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Meem TM, Khan U, Mredul MBR, Awal MA, Rahman MH, Khan MS. A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease. Bioinform Biol Insights 2023; 17:11779322231210098. [PMID: 38033382 PMCID: PMC10683407 DOI: 10.1177/11779322231210098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/07/2023] [Indexed: 12/02/2023] Open
Abstract
Huntington disease (HD) is a degenerative brain disease caused by the expansion of CAG (cytosine-adenine-guanine) repeats, which is inherited as a dominant trait and progressively worsens over time possessing threat. Although HD is monogenetic, the specific pathophysiology and biomarkers are yet unknown specifically, also, complex to diagnose at an early stage, and identification is restricted in accuracy and precision. This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them (DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs interactions (FOXC1, GATA2, etc), TF-microRNA (miRNA) interactions (hsa-miR-340, hsa-miR-34a, etc), protein-drug interactions, and disorders associated with DEGs were predicted. Furthermore, we used gene set enrichment analysis (GSEA) to emphasize relevant gene ontology terms (eg, TF activity, sequence-specific DNA binding) linked to DEGs in HD. Disease interactions revealed the diseases that are linked to HD, and the prospective small drug molecules like cytarabine and arsenite was predicted against HD. This study reveals molecular biomarkers at the RNA and protein levels that may be beneficial to improve the understanding of molecular mechanisms, early diagnosis, as well as prospective pharmacologic targets for designing beneficial HD treatment.
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Affiliation(s)
- Tahera Mahnaz Meem
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Umama Khan
- Biotechnology & Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Bazlur Rahman Mredul
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Md Abdul Awal
- Electronics and Communication Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Salauddin Khan
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
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Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V. Vitamin B 6, B 12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease. 3 Biotech 2023; 13:96. [PMID: 36852176 PMCID: PMC9958225 DOI: 10.1007/s13205-023-03525-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Huntington's disease (HD) is an incurable and progressive neurodegenerative disease affecting the basal ganglia of the brain. HD is caused due to expansion of the polyglutamine tract in the protein Huntingtin resulting in aggregates. The increased PolyQ length results in aggregation of protein Huntingtin leading to neuronal cell death. Vitamin B6, B12 and folate are deficient in many neurodegenerative diseases. We performed an integrated analysis of transcriptomic, metabolomic and cofactor-protein network of vitamin B6, B12 and folate was performed. Our results show considerable overlap of pathways modulated by Vitamin B6, B12 and folate with those obtained from transcriptomic and metabolomic data of HD patients and model systems. Further, in yeast model of HD we showed treatment of B6, B12 or folate either alone or in combination showed impaired aggregate formation. Transcriptomic analysis of yeast model treated with B6, B12 and folate showed upregulation of pathways like ubiquitin mediated proteolysis, autophagy, peroxisome, fatty acid, lipid and nitrogen metabolism. Metabolomic analysis of yeast model shows deregulation of pathways like aminoacyl-tRNA biosynthesis, metabolism of various amino acids, nitrogen metabolism and glutathione metabolism. Integrated transcriptomic and metabolomic analysis of yeast model showed concordance in the pathways obtained. Knockout of Peroxisomal (PXP1 and PEX7) and Autophagy (ATG5) genes in yeast increased aggregates which is mitigated by vitamin B6, B12 and folate treatment. Taken together our results show a role for Vitamin B6, B12 and folate mediated modulation of pathways important for preventing protein aggregation with potential implications for HD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03525-y.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - K. Raksha Rao
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - R. Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Durga Prasad Patnana
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
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Rahman MH, Peng S, Hu X, Chen C, Rahman MR, Uddin S, Quinn JM, Moni MA. A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17031035. [PMID: 32041280 PMCID: PMC7037290 DOI: 10.3390/ijerph17031035] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 12/21/2022]
Abstract
Neurological diseases (NDs) are progressive disorders, the progression of which can be significantly affected by a range of common diseases that present as comorbidities. Clinical studies, including epidemiological and neuropathological analyses, indicate that patients with type 2 diabetes (T2D) have worse progression of NDs, suggesting pathogenic links between NDs and T2D. However, finding causal or predisposing factors that link T2D and NDs remains challenging. To address these problems, we developed a high-throughput network-based quantitative pipeline using agnostic approaches to identify genes expressed abnormally in both T2D and NDs, to identify some of the shared molecular pathways that may underpin T2D and ND interaction. We employed gene expression transcriptomic datasets from control and disease-affected individuals and identified differentially expressed genes (DEGs) in tissues of patients with T2D and ND when compared to unaffected control individuals. One hundred and ninety seven DEGs (99 up-regulated and 98 down-regulated in affected individuals) that were common to both the T2D and the ND datasets were identified. Functional annotation of these identified DEGs revealed the involvement of significant cell signaling associated molecular pathways. The overlapping DEGs (i.e., seen in both T2D and ND datasets) were then used to extract the most significant GO terms. We performed validation of these results with gold benchmark databases and literature searching, which identified which genes and pathways had been previously linked to NDs or T2D and which are novel. Hub proteins in the pathways were identified (including DNM2, DNM1, MYH14, PACSIN2, TFRC, PDE4D, ENTPD1, PLK4, CDC20B, and CDC14A) using protein-protein interaction analysis which have not previously been described as playing a role in these diseases. To reveal the transcriptional and post-transcriptional regulators of the DEGs we used transcription factor (TF) interactions analysis and DEG-microRNAs (miRNAs) interaction analysis, respectively. We thus identified the following TFs as important in driving expression of our T2D/ND common genes: FOXC1, GATA2, FOXL1, YY1, E2F1, NFIC, NFYA, USF2, HINFP, MEF2A, SRF, NFKB1, USF2, HINFP, MEF2A, SRF, NFKB1, PDE4D, CREB1, SP1, HOXA5, SREBF1, TFAP2A, STAT3, POU2F2, TP53, PPARG, and JUN. MicroRNAs that affect expression of these genes include mir-335-5p, mir-16-5p, mir-93-5p, mir-17-5p, mir-124-3p. Thus, our transcriptomic data analysis identifies novel potential links between NDs and T2D pathologies that may underlie comorbidity interactions, links that may include potential targets for therapeutic intervention. In sum, our neighborhood-based benchmarking and multilayer network topology methods identified novel putative biomarkers that indicate how type 2 diabetes (T2D) and these neurological diseases interact and pathways that, in the future, may be targeted for treatment.
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Affiliation(s)
- Md Habibur Rahman
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Silong Peng
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyuan Hu
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chen Chen
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; (M.H.R.); (S.P.); (X.H.); (C.C.)
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Enayetpur, Sirajgonj 6751, Bangladesh;
| | - Shahadat Uddin
- Complex Systems Research Group & Project Management Program, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Julian M.W. Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Correspondence:
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Tsuang DW, Greenwood TA, Jayadev S, Davis M, Shutes-David A, Bird TD. A Genetic Study of Psychosis in Huntington's Disease: Evidence for the Involvement of Glutamate Signaling Pathways. J Huntingtons Dis 2019; 7:51-59. [PMID: 29480208 DOI: 10.3233/jhd-170277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Psychotic symptoms of delusions and hallucinations occur in about 5% of persons with Huntington's disease (HD). The mechanisms underlying these occurrences are unknown, but the same symptoms also occur in schizophrenia, and thus genetic risk factors for schizophrenia may be relevant to the development of psychosis in HD. OBJECTIVE To investigate the possible role of genes associated with schizophrenia in the occurrence of psychotic symptoms in HD. METHODS DNA from subjects with HD and psychosis (HD+P; n = 47), subjects with HD and no psychosis (HD-P; n = 126), and controls (CTLs; n = 207) was genotyped using the Infinium PsychArray-24 v1.1 BeadChip. The allele frequencies of single-nucleotide polymorphisms (SNPs) that were previously associated with schizophrenia and related psychiatric disorders were compared between these groups. RESULTS Of the 30 candidate genes tested, 10 showed an association with psychosis in HD. The majority of these genes, including CTNNA2, DRD2, ERBB4, GRID2, GRIK4, GRM1, NRG1, PCNT, RELN, and SLC1A2, demonstrate network interactions related to glutamate signaling. CONCLUSIONS This study suggests genetic associations between several previously identified candidate genes for schizophrenia and the occurrence of psychotic symptoms in HD. These data support the potential role of genes related to glutamate signaling in HD psychosis.
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Affiliation(s)
- Debby W Tsuang
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Tiffany A Greenwood
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Marie Davis
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Andrew Shutes-David
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA.,Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Thomas D Bird
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
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5
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Stuitje G, van Belzen MJ, Gardiner SL, van Roon-Mom WMC, Boogaard MW, Tabrizi SJ, Roos RAC, Aziz NA. Age of onset in Huntington's disease is influenced by CAG repeat variations in other polyglutamine disease-associated genes. Brain 2019; 140:e42. [PMID: 28549075 DOI: 10.1093/brain/awx122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Geerte Stuitje
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martine J van Belzen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sarah L Gardiner
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Merel W Boogaard
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, UCL Huntington's Disease Centre, University College London Institute of Neurology, London, UK
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - N A Aziz
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Neurodegenerative Disease, UCL Huntington's Disease Centre, University College London Institute of Neurology, London, UK
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6
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Kumar S, Yadav N, Pandey S, Thelma BK. Advances in the discovery of genetic risk factors for complex forms of neurodegenerative disorders: contemporary approaches, success, challenges and prospects. J Genet 2018. [DOI: 10.1007/s12041-018-0953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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7
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Weydt P, Dupuis L, Petersen Å. Thermoregulatory disorders in Huntington disease. HANDBOOK OF CLINICAL NEUROLOGY 2018; 157:761-775. [PMID: 30459039 DOI: 10.1016/b978-0-444-64074-1.00047-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Huntington disease (HD) is a paradigmatic autosomal-dominant adult-onset neurodegenerative disease. Since the identification of an abnormal expansion of a trinucleotide repeat tract in the huntingtin gene as the underlying genetic defect, a broad range of transgenic animal models of the disease has become available and these have helped to unravel the relevant molecular pathways in unprecedented detail. Of note, some of the most informative of these models develop thermoregulatory defects such as hypothermia, problems with adaptive thermogenesis, and an altered circadian temperature rhythm. Both central, e.g., in the hypothalamus and peripheral, i.e., the brown adipose tissue and skeletal muscle, problems contribute to the phenotype. Importantly, these structures and pathways are also affected in human HD. Yet, currently the evidence for bona fide thermodysregulation in human HD patients remains anecdotal. This may be due to a lack of reliable tools for monitoring body temperature in an outpatient setting. Regardless, study of the temperature phenotype has contributed to the identification of unexpected molecular targets, such as the PGC-1α pathway.
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Affiliation(s)
- Patrick Weydt
- Department of Neurodegenerative Diseases and Gerontopsychiatry/Neurology, University of Bonn Medical Center, Bonn, Germany.
| | - Luc Dupuis
- Faculty of Medicine, University of Strasbourg, Strasbourg, France
| | - Åsa Petersen
- Translational Neuroendocrine Research Unit, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
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8
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Risk factors for the onset and progression of Huntington disease. Neurotoxicology 2017; 61:79-99. [PMID: 28111121 DOI: 10.1016/j.neuro.2017.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 01/10/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder characterized by chorea, behavioural and psychiatric manifestations, and dementia, caused by a CAG triplet repeat expansion in the huntingtin gene. Systematic review of the literature was conducted to determine the risk factors for the onset and progression of HD. Multiple databases were searched, using terms specific to Huntington disease and to studies of aetiology, risk, prevention and genetics, limited to studies on human subjects published in English or French between 1950 and 2010. Two reviewers independently screened the abstracts and identified potentially relevant articles for full-text review using predetermined inclusion criteria. Three major categories of risk factors for onset of HD were identified: CAG repeat length in the huntingtin gene, CAG instability, and genetic modifiers. Of these, CAG repeat length in the huntingtin gene is the most important risk factor. For the progression of HD: genetic, demographic, past medical/clinical and environmental risk factors have been studied. Of these factors, genetic factors appear to play the most important role in the progression of HD. Among the potential risk factors, CAG repeat length in the mutant allele was found to be a relatively consistent and significant risk factor for the progression of HD, especially in motor, cognitive, and other neurological symptom deterioration. In addition, there were many consistent results in the literature indicating that a higher number of CAG repeats was associated with shorter survival, faster institutionalization, and earlier percutaneous endoscopic gastrostomy.
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9
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Arning L. The search for modifier genes in Huntington disease – Multifactorial aspects of a monogenic disorder. Mol Cell Probes 2016; 30:404-409. [DOI: 10.1016/j.mcp.2016.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/29/2016] [Accepted: 06/29/2016] [Indexed: 11/24/2022]
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10
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Mo C, Hannan AJ, Renoir T. Environmental factors as modulators of neurodegeneration: Insights from gene–environment interactions in Huntington's disease. Neurosci Biobehav Rev 2015; 52:178-92. [DOI: 10.1016/j.neubiorev.2015.03.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/13/2015] [Accepted: 03/03/2015] [Indexed: 12/11/2022]
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Berggren KL, Chen J, Fox J, Miller J, Dodds L, Dugas B, Vargas L, Lothian A, McAllum E, Volitakis I, Roberts B, Bush AI, Fox JH. Neonatal iron supplementation potentiates oxidative stress, energetic dysfunction and neurodegeneration in the R6/2 mouse model of Huntington's disease. Redox Biol 2015; 4:363-74. [PMID: 25703232 PMCID: PMC4348428 DOI: 10.1016/j.redox.2015.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 02/08/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion that encodes a polyglutamine tract in huntingtin (htt) protein. Dysregulation of brain iron homeostasis, oxidative stress and neurodegeneration are consistent features of the HD phenotype. Therefore, environmental factors that exacerbate oxidative stress and iron dysregulation may potentiate HD. Iron supplementation in the human population is common during infant and adult-life stages. In this study, iron supplementation in neonatal HD mice resulted in deterioration of spontaneous motor running activity, elevated levels of brain lactate and oxidized glutathione consistent with increased energetic dysfunction and oxidative stress, and increased striatal and motor cortical neuronal atrophy, collectively demonstrating potentiation of the disease phenotype. Oxidative stress, energetic, and anatomic markers of degeneration were not affected in wild-type littermate iron-supplemented mice. Further, there was no effect of elevated iron intake on disease outcomes in adult HD mice. We have demonstrated an interaction between the mutant huntingtin gene and iron supplementation in neonatal HD mice. Findings indicate that elevated neonatal iron intake potentiates mouse HD and promotes oxidative stress and energetic dysfunction in brain. Neonatal-infant dietary iron intake level may be an environmental modifier of human HD.
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Affiliation(s)
- Kiersten L Berggren
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Jianfang Chen
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA; Neuroscience Graduate Program, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Julia Fox
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Jonathan Miller
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Lindsay Dodds
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Bryan Dugas
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Liset Vargas
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
| | - Amber Lothian
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Erin McAllum
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Irene Volitakis
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Blaine Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ashley I Bush
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Jonathan H Fox
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA; Neuroscience Graduate Program, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82070, USA.
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12
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Affiliation(s)
- Larissa Arning
- Human Genetics, Ruhr University, 44780, Bochum, Germany,
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13
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Genetics of Huntington's disease and related disorders. Drug Discov Today 2014; 19:985-9. [PMID: 24657309 DOI: 10.1016/j.drudis.2014.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/07/2014] [Indexed: 02/05/2023]
Abstract
Huntington's disease is the most frequent form of the hereditary choreas and has a multifaceted phenotype including cognitive and psychiatric impairment. The disorder is due to a dynamic mutation, which also influences the onset age of the disorder. Other genetic modifiers of the HD phenotypes have been suggested but often not confirmed by independent studies. Several syndromes with similar presentation have different genetic backgrounds, including the neuroacanthocytoses, mainly choreoacanthocytosis and MacLeod syndrome as a result of mutations in chorein and Kell protein, respectively, but also benign hereditary chorea, owing to mutations in NKX-2-1, and paroxysmal kinesigenic dyskinesia, as a result of recently found mutations in the proline-rich transmembrane protein 2, PRRT2. Chorea can also be a major feature in other neurogenetic disorders, including the spinocerebellar ataxias and also in neurometabolic disorders.
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Weydt P, Soyal SM, Landwehrmeyer GB, Patsch W. A single nucleotide polymorphism in the coding region of PGC-1α is a male-specific modifier of Huntington disease age-at-onset in a large European cohort. BMC Neurol 2014; 14:1. [PMID: 24383721 PMCID: PMC3880172 DOI: 10.1186/1471-2377-14-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 12/12/2022] Open
Abstract
Background Genetic modifiers are important clues for the identification of therapeutic targets in neurodegenerative diseases. Huntington disease (HD) is one of the most common autosomal dominant inherited neurodegenerative diseases. The clinical symptoms include motor abnormalities, cognitive decline and behavioral disturbances. Symptom onset is typically between 40 and 50 years of age, but can vary by several decades in extreme cases and this is in part determined by modifying genetic factors. The metabolic master regulator PGC-1α, coded by the PPARGC1A gene, coordinates cellular respiration and was shown to play a role in neurodegenerative diseases, including HD. Methods Using a candidate gene approach we analyzed a large European cohort (n = 1706) from the REGISTRY study for associations between PPARGC1A genotype and age at onset (AO) in HD. Results We report that a coding variant (rs3736265) in PPARGC1A is associated with an earlier motor AO in men but not women carrying the HD mutation. Conclusions These results further strengthen the evidence for a role of PGC-1α in HD and unexpectedly suggest a gender effect.
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Kloster E, Saft C, Epplen JT, Arning L. CNR1 variation is associated with the age at onset in Huntington disease. Eur J Med Genet 2013; 56:416-9. [DOI: 10.1016/j.ejmg.2013.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/27/2013] [Indexed: 11/15/2022]
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16
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Metzger S, Walter C, Riess O, Roos RAC, Nielsen JE, Craufurd D, Nguyen HP. The V471A polymorphism in autophagy-related gene ATG7 modifies age at onset specifically in Italian Huntington disease patients. PLoS One 2013; 8:e68951. [PMID: 23894380 PMCID: PMC3718802 DOI: 10.1371/journal.pone.0068951] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/09/2013] [Indexed: 11/19/2022] Open
Abstract
The cause of Huntington disease (HD) is a polyglutamine repeat expansion of more than 36 units in the huntingtin protein, which is inversely correlated with the age at onset of the disease. However, additional genetic factors are believed to modify the course and the age at onset of HD. Recently, we identified the V471A polymorphism in the autophagy-related gene ATG7, a key component of the autophagy pathway that plays an important role in HD pathogenesis, to be associated with the age at onset in a large group of European Huntington disease patients. To confirm this association in a second independent patient cohort, we analysed the ATG7 V471A polymorphism in additional 1,464 European HD patients of the "REGISTRY" cohort from the European Huntington Disease Network (EHDN). In the entire REGISTRY cohort we could not confirm a modifying effect of the ATG7 V471A polymorphism. However, analysing a modifying effect of ATG7 in these REGISTRY patients and in patients of our previous HD cohort according to their ethnic origin, we identified a significant effect of the ATG7 V471A polymorphism on the HD age at onset only in the Italian population (327 patients). In these Italian patients, the polymorphism is associated with a 6-years earlier disease onset and thus seems to have an aggravating effect. We could specify the role of ATG7 as a genetic modifier for HD particularly in the Italian population. This result affirms the modifying influence of the autophagic pathway on the course of HD, but also suggests population-specific modifying mechanisms in HD pathogenesis.
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Affiliation(s)
- Silke Metzger
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Rare Disease Center, University of Tuebingen, Tuebingen, Germany
| | - Carolin Walter
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Rare Disease Center, University of Tuebingen, Tuebingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Rare Disease Center, University of Tuebingen, Tuebingen, Germany
| | - Raymund A. C. Roos
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jørgen E. Nielsen
- Memory Disorders Research Unit, Neurogenetics Clinic, Section 6702, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Institute of Cellular and Molecular Medicine, Section of Neurogenetics, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - David Craufurd
- Genetic Medicine, University of Manchester, Manchester Academic Health Sciences Centre and Central Manchester University Hospitals NHS Foundation Trust, St. Mary’s Hospital, Manchester, United Kingdom
| | | | - Huu Phuc Nguyen
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- Rare Disease Center, University of Tuebingen, Tuebingen, Germany
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Tsai YC, Metzger S, Riess O, Soehn AS, Nguyen HP. Genetic analysis of polymorphisms in the kalirin gene for association with age-at-onset in European Huntington disease patients. BMC MEDICAL GENETICS 2012; 13:48. [PMID: 22720673 PMCID: PMC3433364 DOI: 10.1186/1471-2350-13-48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 06/21/2012] [Indexed: 01/01/2023]
Abstract
Background Huntington disease (HD) is caused by an expanded CAG repeat in the HD gene. Although the length of the CAG repeat strongly correlates with the age-at-onset (AAO), AAO in HD individuals may differ dramatically in spite of similar expanded CAG repeat lengths. Additional genetic or environmental factors are thought to influence the disease onset. Several modifier genes have been discovered so far but they do not fully explain the variability of AAO in HD. To potentially identify a novel genetic modifier, we analyzed single nucleotide polymorphisms (SNPs) in the kalirin (KALRN) gene. Kalirin is a protein crucially involved in spine plasticity and its interaction with huntingtin-associated protein-1 (HAP-1) and a potential protein dysfunction might contribute to spine pathogenesis in HD. Methods The selected SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and association of SNPs with AAO was investigated with the framework of linear models in an analysis of variance and covariance. Results Eleven SNPs in the kalirin gene were examined in an association study in European HD patients. The ten coding SNPs under investigation were monomorphic, whereas SNP rs10934657 in the promoter region showed a minor allele frequency >1%. An analysis of covariance together with the influence of the expanded HD allele was applied in 680 HD patients. SNP rs10934657 did not affect the AAO of the examined HD population. Conclusions The results did not reveal an association between the analyzed kalirin polymorphisms and the AAO in HD. However, it does not exclude other SNPs of the kalirin gene as susceptible genetic modifiers.
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Affiliation(s)
- Yu-Chun Tsai
- Department of Medical Genetics, University of Tuebingen, Calwerstr 7, Tuebingen, 72076, Germany
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