1
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Xiang Y, Song X, Long D. Ferroptosis regulation through Nrf2 and implications for neurodegenerative diseases. Arch Toxicol 2024; 98:579-615. [PMID: 38265475 PMCID: PMC10861688 DOI: 10.1007/s00204-023-03660-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/07/2023] [Indexed: 01/25/2024]
Abstract
This article provides an overview of the background knowledge of ferroptosis in the nervous system, as well as the key role of nuclear factor E2-related factor 2 (Nrf2) in regulating ferroptosis. The article takes Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) as the starting point to explore the close association between Nrf2 and ferroptosis, which is of clear and significant importance for understanding the mechanism of neurodegenerative diseases (NDs) based on oxidative stress (OS). Accumulating evidence links ferroptosis to the pathogenesis of NDs. As the disease progresses, damage to the antioxidant system, excessive OS, and altered Nrf2 expression levels, especially the inhibition of ferroptosis by lipid peroxidation inhibitors and adaptive enhancement of Nrf2 signaling, demonstrate the potential clinical significance of Nrf2 in detecting and identifying ferroptosis, as well as targeted therapy for neuronal loss and mitochondrial dysfunction. These findings provide new insights and possibilities for the treatment and prevention of NDs.
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Affiliation(s)
- Yao Xiang
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China
| | - Xiaohua Song
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China
| | - Dingxin Long
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China.
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, Hengyang Medical School, University of South China, Hengyang, 421001, People's Republic of China.
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2
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Wilton DK, Mastro K, Heller MD, Gergits FW, Willing CR, Fahey JB, Frouin A, Daggett A, Gu X, Kim YA, Faull RLM, Jayadev S, Yednock T, Yang XW, Stevens B. Microglia and complement mediate early corticostriatal synapse loss and cognitive dysfunction in Huntington's disease. Nat Med 2023; 29:2866-2884. [PMID: 37814059 PMCID: PMC10667107 DOI: 10.1038/s41591-023-02566-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 08/24/2023] [Indexed: 10/11/2023]
Abstract
Huntington's disease (HD) is a devastating monogenic neurodegenerative disease characterized by early, selective pathology in the basal ganglia despite the ubiquitous expression of mutant huntingtin. The molecular mechanisms underlying this region-specific neuronal degeneration and how these relate to the development of early cognitive phenotypes are poorly understood. Here we show that there is selective loss of synaptic connections between the cortex and striatum in postmortem tissue from patients with HD that is associated with the increased activation and localization of complement proteins, innate immune molecules, to these synaptic elements. We also found that levels of these secreted innate immune molecules are elevated in the cerebrospinal fluid of premanifest HD patients and correlate with established measures of disease burden.In preclinical genetic models of HD, we show that complement proteins mediate the selective elimination of corticostriatal synapses at an early stage in disease pathogenesis, marking them for removal by microglia, the brain's resident macrophage population. This process requires mutant huntingtin to be expressed in both cortical and striatal neurons. Inhibition of this complement-dependent elimination mechanism through administration of a therapeutically relevant C1q function-blocking antibody or genetic ablation of a complement receptor on microglia prevented synapse loss, increased excitatory input to the striatum and rescued the early development of visual discrimination learning and cognitive flexibility deficits in these models. Together, our findings implicate microglia and the complement cascade in the selective, early degeneration of corticostriatal synapses and the development of cognitive deficits in presymptomatic HD; they also provide new preclinical data to support complement as a therapeutic target for early intervention.
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Affiliation(s)
- Daniel K Wilton
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US.
| | - Kevin Mastro
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Molly D Heller
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Frederick W Gergits
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Carly Rose Willing
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Jaclyn B Fahey
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Arnaud Frouin
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Anthony Daggett
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at University of California, Los Angeles, CA, USA
| | - Xiaofeng Gu
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at University of California, Los Angeles, CA, USA
| | - Yejin A Kim
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US
| | - Richard L M Faull
- Department of Anatomy with Radiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Suman Jayadev
- Department of Neurology, University of Washington, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ted Yednock
- Annexon Biosciences, South San Francisco, CA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at University of California, Los Angeles, CA, USA
| | - Beth Stevens
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, US.
- Stanley Center, Broad Institute, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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3
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Raposo M, Hübener-Schmid J, Ferreira AF, Vieira Melo AR, Vasconcelos J, Pires P, Kay T, Garcia-Moreno H, Giunti P, Santana MM, Pereira de Almeida L, Infante J, van de Warrenburg BP, de Vries JJ, Faber J, Klockgether T, Casadei N, Admard J, Schöls L, Riess O, Lima M. Blood transcriptome sequencing identifies biomarkers able to track disease stages in spinocerebellar ataxia type 3. Brain 2023; 146:4132-4143. [PMID: 37071051 DOI: 10.1093/brain/awad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/19/2022] [Accepted: 03/27/2023] [Indexed: 04/19/2023] Open
Abstract
Transcriptional dysregulation has been described in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), an autosomal dominant ataxia caused by a polyglutamine expansion in the ataxin-3 protein. As ataxin-3 is ubiquitously expressed, transcriptional alterations in blood may reflect early changes that start before clinical onset and might serve as peripheral biomarkers in clinical and research settings. Our goal was to describe enriched pathways and report dysregulated genes, which can track disease onset, severity or progression in carriers of the ATXN3 mutation (pre-ataxic subjects and patients). Global dysregulation patterns were identified by RNA sequencing of blood samples from 40 carriers of ATXN3 mutation and 20 controls and further compared with transcriptomic data from post-mortem cerebellum samples of MJD patients and controls. Ten genes-ABCA1, CEP72, PTGDS, SAFB2, SFSWAP, CCDC88C, SH2B1, LTBP4, MEG3 and TSPOAP1-whose expression in blood was altered in the pre-ataxic stage and simultaneously, correlated with ataxia severity in the overt disease stage, were analysed by quantitative real-time PCR in blood samples from an independent set of 170 SCA3/MJD subjects and 57 controls. Pathway enrichment analysis indicated the Gαi signalling and the oestrogen receptor signalling to be similarly affected in blood and cerebellum. SAFB2, SFSWAP and LTBP4 were consistently dysregulated in pre-ataxic subjects compared to controls, displaying a combined discriminatory ability of 79%. In patients, ataxia severity was associated with higher levels of MEG3 and TSPOAP1. We propose expression levels of SAFB2, SFSWAP and LTBP4 as well as MEG3 and TSPOAP1 as stratification markers of SCA3/MJD progression, deserving further validation in longitudinal studies and in independent cohorts.
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Affiliation(s)
- Mafalda Raposo
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Jeannette Hübener-Schmid
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72072 Tübingen, Germany
| | - Ana F Ferreira
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Ana Rosa Vieira Melo
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - João Vasconcelos
- Serviço de Neurologia, Hospital do Divino Espírito Santo, 9500-370 Ponta Delgada, Portugal
| | - Paula Pires
- Serviço de Neurologia, Hospital do Santo Espírito da Ilha Terceira, 9700-049 Angra do Heroísmo, Portugal
| | - Teresa Kay
- Serviço de Genética Clínica, Hospital D. Estefânia, 1169-045 Lisboa, Portugal
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London WC1N 3BG, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London WC1N 3BG, UK
| | - Magda M Santana
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3000-075, Portugal
| | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3000-075, Portugal
| | - Jon Infante
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL, Universidad de Cantabria, Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - Bart P van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, 6525 EN Nijmegen, The Netherlands
| | - Jeroen J de Vries
- Department of Neurology, University of Groningen, University Medical Center Groningen, 9700 AD Groningen, The Netherlands
| | - Jennifer Faber
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Ludger Schöls
- Department for Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center for Neurology, University of Tübingen, 72016 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72016 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72072 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Manuela Lima
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
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Benyair R, Giridharan SSP, Rivero-Ríos P, Hasegawa J, Bristow E, Eskelinen EL, Shmueli MD, Fishbain-Yoskovitz V, Merbl Y, Sharkey LM, Paulson HL, Hanson PI, Patnaik S, Al-Ramahi I, Botas J, Marugan J, Weisman LS. Upregulation of the ESCRT pathway and multivesicular bodies accelerates degradation of proteins associated with neurodegeneration. AUTOPHAGY REPORTS 2023; 2:2166722. [PMID: 37064812 PMCID: PMC10101321 DOI: 10.1080/27694127.2023.2166722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many neurodegenerative diseases, including Huntington's disease (HD) and Alzheimer's disease (AD), occur due to an accumulation of aggregation-prone proteins, which results in neuronal death. Studies in animal and cell models show that reducing the levels of these proteins mitigates disease phenotypes. We previously reported a small molecule, NCT-504, which reduces cellular levels of mutant huntingtin (mHTT) in patient fibroblasts as well as mouse striatal and cortical neurons from an HdhQ111 mutant mouse. Here, we show that NCT-504 has a broader potential, and in addition reduces levels of Tau, a protein associated with Alzheimer's disease, as well as other tauopathies. We find that in untreated cells, Tau and mHTT are degraded via autophagy. Notably, treatment with NCT-504 diverts these proteins to multivesicular bodies (MVB) and the ESCRT pathway. Specifically, NCT-504 causes a proliferation of endolysosomal organelles including MVB, and an enhanced association of mHTT and Tau with endosomes and MVB. Importantly, depletion of proteins that act late in the ESCRT pathway blocked NCT-504 dependent degradation of Tau. Moreover, NCT-504-mediated degradation of Tau occurred in cells where Atg7 is depleted, which indicates that this pathway is independent of canonical autophagy. Together, these studies reveal that upregulation of traffic through an ESCRT-dependent MVB pathway may provide a therapeutic approach for neurodegenerative diseases.
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Affiliation(s)
- Ron Benyair
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Sai Srinivas Panapakkam Giridharan
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Pilar Rivero-Ríos
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Junya Hasegawa
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | - Emily Bristow
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
| | | | - Merav D Shmueli
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Merbl
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lisa M Sharkey
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States
| | - Phyllis I Hanson
- Department of Biological Chemistry, University of Michigan School of Medicine, 1150 W. Medical Center Drive, Ann Arbor, Michigan, United States
| | - Samarjit Patnaik
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Jan and Dan Duncan Neurological Research Institute, Houston, Texas, United States
| | - Juan Botas
- Department of Molecular and Human Genetics, Department of Molecular and Cellular Biology, Jan and Dan Duncan Neurological Research Institute, Houston, Texas, United States
| | - Juan Marugan
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Lois S Weisman
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
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5
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Tucci P, Lattanzi R, Severini C, Saso L. Nrf2 Pathway in Huntington's Disease (HD): What Is Its Role? Int J Mol Sci 2022; 23:ijms232315272. [PMID: 36499596 PMCID: PMC9739588 DOI: 10.3390/ijms232315272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease that occurs worldwide. Despite some progress in understanding the onset of HD, drugs that block or delay symptoms are still not available. In recent years, many treatments have been proposed; among them, nuclear transcriptional factor-2 (Nrf2) enhancer compounds have been proposed as potential therapeutic agents to treat HD. Nrf2 triggers an endogenous antioxidant pathway activated in different neurodegenerative disorders. Probably, the stimulation of Nrf2 during either the early phase or before HD symptoms' onset, could slow or prevent striatum degeneration. In this review, we present the scientific literature supporting the role of Nrf2 in HD and the potential prophylactic and therapeutic role of this compound.
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Affiliation(s)
- Paolo Tucci
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Roberta Lattanzi
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Cinzia Severini
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council of Italy (CNR), Viale del Policlinico 155, 00161 Rome, Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Correspondence:
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6
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Current Diagnostic Methods and Non-Coding RNAs as Possible Biomarkers in Huntington’s Disease. Genes (Basel) 2022; 13:genes13112017. [PMID: 36360254 PMCID: PMC9689996 DOI: 10.3390/genes13112017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Whether as a cause or a symptom, RNA transcription is recurrently altered in pathologic conditions. This is also true for non-coding RNAs, with regulatory functions in a variety of processes such as differentiation, cell identity and metabolism. In line with their increasingly recognized roles in cellular pathways, RNAs are also currently evaluated as possible disease biomarkers. They could be informative not only to follow disease progression and assess treatment efficacy in clinics, but also to aid in the development of new therapeutic approaches. This is especially important for neurological and genetic disorders, where the administration of appropriate treatment during the disease prodromal stage could significantly delay, if not halt, disease progression. In this review we focus on the current status of biomarkers in Huntington’s Disease (HD), a fatal hereditary and degenerative disease condition. First, we revise the sources and type of wet biomarkers currently in use. Then, we explore the feasibility of different RNA types (miRNA, ncRNA, circRNA) as possible biomarker candidates, discussing potential advantages, disadvantages, sources of origin and the ongoing investigations on this topic.
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7
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Papoutsi M, Flower M, Hensman Moss DJ, Holmans P, Estevez-Fraga C, Johnson EB, Scahill RI, Rees G, Langbehn D, Tabrizi SJ. Intellectual enrichment and genetic modifiers of cognition and brain volume in Huntington's disease. Brain Commun 2022; 4:fcac279. [PMID: 36519153 PMCID: PMC9732861 DOI: 10.1093/braincomms/fcac279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/22/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
An important step towards the development of treatments for cognitive impairment in ageing and neurodegenerative diseases is to identify genetic and environmental modifiers of cognitive function and understand the mechanism by which they exert an effect. In Huntington's disease, the most common autosomal dominant dementia, a small number of studies have identified intellectual enrichment, i.e. a cognitively stimulating lifestyle and genetic polymorphisms as potential modifiers of cognitive function. The aim of our study was to further investigate the relationship and interaction between genetic factors and intellectual enrichment on cognitive function and brain atrophy in Huntington's disease. For this purpose, we analysed data from Track-HD, a multi-centre longitudinal study in Huntington's disease gene carriers and focused on the role of intellectual enrichment (estimated at baseline) and the genes FAN1, MSH3, BDNF, COMT and MAPT in predicting cognitive decline and brain atrophy. We found that carrying the 3a allele in the MSH3 gene had a positive effect on global cognitive function and brain atrophy in multiple cortical regions, such that 3a allele carriers had a slower rate of cognitive decline and atrophy compared with non-carriers, in agreement with its role in somatic instability. No other genetic predictor had a significant effect on cognitive function and the effect of MSH3 was independent of intellectual enrichment. Intellectual enrichment also had a positive effect on cognitive function; participants with higher intellectual enrichment, i.e. those who were better educated, had higher verbal intelligence and performed an occupation that was intellectually engaging, had better cognitive function overall, in agreement with previous studies in Huntington's disease and other dementias. We also found that intellectual enrichment interacted with the BDNF gene, such that the positive effect of intellectual enrichment was greater in Met66 allele carriers than non-carriers. A similar relationship was also identified for changes in whole brain and caudate volume; the positive effect of intellectual enrichment was greater for Met66 allele carriers, rather than for non-carriers. In summary, our study provides additional evidence for the beneficial role of intellectual enrichment and carrying the 3a allele in MSH3 in cognitive function in Huntington's disease and their effect on brain structure.
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Affiliation(s)
- Marina Papoutsi
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
- Ixico plc, London, UK
| | - Michael Flower
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Davina J Hensman Moss
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Carlos Estevez-Fraga
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Eileanoir B Johnson
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Rachael I Scahill
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Geraint Rees
- Wellcome Centre for Human Neuroimaging, Queen Square Institute of Neurology, University College London, London, UK
- Institute of Cognitive Neuroscience, University College London, London, UK
| | - Douglas Langbehn
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sarah J Tabrizi
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute at University College London, London, UK
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8
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Lawlor M, Zigo M, Kerns K, Cho IK, Easley IV CA, Sutovsky P. Spermatozoan Metabolism as a Non-Traditional Model for the Study of Huntington’s Disease. Int J Mol Sci 2022; 23:ijms23137163. [PMID: 35806166 PMCID: PMC9266437 DOI: 10.3390/ijms23137163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
Huntington’s Disease (HD) is a fatal autosomal dominant neurodegenerative disease manifested through motor dysfunction and cognitive deficits. Decreased fertility is also observed in HD animal models and HD male patients, due to altered spermatogenesis and sperm function, thus resulting in reduced fertilization potential. Although some pharmaceuticals are currently utilized to mitigate HD symptoms, an effective treatment that remedies the pathogenesis of the disease is yet to be approved by the FDA. Identification of genes and relevant diagnostic biomarkers and therapeutic target pathways including glycolysis and mitochondrial complex-I-dependent respiration may be advantageous for early diagnosis, management, and treatment of the disease. This review addresses the HD pathway in neuronal and sperm metabolism, including relevant gene and protein expression in both neurons and spermatozoa, indicated in the pathogenesis of HD. Furthermore, zinc-containing and zinc-interacting proteins regulate and/or are regulated by zinc ion homeostasis in both neurons and spermatozoa. Therefore, this review also aims to explore the comparative role of zinc in both neuronal and sperm function. Ongoing studies aim to characterize the products of genes implicated in HD pathogenesis that are expressed in both neurons and spermatozoa to facilitate studies of future treatment avenues in HD and HD-related male infertility. The emerging link between zinc homeostasis and the HD pathway could lead to new treatments and diagnostic methods linking genetic sperm defects with somatic comorbidities.
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Affiliation(s)
- Meghan Lawlor
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA; (M.L.); (M.Z.); (K.K.)
| | - Michal Zigo
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA; (M.L.); (M.Z.); (K.K.)
| | - Karl Kerns
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA; (M.L.); (M.Z.); (K.K.)
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - In Ki Cho
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; (I.K.C.); (C.A.E.IV)
- Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Charles A. Easley IV
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA; (I.K.C.); (C.A.E.IV)
- Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Peter Sutovsky
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA; (M.L.); (M.Z.); (K.K.)
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, MO 65211, USA
- Correspondence: ; Tel.: +1-(573)-882-3329
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9
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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: 1] [Impact Index Per Article: 0.5] [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.
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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
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10
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Ferguson LB, Roberts AJ, Mayfield RD, Messing RO. Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice. PLoS Comput Biol 2022; 18:e1009800. [PMID: 35176017 PMCID: PMC8853518 DOI: 10.1371/journal.pcbi.1009800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023] Open
Abstract
Alcohol Use Disorder (AUD) is a chronic, relapsing syndrome diagnosed by a heterogeneous set of behavioral signs and symptoms. There are no laboratory tests that provide direct objective evidence for diagnosis. Microarray and RNA-Seq technologies enable genome-wide transcriptome profiling at low costs and provide an opportunity to identify biomarkers to facilitate diagnosis, prognosis, and treatment of patients. However, access to brain tissue in living patients is not possible. Blood contains cellular and extracellular RNAs that provide disease-relevant information for some brain diseases. We hypothesized that blood gene expression profiles can be used to diagnose AUD. We profiled brain (prefrontal cortex, amygdala, and hypothalamus) and blood gene expression levels in C57BL/6J mice using RNA-seq one week after chronic intermittent ethanol (CIE) exposure, a mouse model of alcohol dependence. We found a high degree of preservation (rho range: [0.50, 0.67]) between blood and brain transcript levels. There was small overlap between blood and brain DEGs, and considerable overlap of gene networks perturbed after CIE related to cell-cell signaling (e.g., GABA and glutamate receptor signaling), immune responses (e.g., antigen presentation), and protein processing / mitochondrial functioning (e.g., ubiquitination, oxidative phosphorylation). Blood gene expression data were used to train classifiers (logistic regression, random forest, and partial least squares discriminant analysis), which were highly accurate at predicting alcohol dependence status (maximum AUC: 90.1%). These results suggest that gene expression profiles from peripheral blood samples contain a biological signature of alcohol dependence that can discriminate between CIE and Air subjects.
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Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America
| | - Amanda J. Roberts
- Animal Models Core Facility, The Scripps Research Institute, San Diego, California, United States of America
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, Texas, United States of America
- Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America
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11
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Kuijper EC, Toonen LJA, Overzier M, Tsonaka R, Hettne K, Roos M, van Roon-Mom WMC, Mina E. Huntington Disease Gene Expression Signatures in Blood Compared to Brain of YAC128 Mice as Candidates for Monitoring of Pathology. Mol Neurobiol 2022; 59:2532-2551. [PMID: 35091961 DOI: 10.1007/s12035-021-02680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]
Abstract
While the genetic cause of Huntington disease (HD) is known since 1993, still no cure exists. Therapeutic development would benefit from a method to monitor disease progression and treatment efficacy, ideally using blood biomarkers. Previously, HD-specific signatures were identified in human blood representing signatures in human brain, showing biomarker potential. Since drug candidates are generally first screened in rodent models, we aimed to identify HD signatures in blood and brain of YAC128 HD mice and compare these with previously identified human signatures. RNA sequencing was performed on blood withdrawn at two time points and four brain regions from YAC128 and control mice. Weighted gene co-expression network analysis was used to identify clusters of co-expressed genes (modules) associated with the HD genotype. These HD-associated modules were annotated via text-mining to determine the biological processes they represented. Subsequently, the processes from mouse blood were compared with mouse brain, showing substantial overlap, including protein modification, cell cycle, RNA splicing, nuclear transport, and vesicle-mediated transport. Moreover, the disease-associated processes shared between mouse blood and brain were highly comparable to those previously identified in human blood and brain. In addition, we identified HD blood-specific pathology, confirming previous findings for peripheral pathology in blood. Finally, we identified hub genes for HD-associated blood modules and proposed a strategy for gene selection for development of a disease progression monitoring panel.
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Affiliation(s)
- Elsa C Kuijper
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands.
| | - Lodewijk J A Toonen
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Maurice Overzier
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data Sciences, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Kristina Hettne
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Willeke M C van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
| | - Eleni Mina
- Department of Human Genetics, Leiden University Medical Center, 2333, ZC, Leiden, The Netherlands
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12
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Ahmadi A, Gispert JD, Navarro A, Vilor-Tejedor N, Sadeghi I. Single-cell Transcriptional Changes in Neurodegenerative Diseases. Neuroscience 2021; 479:192-205. [PMID: 34748859 DOI: 10.1016/j.neuroscience.2021.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/25/2023]
Abstract
In recent decades, our understanding of the molecular changes involved in neurodegenerative diseases has been transformed. Single-cell RNA sequencing and single-nucleus RNA sequencing technologies have been applied to provide cellular and molecular details of the brain at the single-cell level. This has expanded our knowledge of the central nervous system and provided insights into the molecular vulnerability of brain cell types and underlying mechanisms in neurodegenerative diseases. In this review, we highlight the recent advances and findings related to neurodegenerative diseases using these cutting-edge technologies.
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Affiliation(s)
- Amirhossein Ahmadi
- Department of Biology, Faculty of Nano and BioScience and Technology, Persian Gulf University, Bushehr 75169, Iran
| | - Juan D Gispert
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Arcadi Navarro
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Natalia Vilor-Tejedor
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Erasmus MC University Medical Center. Department of Clinical Genetics, Rotterdam, the Netherlands.
| | - Iman Sadeghi
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain; Pompeu Fabra University, Barcelona, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
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Isoform-Specific Reduction of the Basic Helix-Loop-Helix Transcription Factor TCF4 Levels in Huntington's Disease. eNeuro 2021; 8:ENEURO.0197-21.2021. [PMID: 34518368 PMCID: PMC8519306 DOI: 10.1523/eneuro.0197-21.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/21/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder with onset of characteristic motor symptoms at midlife, preceded by subtle cognitive and behavioral disturbances. Transcriptional dysregulation emerges early in the disease course and is considered central to HD pathogenesis. Using wild-type (wt) and HD knock-in mouse striatal cell lines we observed a HD genotype-dependent reduction in the protein levels of transcription factor 4 (TCF4), a member of the basic helix-loop-helix (bHLH) family with critical roles in brain development and function. We characterized mouse Tcf4 gene structure and expression of alternative mRNAs and protein isoforms in cell-based models of HD, and in four different brain regions of male transgenic HD mice (R6/1) from young to mature adulthood. The largest decrease in the levels of TCF4 at mRNA and specific protein isoforms were detected in the R6/1 mouse hippocampus. Translating this finding to human disease, we found reduced expression of long TCF4 isoforms in the postmortem hippocampal CA1 area and in the cerebral cortex of HD patients. Additionally, TCF4 protein isoforms showed differential synergism with the proneural transcription factor ASCL1 in activating reporter gene transcription in hippocampal and cortical cultured neurons. Induction of neuronal activity increased these synergistic effects in hippocampal but not in cortical neurons, suggesting brain region-dependent differences in TCF4 functions. Collectively, this study demonstrates isoform-specific changes in TCF4 expression in HD that could contribute to the progressive impairment of transcriptional regulation and neuronal function in this disease.
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Chuang CL, Demontis F. Systemic manifestation and contribution of peripheral tissues to Huntington's disease pathogenesis. Ageing Res Rev 2021; 69:101358. [PMID: 33979693 DOI: 10.1016/j.arr.2021.101358] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Huntington disease (HD) is an autosomal dominant neurodegenerative disease that is caused by expansion of cytosine/adenosine/guanine repeats in the huntingtin (HTT) gene, which leads to a toxic, aggregation-prone, mutant HTT-polyQ protein. Beyond the well-established mechanisms of HD progression in the central nervous system, growing evidence indicates that also peripheral tissues are affected in HD and that systemic signaling originating from peripheral tissues can influence the progression of HD in the brain. Herein, we review the systemic manifestation of HD in peripheral tissues, and the impact of systemic signaling on HD pathogenesis. Mutant HTT induces a body wasting syndrome (cachexia) primarily via its activity in skeletal muscle, bone, adipose tissue, and heart. Additional whole-organism effects induced by mutant HTT include decline in systemic metabolic homeostasis, which stems from derangement of pancreas, liver, gut, hypothalamic-pituitary-adrenal axis, and circadian functions. In addition to spreading via the bloodstream and a leaky blood brain barrier, HTT-polyQ may travel long distance via its uptake by neurons and its axonal transport from the peripheral to the central nervous system. Lastly, signaling factors that are produced and/or secreted in response to therapeutic interventions such as exercise or in response to mutant HTT activity in peripheral tissues may impact HD. In summary, these studies indicate that HD is a systemic disease that is influenced by intertissue signaling and by the action of pathogenic HTT in peripheral tissues. We propose that treatment strategies for HD should include the amelioration of HD symptoms in peripheral tissues. Moreover, harnessing signaling between peripheral tissues and the brain may provide a means for reducing HD progression in the central nervous system.
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Accelerated expansion of pathogenic mitochondrial DNA heteroplasmies in Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:2014610118. [PMID: 34301881 PMCID: PMC8325154 DOI: 10.1073/pnas.2014610118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Decline of mitochondrial function may underlie the pathogenesis of many age-related diseases, such as Huntington’s disease (HD). Mitochondrial oxidative phosphorylation (OXPHOS) system is encoded partially by the mitochondrial genome (mtDNA). By investigating mtDNA in lymphoblast and blood samples of HD patients, we found that the expansion of OXPHOS-impairing mtDNA heteroplasmies (coexistence of mutated and wild-type mtDNA) is a molecular feature associated with the functional, motor, and cognitive aspects of HD progression, suggesting that improving mtDNA quality or restoring mitochondrial function could be a potential target for HD treatments. Mitochondrial dysfunction is found in the brain and peripheral tissues of patients diagnosed with Huntington’s disease (HD), an irreversible neurodegenerative disease of which aging is a major risk factor. Mitochondrial function is encoded by not only nuclear DNA but also DNA within mitochondria (mtDNA). Expansion of mtDNA heteroplasmies (coexistence of mutated and wild-type mtDNA) can contribute to age-related decline of mitochondrial function but has not been systematically investigated in HD. Here, by using a sensitive mtDNA-targeted sequencing method, we studied mtDNA heteroplasmies in lymphoblasts and longitudinal blood samples of HD patients. We found a significant increase in the fraction of mtDNA heteroplasmies with predicted pathogenicity in lymphoblasts from 1,549 HD patients relative to lymphoblasts from 182 healthy individuals. The increased fraction of pathogenic mtDNA heteroplasmies in HD lymphoblasts also correlated with advancing HD stages and worsened disease severity measured by HD motor function, cognitive function, and functional capacity. Of note, elongated CAG repeats in HTT promoted age-dependent expansion of pathogenic mtDNA heteroplasmies in HD lymphoblasts. We then confirmed in longitudinal blood samples of 169 HD patients that expansion of pathogenic mtDNA heteroplasmies was correlated with decline in functional capacity and exacerbation of HD motor and cognitive functions during a median follow-up of 6 y. The results of our study indicate accelerated decline of mtDNA quality in HD, and highlight monitoring mtDNA heteroplasmies longitudinally as a way to investigate the progressive decline of mitochondrial function in aging and age-related diseases.
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Bensalel J, Xu H, Lu ML, Capobianco E, Wei J. RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells. BMC Med Genomics 2021; 14:176. [PMID: 34215255 PMCID: PMC8252266 DOI: 10.1186/s12920-021-01022-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Huntingtin (Htt) protein is the product of the gene mutated in Huntington's disease (HD), a fatal, autosomal dominant, neurodegenerative disorder. Normal Htt is essential for early embryogenesis and the development of the central nervous system. However, the role of Htt in adult tissues is less defined. Following the recent promising clinical trial in which both normal and mutant Htt mRNA were knocked down in HD patients, there is an urgent need to fully understand the molecular consequences of knocking out/down Htt in adult tissues. Htt has been identified as an important transcriptional regulator. Unbiased investigations of transcriptome changes with RNA-sequencing (RNA-Seq) have been done in multiple cell types in HD, further confirming that transcriptional dysregulation is a central pathogenic mechanism in HD. However, there is lack of direct understanding of the transcriptional regulation by normal Htt. METHODS To investigate the transcriptional role of normal Htt, we first knocked out Htt in the human neuroblastoma SH-SY5Y cell line using the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) gene editing approach. We then performed RNA-seq analysis on Htt-null and wild type SH-SY5Y cells to probe the global transcriptome changes induced by Htt deletion. RESULTS In general, Htt has a widespread effect on gene transcription. Functional analysis of the differentially expressed genes (DEGs) using various bioinformatic tools revealed irregularities in pathways related to cell communication and signaling, and more specifically those related to neuron development, neurotransmission and synaptic signaling. We further examined the transcription factors that may regulate these DEGs. Consistent with the disrupted pathways associated with cellular development, we showed that Htt-null cells exhibited slower cell proliferation than wild type cells. We finally validated some of the top DEGS with quantitative RT-PCR. CONCLUSIONS The widespread transcriptome changes in Htt-null cells could be directly caused by the loss of Htt-mediated transcriptional regulation or due to the secondary consequences of disruption in the gene regulatory network. Our study therefore provides valuable information about key genes associated with Htt-mediated transcription and improves our understanding of the molecular mechanisms underlying the cellular functions of normal and mutant Htt.
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Affiliation(s)
- Johanna Bensalel
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Hongyuan Xu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Michael L Lu
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Enrico Capobianco
- Institute of Data Science and Computing, University of Miami, Miami, FL, 33146, USA
| | - Jianning Wei
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA.
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Evolutionary Changes in Pathways and Networks of Genes Expressed in the Brains of Humans and Macaques. J Mol Neurosci 2021; 71:1825-1837. [PMID: 34191269 DOI: 10.1007/s12031-021-01874-y] [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: 03/02/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
As the key organ that separates humans from nonhuman primates, the brain has continuously evolved to adapt to environmental and climatic changes. Although humans share most genetic, molecular, and cellular features with other primates such as macaques, there are significant differences in the structure and function of the brain between humans and these species. Thus, exploring the differences between the brains of human and nonhuman primates in the context of evolution will provide insights into the development, functionality, and diseases of the human central nervous system (CNS). Since the genes involved in many aspects of the human brain are under common pressures of natural selection, their evolutionary features can be analyzed collectively at the pathway level. In this study, the molecular mechanisms underlying human brain capabilities were explored by comparing the evolution features of pathways enriched in genes expressed in the human brain and the macaque brain. We identified 31 pathways with differential evolutionary properties, including those related to neurological diseases, signal transduction, immunological response, and metabolic processes. By analyzing genes differentially expressed in brain regions or development stages between humans and macaques, 9 and 4 pathways with differential evolutionary properties were detected, respectively. We further performed crosstalk analysis on the pathways to obtain an intuitive correlation between the pathways, which is helpful in understanding the mechanisms of interaction between pathways. Our results provide on a comprehensive view of the evolutionary pathways of the human CNS and can serve as a reference for the study of human brain development.
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de Castro IJ, Toner B, Xie SQ, Swingland J, Hodges A, Tabrizi SJ, Turkheimer F, Pombo A, Khalil A. Altered nuclear architecture in blood cells from Huntington's disease patients. Neurol Sci 2021; 43:379-385. [PMID: 33974169 DOI: 10.1007/s10072-021-05289-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.
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Affiliation(s)
- Inês J de Castro
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK. .,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany. .,Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, Im Neuenheimer Feld 344, Heidelberg, 69120, Germany.
| | - Brian Toner
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Sheila Q Xie
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Chromatin and Development Group, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - James Swingland
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,GRIP AI, London, EC2A 3AZ, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Sarah J Tabrizi
- UCL Institute of Neurology, Box 104, National Hospital for Neurology and Neurosurgery Queen Square, University College London, London, WC1N 3BG, UK
| | - Federico Turkheimer
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Huntington's Disease Centre, Department of Neurodegenerative Disease, University College London (UCL) Queen Square Institute of Neurology and the UK Dementia Research Institute, UCL, London, UK
| | - Ana Pombo
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - André Khalil
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA.
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Andrade-Navarro MA, Mühlenberg K, Spruth EJ, Mah N, González-López A, Andreani T, Russ J, Huska MR, Muro EM, Fontaine JF, Amstislavskiy V, Soldatov A, Nietfeld W, Wanker EE, Priller J. RNA Sequencing of Human Peripheral Blood Cells Indicates Upregulation of Immune-Related Genes in Huntington's Disease. Front Neurol 2020; 11:573560. [PMID: 33329316 PMCID: PMC7731869 DOI: 10.3389/fneur.2020.573560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/06/2020] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a trinucleotide repeat expansion in the Huntingtin gene. As disease-modifying therapies for HD are being developed, peripheral blood cells may be used to indicate disease progression and to monitor treatment response. In order to investigate whether gene expression changes can be found in the blood of individuals with HD that distinguish them from healthy controls, we performed transcriptome analysis by next-generation sequencing (RNA-seq). We detected a gene expression signature consistent with dysregulation of immune-related functions and inflammatory response in peripheral blood from HD cases vs. controls, including induction of the interferon response genes, IFITM3, IFI6 and IRF7. Our results suggest that it is possible to detect gene expression changes in blood samples from individuals with HD, which may reflect the immune pathology associated with the disease.
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Affiliation(s)
- Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Katja Mühlenberg
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eike J Spruth
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nancy Mah
- Charité-Universitätsmedizin Berlin, Virchow-Klinikum, Berlin-Brandenburger Centrum für Regenerative Therapien, Berlin, Germany
| | - Adrián González-López
- Klinik f. Anästhesiologie m.S. operative Intensivmedizin, Virchow Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tommaso Andreani
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jenny Russ
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Matthew R Huska
- Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Enrique M Muro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jean-Fred Fontaine
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Alexei Soldatov
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | - Erich E Wanker
- Neuroproteomics, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Centre for Neurodegenerative Diseases, Berlin Institute of Health, Berlin, Germany.,Centre for Clinical Brain Sciences, UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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20
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New developments in Huntington's disease and other triplet repeat diseases: DNA repair turns to the dark side. Neuronal Signal 2020; 4:NS20200010. [PMID: 33224521 PMCID: PMC7672267 DOI: 10.1042/ns20200010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
Huntington’s disease (HD) is a fatal, inherited neurodegenerative disease that causes neuronal death, particularly in medium spiny neurons. HD leads to serious and progressive motor, cognitive and psychiatric symptoms. Its genetic basis is an expansion of the CAG triplet repeat in the HTT gene, leading to extra glutamines in the huntingtin protein. HD is one of nine genetic diseases in this polyglutamine (polyQ) category, that also includes a number of inherited spinocerebellar ataxias (SCAs). Traditionally it has been assumed that HD age of onset and disease progression were solely the outcome of age-dependent exposure of neurons to toxic effects of the inherited mutant huntingtin protein. However, recent genome-wide association studies (GWAS) have revealed significant effects of genetic variants outside of HTT. Surprisingly, these variants turn out to be mostly in genes encoding DNA repair factors, suggesting that at least some disease modulation occurs at the level of the HTT DNA itself. These DNA repair proteins are known from model systems to promote ongoing somatic CAG repeat expansions in tissues affected by HD. Thus, for triplet repeats, some DNA repair proteins seem to abandon their normal genoprotective roles and, instead, drive expansions and accelerate disease. One attractive hypothesis—still to be proven rigorously—is that somatic HTT expansions augment the disease burden of the inherited allele. If so, therapeutic approaches that lower levels of huntingtin protein may need blending with additional therapies that reduce levels of somatic CAG repeat expansions to achieve maximal effect.
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21
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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: 2] [Impact Index Per Article: 0.5] [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.
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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
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22
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Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients. Sci Rep 2020; 10:17547. [PMID: 33067535 PMCID: PMC7567883 DOI: 10.1038/s41598-020-74687-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the expression of DUX4 in skeletal muscles. A number of therapeutic approaches are being developed to antagonize the events preceding and following DUX4 expression that leads to muscular dystrophy. Currently, the possibility to evaluate treatment response in clinical trials is hampered by the lack of objective molecular biomarkers connecting the disease cause to clinical performance. In this study we employed RNA-seq to examine gene expression in PAXgene tubes obtained from two independent cohorts of FSHD patients. Analysis of gene expression profiles did not lead to the identification of genes or pathways differentially expressed in FSHD patients, or associated with disease severity. In particular, we did not find evidence that the DUX4 and PAX7 signatures were differentially expressed. On the other hand, we were able to improve patient classification by including single genes or groups of genes in classification models. The best classifier was ROPN1L, a gene known to be expressed in testis, coincidentally the typical location of DUX4 expression. These improvements in patient classification hold the potential to enrich the FSHD clinical trial toolbox.
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23
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Tabrizi SJ, Flower MD, Ross CA, Wild EJ. Huntington disease: new insights into molecular pathogenesis and therapeutic opportunities. Nat Rev Neurol 2020; 16:529-546. [PMID: 32796930 DOI: 10.1038/s41582-020-0389-4] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
Abstract
Huntington disease (HD) is a neurodegenerative disease caused by CAG repeat expansion in the huntingtin gene (HTT) and involves a complex web of pathogenic mechanisms. Mutant HTT (mHTT) disrupts transcription, interferes with immune and mitochondrial function, and is aberrantly modified post-translationally. Evidence suggests that the mHTT RNA is toxic, and at the DNA level, somatic CAG repeat expansion in vulnerable cells influences the disease course. Genome-wide association studies have identified DNA repair pathways as modifiers of somatic instability and disease course in HD and other repeat expansion diseases. In animal models of HD, nucleocytoplasmic transport is disrupted and its restoration is neuroprotective. Novel cerebrospinal fluid (CSF) and plasma biomarkers are among the earliest detectable changes in individuals with premanifest HD and have the sensitivity to detect therapeutic benefit. Therapeutically, the first human trial of an HTT-lowering antisense oligonucleotide successfully, and safely, reduced the CSF concentration of mHTT in individuals with HD. A larger trial, powered to detect clinical efficacy, is underway, along with trials of other HTT-lowering approaches. In this Review, we discuss new insights into the molecular pathogenesis of HD and future therapeutic strategies, including the modulation of DNA repair and targeting the DNA mutation itself.
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Affiliation(s)
- Sarah J Tabrizi
- Huntington's Disease Centre, University College London, London, UK. .,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK. .,UK Dementia Research Institute, University College London, London, UK.
| | - Michael D Flower
- Huntington's Disease Centre, University College London, London, UK.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute, University College London, London, UK
| | - Christopher A Ross
- Departments of Neurology, Neuroscience and Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Edward J Wild
- Huntington's Disease Centre, University College London, London, UK.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
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24
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Griswold AJ, Sivasankaran SK, Van Booven D, Gardner OK, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Adams LD, Scott AM, Hofmann NK, Vance JM, Cuccaro ML, Bush WS, Martin ER, Byrd GS, Haines JL, Pericak-Vance MA, Beecham GW. Immune and Inflammatory Pathways Implicated by Whole Blood Transcriptomic Analysis in a Diverse Ancestry Alzheimer's Disease Cohort. J Alzheimers Dis 2020; 76:1047-1060. [PMID: 32597797 DOI: 10.3233/jad-190855] [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] [Indexed: 12/31/2022]
Abstract
BACKGROUND Significant work has identified genetic variants conferring risk and protection for Alzheimer's disease (AD), but functional effects of these variants is lacking, particularly in under-represented ancestral populations. Expression studies performed in easily accessible tissue, such as whole blood, can recapitulate some transcriptional changes occurring in brain and help to identify mechanisms underlying neurodegenerative processes. OBJECTIVE We aimed to identify transcriptional differences between AD cases and controls in a cohort of diverse ancestry. METHODS We analyzed the protein coding transcriptome using RNA sequencing from peripheral blood collected from 234 African American (AA) (115 AD, 119 controls) and 240 non-Hispanic Whites (NHW) (121 AD, 119 controls). To identify case-control differentially expressed genes and pathways, we performed stratified, joint, and interaction analyses using linear regression models within and across ancestral groups followed by pathway and gene set enrichment analyses. RESULTS Overall, we identified 418 (291 upregulated, 127 downregulated) and 488 genes (352 upregulated, 136 downregulated) differentially expressed in the AA and NHW datasets, respectively, with only 16 genes commonly differentially expressed in both ancestral groups. Joint analyses provided greater power to detect case-control differences and identified 1,102 differentially expressed genes between cases and controls (812 upregulated, 290 downregulated). Interaction analysis identified only 27 genes with different effects in AA compared to NHW. Pathway and gene-set enrichment analyses revealed differences in immune response-related pathways that were enriched across the analyses despite different underlying gene sets. CONCLUSION These results support the hypothesis of converging underlying pathophysiological processes in AD across ancestral groups.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | | | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Olivia K Gardner
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Aja M Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Goldie S Byrd
- Department of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
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25
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Pérez-Soriano A, Arnal Segura M, Botta-Orfila T, Giraldo D, Fernández M, Compta Y, Fernández-Santiago R, Ezquerra M, Tartaglia GG, Martí MJ. Transcriptomic differences in MSA clinical variants. Sci Rep 2020; 10:10310. [PMID: 32587362 PMCID: PMC7316739 DOI: 10.1038/s41598-020-66221-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
Background: Multiple system atrophy (MSA) is a rare oligodendroglial synucleinopathy of unknown etiopathogenesis including two major clinical variants with predominant parkinsonism (MSA-P) or cerebellar dysfunction (MSA-C). Objective: To identify novel disease mechanisms we performed a blood transcriptomic study investigating differential gene expression changes and biological process alterations in MSA and its clinical subtypes. Methods: We compared the transcriptome from rigorously gender and age-balanced groups of 10 probable MSA-P, 10 probable MSA-C cases, 10 controls from the Catalan MSA Registry (CMSAR), and 10 Parkinson Disease (PD) patients. Results: Gene set enrichment analyses showed prominent positive enrichment in processes related to immunity and inflammation in all groups, and a negative enrichment in cell differentiation and development of the nervous system in both MSA-P and PD, in contrast to protein translation and processing in MSA-C. Gene set enrichment analysis using expression patterns in different brain regions as a reference also showed distinct results between the different synucleinopathies. Conclusions: In line with the two major phenotypes described in the clinic, our data suggest that gene expression and biological processes might be differentially affected in MSA-P and MSA-C. Future studies using larger sample sizes are warranted to confirm these results.
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Affiliation(s)
- Alexandra Pérez-Soriano
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain.,Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain.,Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Magdalena Arnal Segura
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,Human Computational Biology Group, Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Teresa Botta-Orfila
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,Biological Fluids Biobank; IDIBAPS-Hospital Clinic of Barcelona, Barcelona, Catalonia, Spain
| | - Darly Giraldo
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain
| | - Manel Fernández
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain.,María de Maeztu Unit of Excellence (Institute of Neurosciences, University of Barcelona), Ministry of Science, Innovation and Universities, Barcelona, Catalonia, Spain
| | - Yaroslau Compta
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain
| | - Rubén Fernández-Santiago
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain
| | - Mario Ezquerra
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain
| | - Gian G Tartaglia
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,María de Maeztu Unit of Excellence (Institute of Neurosciences, University of Barcelona), Ministry of Science, Innovation and Universities, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca I Estudis Avançats (ICREA), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M J Martí
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain.
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26
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Wertz MH, Pineda SS, Lee H, Kulicke R, Kellis M, Heiman M. Interleukin-6 deficiency exacerbates Huntington's disease model phenotypes. Mol Neurodegener 2020; 15:29. [PMID: 32448329 PMCID: PMC7247164 DOI: 10.1186/s13024-020-00379-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/13/2020] [Indexed: 01/04/2023] Open
Abstract
Huntington’s disease (HD) is an incurable neurodegenerative disorder caused by CAG trinucleotide expansions in the huntingtin gene. Markers of both systemic and CNS immune activation and inflammation have been widely noted in HD and mouse models of HD. In particular, elevation of the pro-inflammatory cytokine interleukin-6 (IL-6) is the earliest reported marker of immune activation in HD, and this elevation has been suggested to contribute to HD pathogenesis. To test the hypothesis that IL-6 deficiency would be protective against the effects of mutant huntingtin, we generated R6/2 HD model mice that lacked IL-6. Contrary to our prediction, IL-6 deficiency exacerbated HD-model associated behavioral phenotypes. Single nuclear RNA Sequencing (snRNA-seq) analysis of striatal cell types revealed that IL-6 deficiency led to the dysregulation of various genes associated with synaptic function, as well as the BDNF receptor Ntrk2. These data suggest that IL-6 deficiency exacerbates the effects of mutant huntingtin through dysregulation of genes of known relevance to HD pathobiology in striatal neurons, and further suggest that modulation of IL-6 to a level that promotes proper regulation of genes associated with synaptic function may hold promise as an HD therapeutic target.
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Affiliation(s)
- Mary H Wertz
- Picower Institute for Learning and Memory, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - S Sebastian Pineda
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139, USA
| | - Hyeseung Lee
- Picower Institute for Learning and Memory, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ruth Kulicke
- Picower Institute for Learning and Memory, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139, USA
| | - Myriam Heiman
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, 02139, USA. .,Picower Institute for Learning and Memory, Cambridge, MA, 02139, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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27
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Golriz Khatami S, Mubeen S, Hofmann-Apitius M. Data science in neurodegenerative disease: its capabilities, limitations, and perspectives. Curr Opin Neurol 2020; 33:249-254. [PMID: 32073441 PMCID: PMC7077964 DOI: 10.1097/wco.0000000000000795] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW With the advancement of computational approaches and abundance of biomedical data, a broad range of neurodegenerative disease models have been developed. In this review, we argue that computational models can be both relevant and useful in neurodegenerative disease research and although the current established models have limitations in clinical practice, artificial intelligence has the potential to overcome deficiencies encountered by these models, which in turn can improve our understanding of disease. RECENT FINDINGS In recent years, diverse computational approaches have been used to shed light on different aspects of neurodegenerative disease models. For example, linear and nonlinear mixed models, self-modeling regression, differential equation models, and event-based models have been applied to provide a better understanding of disease progression patterns and biomarker trajectories. Additionally, the Cox-regression technique, Bayesian network models, and deep-learning-based approaches have been used to predict the probability of future incidence of disease, whereas nonnegative matrix factorization, nonhierarchical cluster analysis, hierarchical agglomerative clustering, and deep-learning-based approaches have been employed to stratify patients based on their disease subtypes. Furthermore, the interpretation of neurodegenerative disease data is possible through knowledge-based models which use prior knowledge to complement data-driven analyses. These knowledge-based models can include pathway-centric approaches to establish pathways perturbed in a given condition, as well as disease-specific knowledge maps, which elucidate the mechanisms involved in a given disease. Collectively, these established models have revealed high granular details and insights into neurodegenerative disease models. SUMMARY In conjunction with increasingly advanced computational approaches, a wide spectrum of neurodegenerative disease models, which can be broadly categorized into data-driven and knowledge-driven, have been developed. We review the state of the art data and knowledge-driven models and discuss the necessary steps which are vital to bring them into clinical application.
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Affiliation(s)
- Sepehr Golriz Khatami
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sarah Mubeen
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin
- Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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28
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Huang YS, Ogbechi J, Clanchy FI, Williams RO, Stone TW. IDO and Kynurenine Metabolites in Peripheral and CNS Disorders. Front Immunol 2020; 11:388. [PMID: 32194572 PMCID: PMC7066259 DOI: 10.3389/fimmu.2020.00388] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
The importance of the kynurenine pathway in normal immune system function has led to an appreciation of its possible contribution to autoimmune disorders such as rheumatoid arthritis. Indoleamine-2,3-dioxygenase (IDO) activity exerts a protective function, limiting the severity of experimental arthritis, whereas deletion or inhibition exacerbates the symptoms. Other chronic disorder with an inflammatory component, such as atherosclerosis, are also suppressed by IDO activity. It is suggested that this overall anti-inflammatory activity is mediated by a change in the relative production or activity of Th17 and regulatory T cell populations. Kynurenines may play an anti-inflammatory role also in CNS disorders such as Huntington's disease, Alzheimer's disease and multiple sclerosis, in which signs of inflammation and neurodegeneration are involved. The possibility is discussed that in Huntington's disease kynurenines interact with other anti-inflammatory molecules such as Human Lymphocyte Antigen-G which may be relevant in other disorders. Kynurenine involvement may account for the protection afforded to animals with cerebral malaria and trypanosomiasis when they are treated with an inhibitor of kynurenine-3-monoxygenase (KMO). There is some evidence that changes in IL-10 may contribute to this protection and the relationship between kynurenines and IL-10 in arthritis and other inflammatory conditions should be explored. In addition, metabolites of kynurenine downstream of KMO, such as anthranilic acid and 3-hydroxy-anthranilic acid can influence inflammation, and the ratio of these compounds is a valuable biomarker of inflammatory status although the underlying molecular mechanisms of the changes require clarification. Hence it is essential that more effort be expended to identify their sites of action as potential targets for drug development. Finally, we discuss increasing awareness of the epigenetic regulation of IDO, for example by DNA methylation, a phenomenon which may explain differences between individuals in their susceptibility to arthritis and other inflammatory disorders.
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Affiliation(s)
- Yi-Shu Huang
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Joy Ogbechi
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Felix I Clanchy
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Richard O Williams
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Trevor W Stone
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
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29
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Shi Y, Liu H, Yang C, Xu K, Cai Y, Wang Z, Zhao Z, Shao T, Li Y. Transcriptomic Analyses for Identification and Prioritization of Genes Associated With Alzheimer's Disease in Humans. Front Bioeng Biotechnol 2020; 8:31. [PMID: 32154224 PMCID: PMC7047416 DOI: 10.3389/fbioe.2020.00031] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), as important ncRNA regulators, play crucial roles in the regulation of various biological processes, and their aberrant expression is related to the occurrence and development of diseases, which is gradually validated by more and more studies. Alzheimer’s disease (AD) is a chronic neurodegenerative disease that often develops slowly and gradually deteriorates over time. However, which functions the lncRNAs perform in AD are almost unknown. In this study, we performed transcriptome analysis in AD, containing 12,892 known lncRNAs and 19,053 protein-coding genes (PCGs). Further, 14 down-regulated and 39 up-regulated lncRNAs were identified, compared with normal brain samples, which indicated that these lncRNAs might play critical roles in the pathogenesis of AD. In addition, 19 down-regulated and 28 up-regulated PCGs were also detected. Using the differentially expressed lncRNAs and PCGs through the WGCNA method, an lncRNA–mRNA co-expressed network was constructed. The results showed that lncRNAs RP3-522J7, MIR3180-2, and MIR3180-3 were frequently co-expressed with known AD risk PCGs. Interestingly, PCGs in the network are significantly enriched in brain- or AD-related biological functions, including the brain renin–angiotensin system, cell adhesion, neuroprotective role of THOP1 in AD, and so on. Furthermore, it was shown that 18 lncRNAs and 7 PCGs were highly expressed in normal brain tissue relative to other normal tissue types, suggesting their potential as diagnostic markers of AD, especially RP3-522J7, MIR3180-2, MIR3180-3, and CTA-929C8. In total, our study identified a compendium of AD-related dysregulated lncRNAs and characterized the corresponding biological functions of these lncRNAs in AD, which will be helpful to understand the molecular basis and pathogenesis of AD.
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Affiliation(s)
- Yuchen Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Changbo Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yangyang Cai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yixue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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30
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Al-Dalahmah O, Sosunov AA, Shaik A, Ofori K, Liu Y, Vonsattel JP, Adorjan I, Menon V, Goldman JE. Single-nucleus RNA-seq identifies Huntington disease astrocyte states. Acta Neuropathol Commun 2020; 8:19. [PMID: 32070434 PMCID: PMC7029580 DOI: 10.1186/s40478-020-0880-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/05/2020] [Indexed: 11/17/2022] Open
Abstract
Huntington Disease (HD) is an inherited movement disorder caused by expanded CAG repeats in the Huntingtin gene. We have used single nucleus RNASeq (snRNASeq) to uncover cellular phenotypes that change in the disease, investigating single cell gene expression in cingulate cortex of patients with HD and comparing the gene expression to that of patients with no neurological disease. In this study, we focused on astrocytes, although we found significant gene expression differences in neurons, oligodendrocytes, and microglia as well. In particular, the gene expression profiles of astrocytes in HD showed multiple signatures, varying in phenotype from cells that had markedly upregulated metallothionein and heat shock genes, but had not completely lost the expression of genes associated with normal protoplasmic astrocytes, to astrocytes that had substantially upregulated glial fibrillary acidic protein (GFAP) and had lost expression of many normal protoplasmic astrocyte genes as well as metallothionein genes. When compared to astrocytes in control samples, astrocyte signatures in HD also showed downregulated expression of a number of genes, including several associated with protoplasmic astrocyte function and lipid synthesis. Thus, HD astrocytes appeared in variable transcriptional phenotypes, and could be divided into several different “states”, defined by patterns of gene expression. Ultimately, this study begins to fill the knowledge gap of single cell gene expression in HD and provide a more detailed understanding of the variation in changes in gene expression during astrocyte “reactions” to the disease.
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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: 12] [Impact Index Per Article: 2.4] [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.
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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.
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Zadel M, Maver A, Kovanda A, Peterlin B. Transcriptomic Biomarkers for Huntington's Disease: Are Gene Expression Signatures in Whole Blood Reliable Biomarkers? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 22:283-294. [PMID: 29652574 DOI: 10.1089/omi.2017.0206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Huntington's disease (HD) is a severe neurodegenerative disorder manifesting as progressive impairment of motor function, cognitive decline, psychiatric symptoms, and immunological and endocrine dysfunction. We explored the consistency of blood transcriptomic biomarkers in HD based on a novel Slovene patient cohort and expert review of previous studies. HumanHT-12 v4 BeadChip microarrays were performed on the whole blood samples of a cohort of 23 HD mutation carriers and 23 controls to identify differentially expressed (DE) transcripts. In addition, we performed an expert review of DE transcripts identified in comparable HD studies from whole blood, to identify any consistent signature of HD. In the Slovene cohort, we identified 740 DE transcripts (p < 0.01 and a false discovery rate (FDR) of <0.1) of which 414 were downregulated and 326 were upregulated. Pathway analyses of DE transcripts showed enrichment for pathways involved in systemic, rather than neural processes in HD. With an expert review of comparable studies, we have further identified 15 DE transcripts shared by 3 studies. We suggest transcriptomic changes in blood reflect systemic changes in HD pathogenesis, rather than being a direct result of the neuropathological processes in the central nervous system during HD progression, and thus, have limited value as disease biomarkers.
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Affiliation(s)
- Maja Zadel
- 1 Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Anja Kovanda
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Borut Peterlin
- 2 Clinical Institute of Medical Genetics, University Medical Centre Ljubljana , Ljubljana, Slovenia
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A Functional riboSNitch in the 3' Untranslated Region of FKBP5 Alters MicroRNA-320a Binding Efficiency and Mediates Vulnerability to Chronic Post-Traumatic Pain. J Neurosci 2018; 38:8407-8420. [PMID: 30150364 DOI: 10.1523/jneurosci.3458-17.2018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 01/30/2023] Open
Abstract
Previous studies have shown that common variants of the gene coding for FK506-binding protein 51 (FKBP5), a critical regulator of glucocorticoid sensitivity, affect vulnerability to stress-related disorders. In a previous report, FKBP5 rs1360780 was identified as a functional variant because of its effect on gene methylation. Here we report evidence for a novel functional FKBP5 allele, rs3800373. This study assessed the association between rs3800373 and post-traumatic chronic pain in 1607 women and men from two ethnically diverse human cohorts. The molecular mechanism through which rs3800373 affects adverse outcomes was established via in silico, in vivo, and in vitro analyses. The rs3800373 minor allele predicted worse adverse outcomes after trauma exposure, such that individuals with the minor (risk) allele developed more severe post-traumatic chronic musculoskeletal pain. Among these individuals, peritraumatic circulating FKBP5 expression levels increased as cortisol and glucocorticoid receptor (NR3C1) mRNA levels increased, consistent with increased glucocorticoid resistance. Bioinformatic, in vitro, and mutational analyses indicate that the rs3800373 minor allele reduces the binding of a stress- and pain-associated microRNA, miR-320a, to FKBP5 via altering the FKBP5 mRNA 3'UTR secondary structure (i.e., is a riboSNitch). This results in relatively greater FKBP5 translation, unchecked by miR-320a. Overall, these results identify an important gene-miRNA interaction influencing chronic pain risk in vulnerable individuals and suggest that exogenous methods to achieve targeted reduction in poststress FKBP5 mRNA expression may constitute useful therapeutic strategies.SIGNIFICANCE STATEMENT FKBP5 is a critical regulator of the stress response. Previous studies have shown that dysregulation of the expression of this gene plays a role in the pathogenesis of chronic pain development as well as a number of comorbid neuropsychiatric disorders. In the current study, we identified a functional allele (rs3800373) in the 3'UTR of FKBP5 that influences vulnerability to chronic post-traumatic pain in two ethnic cohorts. Using multiple complementary experimental approaches, we show that the FKBP5 rs3800373 minor allele alters the secondary structure of FKBP5 mRNA, decreasing the binding of a stress- and pain-associated microRNA, miR-320a. This results in relatively greater FKBP5 translation, unchecked by miR-320a, increasing glucocorticoid resistance and increasing vulnerability to post-traumatic pain.
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Holmans PA, Massey TH, Jones L. Genetic modifiers of Mendelian disease: Huntington's disease and the trinucleotide repeat disorders. Hum Mol Genet 2018; 26:R83-R90. [PMID: 28977442 DOI: 10.1093/hmg/ddx261] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
In the decades since the genes and mutations associated with the commoner Mendelian disorders were first discovered, technological advances in genetic analysis have made finding genomic variation a much less onerous task. Recently, the global efforts to collect subjects with Mendelian disorders, to better define the disorders and to empower appropriate clinical trials, along with improved genetic technologies, have allowed the identification of genetic variation that does not cause disease, but substantially modifies disease presentation. The advantage of this is it identifies biological pathways and molecules, that, if modified in people, might alter disease presentation. In Huntington's disease (HD), caused by an expanded CAG repeat tract in HTT, genetic variation has been uncovered that is associated with change in the onset or progression of disease. Some of this variation lies in genes that are part of the DNA damage response, previously suggested to be important in modulating expansion of the repeat tract in germline and somatic cells. The genetic evidence implicates a DNA damage response-related pathway in modulating the pathogenicity of the repeat tracts in HD, and possibly, in other trinucleotide repeat disorders. These findings offer new targets for drug development in these currently intractable disorders.
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Affiliation(s)
- Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Thomas H Massey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases. Eur J Hum Genet 2018; 26:778-785. [PMID: 29487416 PMCID: PMC5974013 DOI: 10.1038/s41431-018-0115-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/21/2017] [Accepted: 01/24/2018] [Indexed: 12/23/2022] Open
Abstract
Although individually uncommon, rare diseases (RDs) collectively affect 6–8% of the population. The unmet need of the rare disease community was recognized by the European Commission which in 2012 funded three flagship projects, RD-Connect, NeurOmics, and EURenOmics, to help move the field forward with the ambition of advancing -omics research and data sharing at their core in line with the goals of IRDiRC (International Rare Disease Research Consortium). NeurOmics and EURenOmics generate -omics data and improve diagnosis and therapy in rare renal and neurological diseases, with RD-Connect developing an infrastructure to facilitate the sharing, systematic integration and analysis of these data. Here, we summarize the achievements of these three projects, their impact on the RD community and their vision for the future. We also report from the Joint Outreach Day organized by the three projects on the 3rd of May 2017 in Berlin. The workshop stimulated an open, multi-stakeholder discussion on the challenges of the rare diseases, and highlighted the cross-project cooperation and the common goal: the use of innovative genomic technologies in rare disease research.
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St-Amour I, Turgeon A, Goupil C, Planel E, Hébert SS. Co-occurrence of mixed proteinopathies in late-stage Huntington's disease. Acta Neuropathol 2018; 135:249-265. [PMID: 29134321 DOI: 10.1007/s00401-017-1786-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022]
Abstract
Accumulating evidence highlights the potential role of mixed proteinopathies (i.e., abnormal protein aggregation) in the development of clinical manifestations of neurodegenerative diseases (NDD). Huntington's disease (HD) is an inherited NDD caused by autosomal-dominant expanded CAG trinucleotide repeat mutation in the gene coding for Huntingtin (Htt). Previous studies have suggested the coexistence of phosphorylated-Tau, α-synuclein (α-Syn) and TAR DNA-binding protein 43 (TDP-43) inclusions in HD. However, definite evidence that HD pathology in humans can be accompanied by other proteinopathies is still lacking. Using human post-mortem putamen samples from 31 controls and 56 HD individuals, we performed biochemical analyses of the expression, oligomerization and aggregation of Tau, α-Syn, TDP-43, and Amyloid precursor protein (APP)/Aβ. In HD brain, we observed reduced soluble protein (but not mRNA) levels of Htt, α-Syn, and Tau. Our results also support abnormal phosphorylation of Tau in more advanced stages of disease. Aberrant splicing of Tau exons 2, 3 (exclusion) and 10 (inclusion) was also detected in HD patients, leading to higher 0N4R and lower 1N3R isoforms. Finally, following formic acid extraction, we observed increased aggregation of TDP-43, α-Syn, and phosphorylated-Tau during HD progression. Notably, we observed that 88% of HD patients with Vonsattel grade 4 neuropathology displayed at least one non-Htt proteinopathy compared to 29% in controls. Interestingly, α-Syn aggregation correlated with Htt, TDP-43 and phosphorylated-Tau in HD but not in controls. The impact of this work is twofold: (1) it provides compelling evidences that Tau, α-Syn and TDP-43 proteinopathies are increased in HD, and (2) it suggests the involvement of common mechanisms leading to abnormal accumulation of aggregation-prone proteins in NDD. Further studies will be needed to decipher the impact of these proteinopathies on clinical manifestation of HD.
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Affiliation(s)
- Isabelle St-Amour
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, CHUL, 2705 Boul. Laurier, P0-9800, Québec, QC, G1V 4G2, Canada
- Département de psychiatrie et de neurosciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Andréanne Turgeon
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, CHUL, 2705 Boul. Laurier, P0-9800, Québec, QC, G1V 4G2, Canada
- Département de psychiatrie et de neurosciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Claudia Goupil
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, CHUL, 2705 Boul. Laurier, P0-9800, Québec, QC, G1V 4G2, Canada
- Département de psychiatrie et de neurosciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Emmanuel Planel
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, CHUL, 2705 Boul. Laurier, P0-9800, Québec, QC, G1V 4G2, Canada
- Département de psychiatrie et de neurosciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Sébastien S Hébert
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, CHUL, 2705 Boul. Laurier, P0-9800, Québec, QC, G1V 4G2, Canada.
- Département de psychiatrie et de neurosciences, Université Laval, Québec, QC, G1V 0A6, Canada.
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