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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Ebrahimzadeh K, Noroozi R. The emerging role of long non-coding RNAs, microRNAs, and an accelerated epigenetic age in Huntington’s disease. Front Aging Neurosci 2022; 14:987174. [PMID: 36185471 PMCID: PMC9520620 DOI: 10.3389/fnagi.2022.987174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disease with variable clinical manifestations. Recent studies highlighted the contribution of epigenetic alterations to HD progress and onset. The potential crosstalk between different epigenetic layers and players such as aberrant expression of non-coding RNAs and methylation alterations has been found to affect the pathogenesis of HD or mediate the effects of trinucleotide expansion in its pathophysiology. Also, microRNAs have been assessed for their roles in the modulation of HD manifestations, among them are miR-124, miR-128a, hsa-miR-323b-3p, miR-432, miR-146a, miR-19a, miR-27a, miR-101, miR-9*, miR-22, miR-132, and miR-214. Moreover, long non-coding RNAs such as DNM3OS, NEAT1, Meg3, and Abhd11os are suggested to be involved in the pathogenesis of HD. An accelerated DNA methylation age is another epigenetic signature reported recently for HD. The current literature search collected recent findings of dysregulation of miRNAs or lncRNAs as well as methylation changes and epigenetic age in HD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Kaveh Ebrahimzadeh,
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Rezvan Noroozi,
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Neueder A, Kojer K, Hering T, Lavery DJ, Chen J, Birth N, Hallitsch J, Trautmann S, Parker J, Flower M, Sethi H, Haider S, Lee JM, Tabrizi SJ, Orth M. Abnormal molecular signatures of inflammation, energy metabolism, and vesicle biology in human Huntington disease peripheral tissues. Genome Biol 2022; 23:189. [PMID: 36071529 PMCID: PMC9450392 DOI: 10.1186/s13059-022-02752-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/18/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND A major challenge in neurodegenerative diseases concerns identifying biological disease signatures that track with disease progression or respond to an intervention. Several clinical trials in Huntington disease (HD), an inherited, progressive neurodegenerative disease, are currently ongoing. Therefore, we examine whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in HD patients. RESULTS We generate large, high-quality human datasets from skeletal muscle, skin and adipose tissue to probe molecular changes in human premanifest and early manifest HD patients-those most likely involved in clinical trials. The analysis of the transcriptomics and proteomics data shows robust, stage-dependent dysregulation. Gene ontology analysis confirms the involvement of inflammation and energy metabolism in peripheral HD pathogenesis. Furthermore, we observe changes in the homeostasis of extracellular vesicles, where we find consistent changes of genes and proteins involved in this process. In-depth single nucleotide polymorphism data across the HTT gene are derived from the generated primary cell lines. CONCLUSIONS Our 'omics data document the involvement of inflammation, energy metabolism, and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials. The generated data, complemented by the primary cell lines established from peripheral tissues, and a large panel of iPSC lines that can serve as human models of HD are a valuable and unique resource to advance the current understanding of molecular mechanisms driving HD pathogenesis.
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Affiliation(s)
- Andreas Neueder
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Kerstin Kojer
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Tanja Hering
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Daniel J Lavery
- CHDI Foundation, Princeton, NJ, 08540, USA
- Loulou Foundation, Orphan Disease Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jian Chen
- CHDI Foundation, Princeton, NJ, 08540, USA
| | - Nathalie Birth
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | | | - Sonja Trautmann
- Department of Neurology, Ulm University, 89081, Ulm, Germany
| | - Jennifer Parker
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Michael Flower
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Huma Sethi
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Salman Haider
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Michael Orth
- Department of Neurology, Ulm University, 89081, Ulm, Germany.
- Swiss Huntington Centre, Neurozentrum, Siloah AG, Worbstr. 312, 3073, Gümligen, Switzerland.
- University Hospital of Old Age Psychiatry and Psychotherapy, Bern University, Bern, Switzerland.
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Weng YT, Chen HM, Chien T, Chiu FL, Kuo HC, Chern Y. TRAX Provides Neuroprotection for Huntington's Disease Via Modulating a Novel Subset of MicroRNAs. Mov Disord 2022; 37:2008-2020. [PMID: 35997316 DOI: 10.1002/mds.29174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/19/2022] [Accepted: 07/14/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Huntington's disease (HD) is a neurodegenerative disease caused by CAG-repeat expansions (>36) in exon 1 of HTT, which dysregulates multiple cellular machineries. Translin-associated protein X (TRAX) is a scaffold protein with diverse functions, including suppressing the microRNA (miRNA)-mediated silencing by degrading pre-miRNA. To date, the role of TRAX in neurodegenerative diseases remains unknown. OBJECTIVES We delineated the role of TRAX upregulation during HD progression. METHODS Expression of TRAX in the brains of humans and three mouse models with HD were analyzed by immunohistochemistry staining, western blot, and quantitative reverse transcription-polymerase chain reaction. Adeno-associated viruses harboring TRAX short hairpin RNA were intrastriatally injected into HD mice to downregulate TRAX. HD-like symptoms were analyzed by behavioral and biochemical assessments. The miRNA-sequencing and RNA-sequencing analyses were used to identify the TRAX- regulated miRNA-messenger RNA (mRNA) axis during HD progression. The identified gene targets were validated biochemically in mouse and human striatal cells. RESULTS We discovered that TRAX was upregulated in the brains of HD patients and three HD mouse models. Downregulation of TRAX enhanced 83 miRNAs (including miR-330-3p, miR-496a-3p) and subsequently changed the corresponding mRNA networks critical for HD pathogenesis (eg, DARPP-32 and brain-derived neurotrophic factor). Disruption of the TRAX-mediated miRNA-mRNA axis accelerated the progression of HD-like symptoms, including the degeneration of motor function, accumulation of mHTT aggregates, and shortened neurite outgrowth. CONCLUSIONS We demonstrated that TRAX upregulation is authentic and protective in HD. Our study provides a novel layer of regulation for HD pathogenesis and may lead to the development of new therapeutic strategies for HD. © 2022 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Yu-Ting Weng
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hui-Mei Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting Chien
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yijuang Chern
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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An interdependence between GAPVD1 gene polymorphism, expression level and response to interferon beta in patients with multiple sclerosis. J Neuroimmunol 2021; 353:577507. [PMID: 33548618 DOI: 10.1016/j.jneuroim.2021.577507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 11/21/2022]
Abstract
Interferon-β (IFN-β) is among the first drugs used for reducing the symptoms of multiple sclerosis (MS). Many studies show that the genetic predisposition of patients might modulate their response to IFN-β treatment. In this study GAPVD1 gene expression and the genotyping of rs2291858 variant were analysed in 100 responder and 100 non-responder patients with MS treated using IFN-β. Moreover, rs2291858 genotyping was performed for 200 patients with MS and 200 healthy controls. GAPVD1 expression was significantly increased in the responder patients than in non-responders and the distribution of rs2291858 polymorphism was significantly different between them. The GAPVD1 expression level in AA genotype of the responder group was higher than that in other genotypes of these two groups. The results show that the GAPVD1 expression level and rs2291858 genotype probably affect the response to IFN- β in patients with MS.
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Exosomes and exosomal microRNA in non-targeted radiation bystander and abscopal effects in the central nervous system. Cancer Lett 2020; 499:73-84. [PMID: 33160002 DOI: 10.1016/j.canlet.2020.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/24/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
Localized cranial radiotherapy is a dominant treatment for brain cancers. After being subjected to radiation, the central nervous system (CNS) exhibits targeted effects as well as non-targeted radiation bystander effects (RIBE) and abscopal effects (RIAE). Radiation-induced targeted effects in the CNS include autophagy and various changes in tumor cells due to radiation sensitivity, which can be regulated by microRNAs. Non-targeted radiation effects are mainly induced by gap junctional communication between cells, exosomes containing microRNAs can be transduced by intracellular endocytosis to regulate RIBE and RIAE. In this review, we discuss the involvement of microRNAs in radiation-induced targeted effects, as well as exosomes and/or exosomal microRNAs in non-targeted radiation effects in the CNS. As a target pathway, we also discuss the Akt pathway which is regulated by microRNAs, exosomes, and/or exosomal microRNAs in radiation-induced targeted effects and RIBE in CNS tumor cells. As the CNS-derived exosomes can cross the blood-brain-barrier (BBB) into the bloodstream and be isolated from peripheral blood, exosomes and exosomal microRNAs can emerge as promising minimally invasive biomarkers and therapeutic targets for radiation-induced targeted and non-targeted effects in the CNS.
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A genome-wide scan for candidate lethal variants in Thoroughbred horses. Sci Rep 2020; 10:13153. [PMID: 32753654 PMCID: PMC7403398 DOI: 10.1038/s41598-020-68946-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3'UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.
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