric white matter connections at baseline and over 24 months in premanifest Huntington's disease is associated with gene expression profiles enriched for synaptic genes and metabolic genes. Corticostriatal gene expression profiles are predominately associated with motor, parietal, and occipital regions, while interhemispheric expression profiles are associated with frontotemporal regions. We also show that genes with known abnormal transcription in human Huntington's disease and animal models are overrepresented in synaptic gene expression profiles, but not in metabolic gene expression profiles. CONCLUSIONS These findings suggest a dual mechanism of white matter vulnerability in Huntington's disease, in which abnormal transcription of synaptic genes and metabolic disturbance not related to transcription may drive white matter loss.
Collapse
Affiliation(s)
- Peter McColgan
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom
| | - Sarah Gregory
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom
| | - Kiran K Seunarine
- Developmental Imaging and Biophysics Section, UCL Institute of Child Health, Queen Square, London, United Kingdom
| | - Adeel Razi
- Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, Queen Square, London, United Kingdom; Department of Electronic Engineering, NED University of Engineering and Technology, Karachi, Pakistan
| | - Marina Papoutsi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom
| | - Eileanoir Johnson
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom
| | - Alexandra Durr
- APHP Department of Genetics, University Hospital Pitié-Salpêtrière; and ICM (Brain and Spine Institute) INSERM U1127, CNRS UMR7225, Sorbonne Universités - UPMC Paris VI UMR_S1127, Paris, France
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Rachael I Scahill
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom
| | - Chris A Clark
- Developmental Imaging and Biophysics Section, UCL Institute of Child Health, Queen Square, London, United Kingdom
| | - Geraint Rees
- Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, Queen Square, London, United Kingdom; National Hospital for Neurology and Neurosurgery, Queen Square, London, United Kingdom.
| |
Collapse
|
47
|
Garret M, Du Z, Chazalon M, Cho YH, Baufreton J. Alteration of GABAergic neurotransmission in Huntington's disease. CNS Neurosci Ther 2018; 24:292-300. [PMID: 29464851 DOI: 10.1111/cns.12826] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/23/2018] [Accepted: 01/26/2018] [Indexed: 12/16/2022] Open
Abstract
Hereditary Huntington's disease (HD) is characterized by cell dysfunction and death in the brain, leading to progressive cognitive, psychiatric, and motor impairments. Despite molecular and cellular descriptions of the effects of the HD mutation, no effective pharmacological treatment is yet available. In addition to well-established alterations of glutamatergic and dopaminergic neurotransmitter systems, it is becoming clear that the GABAergic systems are also impaired in HD. GABA is the major inhibitory neurotransmitter in the brain, and GABAergic neurotransmission has been postulated to be modified in many neurological and psychiatric diseases. In addition, GABAergic neurotransmission is the target of many drugs that are in wide clinical use. Here, we summarize data demonstrating the occurrence of alterations of GABAergic markers in the brain of HD carriers as well as in rodent models of the disease. In particular, we pinpoint HD-related changes in the expression of GABAA receptors (GABAA Rs). On the basis that a novel GABA pharmacology of GABAA Rs established with more selective drugs is emerging, we argue that clinical treatments acting specifically on GABAergic neurotransmission may be an appropriate strategy for improving symptoms linked to the HD mutation.
Collapse
Affiliation(s)
- Maurice Garret
- Université de Bordeaux, INCIA, UMR 5287, Bordeaux, France.,CNRS, INCIA, UMR 5287, Bordeaux, France
| | - Zhuowei Du
- Université de Bordeaux, INCIA, UMR 5287, Bordeaux, France.,CNRS, INCIA, UMR 5287, Bordeaux, France
| | - Marine Chazalon
- Institut des Maladies Neurodégénératives, Université de Bordeaux, UMR 5293, Bordeaux, France.,Institut des Maladies Neurodégénératives, CNRS, UMR 5293, Bordeaux, France
| | - Yoon H Cho
- Université de Bordeaux, INCIA, UMR 5287, Bordeaux, France.,CNRS, INCIA, UMR 5287, Bordeaux, France
| | - Jérôme Baufreton
- Institut des Maladies Neurodégénératives, Université de Bordeaux, UMR 5293, Bordeaux, France.,Institut des Maladies Neurodégénératives, CNRS, UMR 5293, Bordeaux, France
| |
Collapse
|
48
|
Puigdellívol M, Saavedra A, Pérez-Navarro E. Cognitive dysfunction in Huntington's disease: mechanisms and therapeutic strategies beyond BDNF. Brain Pathol 2018; 26:752-771. [PMID: 27529673 DOI: 10.1111/bpa.12432] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/08/2016] [Indexed: 12/15/2022] Open
Abstract
One of the main focuses in Huntington's disease (HD) research, as well as in most neurodegenerative diseases, is the development of new therapeutic strategies, as currently there is no treatment to delay or prevent the progression of the disease. Neuronal dysfunction and neuronal death in HD are caused by a combination of interrelated pathogenic processes that lead to motor, cognitive and psychiatric symptoms. Understanding how mutant huntingtin impacts on a plethora of cellular functions could help to identify new molecular targets. Although HD has been classically classified as a neurodegenerative disease affecting voluntary movement, lately cognitive dysfunction is receiving increased attention as it is very invalidating for patients. Thus, an ambitious goal in HD research is to find altered molecular mechanisms that contribute to cognitive decline. In this review, we have focused on those findings related to corticostriatal and hippocampal cognitive dysfunction in HD, as well as on the underlying molecular mechanisms, which constitute potential therapeutic targets. These include alterations in synaptic plasticity, transcriptional machinery and neurotrophic and neurotransmitter signaling.
Collapse
Affiliation(s)
- Mar Puigdellívol
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER) sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Ana Saavedra
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER) sobre Enfermedades Neurodegenerativas (CIBERNED), Spain.,Institut de Neurociències, Universitat de Barcelona, Catalonia, Spain
| | - Esther Pérez-Navarro
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER) sobre Enfermedades Neurodegenerativas (CIBERNED), Spain.,Institut de Neurociències, Universitat de Barcelona, Catalonia, Spain
| |
Collapse
|
49
|
Dong X, Cong S. Identification of differentially expressed genes and regulatory relationships in Huntington's disease by bioinformatics analysis. Mol Med Rep 2018; 17:4317-4326. [PMID: 29328442 PMCID: PMC5802203 DOI: 10.3892/mmr.2018.8410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022] Open
Abstract
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock-in cell model STHdhQ111/Q111 were predicted. DEGs between the HD and control samples were screened using the limma package in R. Functional and pathway enrichment analyses were conducted using the database for annotation, visualization and integrated discovery software. A protein-protein interaction (PPI) network was established by the search tool for the retrieval of interacting genes and visualized by Cytoscape. Module analysis of the PPI network was performed utilizing MCODE. A total of 471 DEGs were identified, including ribonuclease A family member 4 (RNASE4). In addition, 41 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways, as well as several significant Gene Ontology terms (including cytokine-cytokine receptor interaction and cytosolic DNA-sensing) were identified. A total of 18 significant modules were identified from the PPI network. Furthermore, a novel transcriptional regulatory relationship was identified, namely signal transducer and activator of transcription 3 (STAT3), which is regulated by miRNA-124 in HD. In conclusion, deregulation of 18 critical genes may contribute to the occurrence of HD. RNASE4, STAT3, and miRNA-124 may have a regulatory association with the pathological mechanisms in HD.
Collapse
Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| |
Collapse
|
50
|
Keo A, Aziz NA, Dzyubachyk O, van der Grond J, van Roon-Mom WMC, Lelieveldt BPF, Reinders MJT, Mahfouz A. Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington's Disease. Front Mol Neurosci 2017; 10:399. [PMID: 29249939 PMCID: PMC5714896 DOI: 10.3389/fnmol.2017.00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and spinobulbar muscular atrophy. The expanded CAG repeat length in the causative gene is negatively related to the age-at-onset (AAO) of clinical symptoms. In addition to the expanded CAG repeat length in the causative gene, the normal CAG repeats in the other polyQ genes can affect the AAO, suggesting functional interactions between the polyQ genes. However, there is no detailed assessment of the relationships among polyQ genes in pathologically relevant brain regions. We used gene co-expression analysis to study the functional relationships among polyQ genes in different brain regions using the Allen Human Brain Atlas (AHBA), a spatial map of gene expression in the healthy brain. We constructed co-expression networks for seven anatomical brain structures, as well as a region showing a specific pattern of atrophy in HD patients detected by magnetic resonance imaging (MRI) of the brain. In this HD-associated region, we found that ATN1 and ATXN2 were co-expressed and shared co-expression partners which were enriched for DNA repair genes. We observed a similar co-expression pattern in the frontal lobe, parietal lobe, and striatum in which this relation was most pronounced. Given that the co-expression patterns for these anatomical structures were similar to those for the HD-associated region, our results suggest that their disruption is likely involved in HD pathology. Moreover, ATN1 and ATXN2 also shared many co-expressed genes with HTT, the causative gene of HD, across the brain. Although this triangular relationship among these three polyQ genes may also be dysregulated in other polyQ diseases, stronger co-expression patterns between ATN1 and ATXN2 observed in the HD-associated region, especially in the striatum, may be more specific to HD.
Collapse
Affiliation(s)
- Arlin Keo
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - N Ahmad Aziz
- Department of Neurology, Leiden University Medical Center, Leiden, Netherlands
| | - Oleh Dzyubachyk
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Boudewijn P F Lelieveldt
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcel J T Reinders
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - Ahmed Mahfouz
- Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands.,Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| |
Collapse
|