1
|
Griñán-Ferré C, Bellver-Sanchis A, Guerrero A, Pallàs M. Advancing personalized medicine in neurodegenerative diseases: The role of epigenetics and pharmacoepigenomics in pharmacotherapy. Pharmacol Res 2024; 205:107247. [PMID: 38834164 DOI: 10.1016/j.phrs.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
About 80 % of brain disorders have a genetic basis. The pathogenesis of most neurodegenerative diseases is associated with a myriad of genetic defects, epigenetic alterations (DNA methylation, histone/chromatin remodeling, miRNA dysregulation), and environmental factors. The emergence of new sequencing technologies and tools to study the epigenome has led to identifying predictive biomarkers for earlier diagnosis, opening up the possibility of prophylactical interventions. As a result, advances in pharmacogenetics and pharmacoepigenomics now allow for personalized treatments based on the profile of each patient and the specific genetic and epigenetic mechanisms involved. This Review highlights the complexity of neurodegenerative diseases and the variability in patient responses to pharmacotherapy, emphasizing the influence of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of drugs used to treat those conditions. We specifically discuss the potential modulatory effect of several genetic polymorphisms associated with an increased risk of developing different neurodegenerative diseases. We explore genetic and genomic technologies and the potential of analyzing individual-specific drug metabolism to predict and influence drug response and associated clinical outcomes. We also provide insights into the mechanism of action of the drugs under investigation and their potential impact on disease-modifying pathways. Finally, the Review underscores the great potential of this field to enhance the effectiveness and safety of drug treatments through personalized medicine.
Collapse
Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Aina Bellver-Sanchis
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Ana Guerrero
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències-Universitat de Barcelona, Avda. Joan XXIII, 27, Barcelona 08028, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
2
|
Ramos-Campoy O, Comas-Albertí A, Hervás D, Borrego-Écija S, Bosch B, Sandoval J, Fort-Aznar L, Moreno-Izco F, Fernández-Villullas G, Molina-Porcel L, Balasa M, Lladó A, Sánchez-Valle R, Antonell A. Genome-Wide DNA Methylation in Early-Onset-Dementia Patients Brain Tissue and Lymphoblastoid Cell Lines. Int J Mol Sci 2024; 25:5445. [PMID: 38791483 PMCID: PMC11121630 DOI: 10.3390/ijms25105445] [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: 04/23/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Epigenetics, a potential underlying pathogenic mechanism of neurodegenerative diseases, has been in the scope of several studies performed so far. However, there is a gap in regard to analyzing different forms of early-onset dementia and the use of Lymphoblastoid cell lines (LCLs). We performed a genome-wide DNA methylation analysis on sixty-four samples (from the prefrontal cortex and LCLs) including those taken from patients with early-onset forms of Alzheimer's disease (AD) and frontotemporal dementia (FTD) and healthy controls. A beta regression model and adjusted p-values were used to obtain differentially methylated positions (DMPs) via pairwise comparisons. A correlation analysis of DMP levels with Clariom D array gene expression data from the same cohort was also performed. The results showed hypermethylation as the most frequent finding in both tissues studied in the patient groups. Biological significance analysis revealed common pathways altered in AD and FTD patients, affecting neuron development, metabolism, signal transduction, and immune system pathways. These alterations were also found in LCL samples, suggesting the epigenetic changes might not be limited to the central nervous system. In the brain, CpG methylation presented an inverse correlation with gene expression, while in LCLs, we observed mainly a positive correlation. This study enhances our understanding of the biological pathways that are associated with neurodegeneration, describes differential methylation patterns, and suggests LCLs are a potential cell model for studying neurodegenerative diseases in earlier clinical phases than brain tissue.
Collapse
Affiliation(s)
- Oscar Ramos-Campoy
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Aina Comas-Albertí
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - David Hervás
- Department of Applied Statistics and Operations Research and Quality, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sergi Borrego-Écija
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Beatriz Bosch
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Juan Sandoval
- Epigenomics Core Facility, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Laura Fort-Aznar
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Fermín Moreno-Izco
- Cognitive Disorders Unit, Department of Neurology, Hospital Universitario Donostia, 20014 San Sebastian, Spain
- Instituto de Investigación Sanitaria Biogipuzkoa, Neurosciences Area, Group of Neurodegenerative Diseases, 20014 San Sebastian, Spain
| | - Guadalupe Fernández-Villullas
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Neurological Tissue Bank, Biobank-Hospital Clinic-IDIBAPS, 08036 Barcelona, Spain
| | - Mircea Balasa
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Anna Antonell
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| |
Collapse
|
3
|
Ren Q, Liu Z, Wu L, Yin G, Xie X, Kong W, Zhou J, Liu S. C/EBPβ: The structure, regulation, and its roles in inflammation-related diseases. Biomed Pharmacother 2023; 169:115938. [PMID: 38000353 DOI: 10.1016/j.biopha.2023.115938] [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: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023] Open
Abstract
Inflammation, a mechanism of the human body, has been implicated in many diseases. Inflammatory responses include the release of inflammatory mediators by activating various signaling pathways. CCAAT/enhancer binding protein β (C/EBPβ), a transcription factor in the C/EBP family, contains the leucine zipper (bZIP) domain. The expression of C/EBPβ is mediated at the transcriptional and post-translational levels, such as phosphorylation, acetylation, methylation, and SUMOylation. C/EBPβ has been involved in inflammatory responses by mediating several signaling pathways, such as MAPK/NF-κB and IL-6/JAK/STAT3 pathways. C/EBPβ plays an important role in the pathological development of inflammation-related diseases, such as osteoarthritis, pneumonia, hepatitis, inflammatory bowel diseases, and rheumatoid arthritis. Here, we comprehensively discuss the structure and biological effects of C/EBPβ and its role in inflammatory diseases.
Collapse
Affiliation(s)
- Qun Ren
- Department of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Zhaowen Liu
- Department of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Longhuo Wu
- Department of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Guoqiang Yin
- Ganzhou People's Hospital Affiliated to Nanchang University, Ganzhou 341000, China
| | - Xunlu Xie
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China
| | - Weihao Kong
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China
| | - Jianguo Zhou
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China
| | - Shiwei Liu
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China.
| |
Collapse
|
4
|
Grossman M, Seeley WW, Boxer AL, Hillis AE, Knopman DS, Ljubenov PA, Miller B, Piguet O, Rademakers R, Whitwell JL, Zetterberg H, van Swieten JC. Frontotemporal lobar degeneration. Nat Rev Dis Primers 2023; 9:40. [PMID: 37563165 DOI: 10.1038/s41572-023-00447-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/12/2023] [Indexed: 08/12/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) is one of the most common causes of early-onset dementia and presents with early social-emotional-behavioural and/or language changes that can be accompanied by a pyramidal or extrapyramidal motor disorder. About 20-25% of individuals with FTLD are estimated to carry a mutation associated with a specific FTLD pathology. The discovery of these mutations has led to important advances in potentially disease-modifying treatments that aim to slow progression or delay disease onset and has improved understanding of brain functioning. In both mutation carriers and those with sporadic disease, the most common underlying diagnoses are linked to neuronal and glial inclusions containing tau (FTLD-tau) or TDP-43 (FTLD-TDP), although 5-10% of patients may have inclusions containing proteins from the FUS-Ewing sarcoma-TAF15 family (FTLD-FET). Biomarkers definitively identifying specific pathological entities in sporadic disease have been elusive, which has impeded development of disease-modifying treatments. Nevertheless, disease-monitoring biofluid and imaging biomarkers are becoming increasingly sophisticated and are likely to serve as useful measures of treatment response during trials of disease-modifying treatments. Symptomatic trials using novel approaches such as transcranial direct current stimulation are also beginning to show promise.
Collapse
Affiliation(s)
- Murray Grossman
- Department of Neurology and Penn Frontotemporal Degeneration Center, University of Pennsylvania, Philadelphia, PA, USA
| | - William W Seeley
- Departments of Neurology and Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
| | - Adam L Boxer
- Departments of Neurology and Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Argye E Hillis
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Peter A Ljubenov
- Departments of Neurology and Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Miller
- Departments of Neurology and Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Olivier Piguet
- School of Psychology and Brain and Mind Center, University of Sydney, Sydney, New South Wales, Australia
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The University of Gothenburg, Mölndal, Sweden
- Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | |
Collapse
|
5
|
Hosaka T, Tsuji H, Kwak S. Roles of Aging, Circular RNAs, and RNA Editing in the Pathogenesis of Amyotrophic Lateral Sclerosis: Potential Biomarkers and Therapeutic Targets. Cells 2023; 12:1443. [PMID: 37408276 DOI: 10.3390/cells12101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable motor neuron disease caused by upper and lower motor neuron death. Despite advances in our understanding of ALS pathogenesis, effective treatment for this fatal disease remains elusive. As aging is a major risk factor for ALS, age-related molecular changes may provide clues for the development of new therapeutic strategies. Dysregulation of age-dependent RNA metabolism plays a pivotal role in the pathogenesis of ALS. In addition, failure of RNA editing at the glutamine/arginine (Q/R) site of GluA2 mRNA causes excitotoxicity due to excessive Ca2+ influx through Ca2+-permeable α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors, which is recognized as an underlying mechanism of motor neuron death in ALS. Circular RNAs (circRNAs), a circular form of cognate RNA generated by back-splicing, are abundant in the brain and accumulate with age. Hence, they are assumed to play a role in neurodegeneration. Emerging evidence has demonstrated that age-related dysregulation of RNA editing and changes in circRNA expression are involved in ALS pathogenesis. Herein, we review the potential associations between age-dependent changes in circRNAs and RNA editing, and discuss the possibility of developing new therapies and biomarkers for ALS based on age-related changes in circRNAs and dysregulation of RNA editing.
Collapse
Affiliation(s)
- Takashi Hosaka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- University of Tsukuba Hospital/Jichi Medical University Joint Ibaraki Western Regional Clinical Education Center, Chikusei 308-0813, Japan
- Department of Internal Medicine, Ibaraki Western Medical Center, Chikusei 308-0813, Japan
| | - Hiroshi Tsuji
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Shin Kwak
- Department of Neurology, Tokyo Medical University, Tokyo 160-0023, Japan
| |
Collapse
|
6
|
Fu X, He Y, Xie Y, Lu Z. A conjoint analysis of bulk RNA-seq and single-nucleus RNA-seq for revealing the role of ferroptosis and iron metabolism in ALS. Front Neurosci 2023; 17:1113216. [PMID: 36937665 PMCID: PMC10017473 DOI: 10.3389/fnins.2023.1113216] [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: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive and selective degeneration of motor neurons in the motor cortex of brain and spinal cord. Ferroptosis is a newly discovered form of cell death and reported to mediate selective motor neuron death in the mouse model of ALS. The growing awareness of ferroptosis and iron metabolism dysfunction in ALS prompted us to investigate the expression pattern of ferroptosis and iron metabolism-related genes (FIRGs) in ALS. Here, we performed a conjoint analysis of bulk-RNA sequence and single-nucleus RNA sequence data using the datasets from Gene Expression Omnibus (GEO) to reveal the role of FIRGs in ALS, especially in selective motor neuron death of ALS. We first investigated the differentially expressed genes (DEGs) between ALS and non-neurological controls. Weighted gene co-expression network analysis constructed the gene co-expression network and identified three modules closely associated with ALS. Fifteen FIRGs was identified as target genes based on least absolute shrinkage and selection operator regression analysis as follows: ACSL4, ANO6, ATP6V0E1, B2M, CD44, CHMP5, CYBB, CYBRD1, HIF1A, MOSPD1, NCF2, SDCBP, STEAP2, TMEM14C, ULK1. These genes could differentiate ALS patients from non-neurological controls (p < 2.2e-16) and had a valid value in predicting and diagnosing ALS (AUC = 0.881 in primary dataset and AUC = 0.768 in validation dataset). Then we performed the functional enrichment analysis of DEGs between ALS cases, the most significantly influenced by target genes, and non-neurological controls. The result indicated that the most significantly influenced functions in ALS pathogenesis by these identified FIRGs are synapse pathways, calcium signaling pathway, cAMP signaling pathway, and phagosome and several immune pathways. At last, the analysis of single- nuclear seq found that CHMP5, one of the 15 FIRGs identified by bulk single-nucleus RNA-seq data, was expressed significantly higher in ALS than pathologically normal (PN), specifically in excitatory neuron populations with layer 2 and layer 3 markers (Ex L2_L3), layer 3 and layer 5 markers (Ex L3_L5). Taken together, our study indicates the positive correlation between FIRGs and ALS, presents potential markers for ALS diagnosis and provides new research directions of CHMP5 function in selective motor neuron death in ALS.
Collapse
Affiliation(s)
- Xiujuan Fu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yizi He
- Department of Lymphoma and Hematology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yongzhi Xie
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yongzhi Xie,
| | - Zuneng Lu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
- Zuneng Lu,
| |
Collapse
|
7
|
Huseby CJ, Delvaux E, Brokaw DL, Coleman PD. Blood RNA transcripts reveal similar and differential alterations in fundamental cellular processes in Alzheimer's disease and other neurodegenerative diseases. Alzheimers Dement 2022. [DOI: 10.1002/alz.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Carol J. Huseby
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Elaine Delvaux
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Danielle L. Brokaw
- University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Paul D. Coleman
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| |
Collapse
|
8
|
Sundaramoorthy TH, Castanho I. The Neuroepigenetic Landscape of Vertebrate and Invertebrate Models of Neurodegenerative Diseases. Epigenet Insights 2022; 15:25168657221135848. [PMID: 36353727 PMCID: PMC9638687 DOI: 10.1177/25168657221135848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Vertebrate and invertebrate models of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, have been paramount to our understanding of the pathophysiology of these conditions; however, the brain epigenetic landscape is less well established in these disease models. DNA methylation, histone modifications, and microRNAs are among commonly studied mechanisms of epigenetic regulation. Genome-wide studies and candidate studies of specific methylation marks, histone marks, and microRNAs have demonstrated the dysregulation of these mechanisms in models of neurodegenerative diseases; however, the studies to date are scarce and inconclusive and the implications of many of these changes are still not fully understood. In this review, we summarize epigenetic changes reported to date in the brain of vertebrate and invertebrate models used to study neurodegenerative diseases, specifically diseases affecting the aging population. We also discuss caveats of epigenetic research so far and the use of disease models to understand neurodegenerative diseases, with the aim of improving the use of model organisms in this context in future studies.
Collapse
Affiliation(s)
| | - Isabel Castanho
- University of Exeter Medical School,
University of Exeter, Exeter, UK
- Beth Israel Deaconess Medical Center,
Boston, MA, USA
- Harvard Medical School, Boston, MA,
USA
| |
Collapse
|
9
|
van Zundert B, Montecino M. Epigenetic Changes and Chromatin Reorganization in Brain Function: Lessons from Fear Memory Ensemble and Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms232012081. [PMID: 36292933 PMCID: PMC9602769 DOI: 10.3390/ijms232012081] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Healthy brain functioning in mammals requires a continuous fine-tuning of gene expression. Accumulating evidence over the last three decades demonstrates that epigenetic mechanisms and dynamic changes in chromatin organization are critical components during the control of gene transcription in neural cells. Recent genome-wide analyses show that the regulation of brain genes requires the contribution of both promoter and long-distance enhancer elements, which must functionally interact with upregulated gene expression in response to physiological cues. Hence, a deep comprehension of the mechanisms mediating these enhancer–promoter interactions (EPIs) is critical if we are to understand the processes associated with learning, memory and recall. Moreover, the onset and progression of several neurodegenerative diseases and neurological alterations are found to be strongly associated with changes in the components that support and/or modulate the dynamics of these EPIs. Here, we overview relevant discoveries in the field supporting the role of the chromatin organization and of specific epigenetic mechanisms during the control of gene transcription in neural cells from healthy mice subjected to the fear conditioning paradigm, a relevant model to study memory ensemble. Additionally, special consideration is dedicated to revising recent results generated by investigators working with animal models and human postmortem brain tissue to address how changes in the epigenome and chromatin architecture contribute to transcriptional dysregulation in Alzheimer’s disease, a widely studied neurodegenerative disease. We also discuss recent developments of potential new therapeutic strategies involving epigenetic editing and small chromatin-modifying molecules (or epidrugs).
Collapse
Affiliation(s)
- Brigitte van Zundert
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
- CARE Biomedical Research Center, Santiago 8330005, Chile
- Correspondence: (B.v.Z.); (M.M.)
| | - Martin Montecino
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
- Millennium Institute Center for Genome Regulation CRG, Santiago 8370186, Chile
- Correspondence: (B.v.Z.); (M.M.)
| |
Collapse
|
10
|
The pathogenesis of amyotrophic lateral sclerosis: Mitochondrial dysfunction, protein misfolding and epigenetics. Brain Res 2022; 1786:147904. [PMID: 35390335 DOI: 10.1016/j.brainres.2022.147904] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/24/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with multiple complex mechanisms involved. Among them, mitochondrial dysfunction plays an important role in ALS. Multiple studies have shown that mitochondria are closely associated with reactive oxygen species production and oxidative stress and exhibit different functional states in different genetic backgrounds. In this review we explored the roles of Ca2+, autophagy, mitochondrial quality control in the regulation of mitochondrial homeostasis and their relationship with ALS. In addition, we also summarized and analyzed the roles of protein misfolding and abnormal aggregation in the pathogenesis of ALS. Moreover, we also discussed how epigenetic mechanisms such as DNA methylation and protein post-translational modification affect initiation and progression of ALS. Nevertheless, existing events still cannot fully explain the pathogenesis of ALS at present, more studies are required to explore pathological mechanisms of ALS.
Collapse
|
11
|
Beneficial and Dimorphic Response to Combined HDAC Inhibitor Valproate and AMPK/SIRT1 Pathway Activator Resveratrol in the Treatment of ALS Mice. Int J Mol Sci 2022; 23:ijms23031047. [PMID: 35162978 PMCID: PMC8835218 DOI: 10.3390/ijms23031047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal adult-onset neurodegenerative disorder. There is no cure and current treatments fail to slow the progression of the disease. Epigenetic modulation in the acetylation state of NF-kB RelA and the histone 3 (H3) protein, involved in the development of neurodegeneration, is a drugable target for the class-I histone deacetylases (HDAC) inhibitors, entinostat or valproate, and the AMP-activated kinase (AMPK)-sirtuin 1 pathway activator, resveratrol. In this study, we demonstrated that the combination of valproate and resveratrol can restore the normal acetylation state of RelA in the SOD1(G93A) murine model of ALS, in order to obtain the neuroprotective form of NF-kB. We also investigated the sexually dimorphic development of the disease, as well as the sex-sensibility to the treatment administered. We showed that the combined drugs, which rescued AMPK activation, RelA and the histone 3 acetylation state, reduced the motor deficit and the disease pathology associated with motor neuron loss and microglial reactivity, Brain-Derived Neurotrophic Factor (BDNF) and B-cell lymphoma-extra large (Bcl-xL) level decline. Specifically, vehicle-administered males showed earlier onset and slower progression of the disease when compared to females. The treatment, administered at 50 days of life, postponed the time of onset in the male by 22 days, but not in a significant way in females. Nevertheless, in females, the drugs significantly reduced symptom severity of the later phase of the disease and prolonged the mice’s survival. Only minor beneficial effects were produced in the latter stage in males. Overall, this study shows a beneficial and sexually dimorphic response to valproate and resveratrol treatment in ALS mice.
Collapse
|
12
|
Jiang L, Zhang T, Lu K, Qi S. The progress in C9orf72 research: ALS/FTD pathogenesis, functions and structure. Small GTPases 2022; 13:56-76. [PMID: 33663328 PMCID: PMC9707547 DOI: 10.1080/21541248.2021.1892443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hexanucleotide repeat (GGGGCC) expansion in C9orf72 is accounted for a large proportion of the genetic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The hypotheses of how the massive G4C2 repeats in C9orf72 destroy the neurons and lead to ALS/FTD are raised and improving. As a multirole player, C9orf72 exerts critical roles in many cellular processes, including autophagy, membrane trafficking, immune response, and so on. Notably, the partners of C9orf72, through which C9orf72 participates in the cell activities, have been identified. Notably, the structures of the C9orf72-SMCR8-WDR41 complex shed light on its activity as GTPase activating proteins (GAP). In this manuscript, we reviewed the latest research progress in the C9orf72-mediated ALS/FTD, the physiological functions of C9orf72, and the putative function models of C9orf72/C9orf72-containing complex.
Collapse
Affiliation(s)
- Lan Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tizhong Zhang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kefeng Lu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China,CONTACT Shiqian Qi Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China.
These authors contributed equally to this work.
| |
Collapse
|
13
|
Liu E, Karpf L, Bohl D. Neuroinflammation in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia and the Interest of Induced Pluripotent Stem Cells to Study Immune Cells Interactions With Neurons. Front Mol Neurosci 2022; 14:767041. [PMID: 34970118 PMCID: PMC8712677 DOI: 10.3389/fnmol.2021.767041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022] Open
Abstract
Inflammation is a shared hallmark between amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). For long, studies were conducted on tissues of post-mortem patients and neuroinflammation was thought to be only bystander result of the disease with the immune system reacting to dying neurons. In the last two decades, thanks to improving technologies, the identification of causal genes and the development of new tools and models, the involvement of inflammation has emerged as a potential driver of the diseases and evolved as a new area of intense research. In this review, we present the current knowledge about neuroinflammation in ALS, ALS-FTD, and FTD patients and animal models and we discuss reasons of failures linked to therapeutic trials with immunomodulator drugs. Then we present the induced pluripotent stem cell (iPSC) technology and its interest as a new tool to have a better immunopathological comprehension of both diseases in a human context. The iPSC technology giving the unique opportunity to study cells across differentiation and maturation times, brings the hope to shed light on the different mechanisms linking neurodegeneration and activation of the immune system. Protocols available to differentiate iPSC into different immune cell types are presented. Finally, we discuss the interest in studying monocultures of iPS-derived immune cells, co-cultures with neurons and 3D cultures with different cell types, as more integrated cellular approaches. The hope is that the future work with human iPS-derived cells helps not only to identify disease-specific defects in the different cell types but also to decipher the synergistic effects between neurons and immune cells. These new cellular tools could help to find new therapeutic approaches for all patients with ALS, ALS-FTD, and FTD.
Collapse
Affiliation(s)
- Elise Liu
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Léa Karpf
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| |
Collapse
|
14
|
Sun L, Cheng B, Zhou Y, Fan Y, Li W, Qiu Q, Fang Y, Xiao S, Zheng H, Li X. ErbB4 Mutation that Decreased NRG1-ErbB4 Signaling Involved in the Pathogenesis of Amyotrophic Lateral Sclerosis/Frontotemporal Dementia. J Alzheimers Dis 2021; 74:535-544. [PMID: 32065797 DOI: 10.3233/jad-191230] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) includes a large spectrum of neurodegenerative disorders. OBJECTIVE To identify the relationship of ErbB4 mutation and ALS/FTD. METHODS Here, we report an atypical case of frontal variant behavioral abnormalities at the initial stage, a stable plateau stage of 5 years, and paralysis involving both upper and lower motor neurons followed by progressive cognitive dysfunction at the advanced stage. The clinical findings suggested a diagnosis of ALS/FTD, and genetic testing revealed erb-b2 receptor tyrosine kinase 4 (ErbB4) heterozygous mutation (c.2136 T>G, p.I712M), identified in an ALS pedigree previously. We modeled mutant ErbB4 protein through the SWISS-MODEL Server, and speculated on the structural change caused by the mutation. We also identified that ErbB4 (I712M) mutation led to reduced auto-phosphorylation of ErbB4 upon neuregulin-1 (NRG1) stimulation. RESULTS A functional analysis of ErbB4 mutation demonstrated an obviously decreased auto-phosphorylation of ErbB4 involving in the pathogenesis of ALS/FTD. CONCLUSION We firstly found ErbB4 mutation to be identified in ALS/FTD.
Collapse
Affiliation(s)
- Lin Sun
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baoying Cheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Xiamen University, Xiamen, China.,Department of Neuroscience, Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Yuxun Zhou
- The College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Yating Fan
- The College of Chemistry, Chemical Engineering & Biotechnology, Donghua University, Shanghai, China
| | - Wei Li
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Qiu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Fang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shifu Xiao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Honghua Zheng
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, College of Medicine, Xiamen University, Xiamen, China.,Department of Neuroscience, Shenzhen Research Institute of Xiamen University, Shenzhen, China
| | - Xia Li
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
15
|
Natarajan K, Eisfeldt J, Hammond M, Laffita-Mesa JM, Patra K, Khoshnood B, Öijerstedt L, Graff C. Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia. Acta Neuropathol Commun 2021; 9:132. [PMID: 34344473 PMCID: PMC8336016 DOI: 10.1186/s40478-021-01234-2] [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: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 11/10/2022] Open
Abstract
We identified an autosomal dominant progranulin mutation carrier without symptoms of dementia in her lifetime (Reduced Penetrance Mutation Carrier, RedPenMC). This resistance to develop expected pathology presents a unique opportunity to interrogate neurodegenerative mechanisms. We performed multimodal single-nuclei analyses of post-mortem frontal cortex from RedPenMC, including transcriptomics and global levels of chromatin marks. RedPenMC had an increased ratio of GRN-expressing microglia, higher levels of activating histone mark H3k4me3 in microglia and lower levels of the repressive chromatin marks H3k9me1 and H3k9me3 in the frontal cortex than her affected mutation carrier son and evidence of higher protein levels of progranulin in both plasma and brain homogenates. Although the study is limited to one case, the results support that restoring brain progranulin levels may be sufficient to escape neurodegeneration and FTD. In addition to previously identified modifier genes, it is possible that epigenetic marks may contribute to the increased progranulin expression in cases of reduced penetrance. These findings may stimulate similar follow-up studies and new therapeutic approaches.
Collapse
|
16
|
Histone Methylation Regulation in Neurodegenerative Disorders. Int J Mol Sci 2021; 22:ijms22094654. [PMID: 33925016 PMCID: PMC8125694 DOI: 10.3390/ijms22094654] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Advances achieved with molecular biology and genomics technologies have permitted investigators to discover epigenetic mechanisms, such as DNA methylation and histone posttranslational modifications, which are critical for gene expression in almost all tissues and in brain health and disease. These advances have influenced much interest in understanding the dysregulation of epigenetic mechanisms in neurodegenerative disorders. Although these disorders diverge in their fundamental causes and pathophysiology, several involve the dysregulation of histone methylation-mediated gene expression. Interestingly, epigenetic remodeling via histone methylation in specific brain regions has been suggested to play a critical function in the neurobiology of psychiatric disorders, including that related to neurodegenerative diseases. Prominently, epigenetic dysregulation currently brings considerable interest as an essential player in neurodegenerative disorders, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Amyotrophic lateral sclerosis (ALS) and drugs of abuse, including alcohol abuse disorder, where it may facilitate connections between genetic and environmental risk factors or directly influence disease-specific pathological factors. We have discussed the current state of histone methylation, therapeutic strategies, and future perspectives for these disorders. While not somatically heritable, the enzymes responsible for histone methylation regulation, such as histone methyltransferases and demethylases in neurons, are dynamic and reversible. They have become promising potential therapeutic targets to treat or prevent several neurodegenerative disorders. These findings, along with clinical data, may provide links between molecular-level changes and behavioral differences and provide novel avenues through which the epigenome may be targeted early on in people at risk for neurodegenerative disorders.
Collapse
|
17
|
Quezada E, Cappelli C, Diaz I, Jury N, Wightman N, Brown RH, Montecino M, van Zundert B. BET bromodomain inhibitors PFI-1 and JQ1 are identified in an epigenetic compound screen to enhance C9ORF72 gene expression and shown to ameliorate C9ORF72-associated pathological and behavioral abnormalities in a C9ALS/FTD model. Clin Epigenetics 2021; 13:56. [PMID: 33726839 PMCID: PMC7962347 DOI: 10.1186/s13148-021-01039-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/23/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND An intronic GGGGCC (G4C2) hexanucleotide repeat expansion (HRE) in the C9ORF72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), referred to as C9ALS/FTD. No cure or effective treatment exist for C9ALS/FTD. Three major molecular mechanisms have emerged to explain C9ALS/FTD disease mechanisms: (1) C9ORF72 loss-of-function through haploinsufficiency, (2) dipeptide repeat (DPR) proteins mediated toxicity by the translation of the repeat RNAs, and more controversial, (3) RNA-mediated toxicity by bidirectional transcription of the repeats that form intranuclear RNA foci. Recent studies indicate a double-hit pathogenic mechanism in C9ALS/FTD, where reduced C9ORF72 protein levels lead to impaired clearance of toxic DPRs. Here we explored whether pharmacological compounds can revert these pathological hallmarks in vitro and cognitive impairment in a C9ALS/FTD mouse model (C9BAC). We specifically focused our study on small molecule inhibitors targeting chromatin-regulating proteins (epidrugs) with the goal of increasing C9ORF72 gene expression and reduce toxic DPRs. RESULTS We generated luciferase reporter cell lines containing 10 (control) or ≥ 90 (mutant) G4C2 HRE located between exon 1a and 1b of the human C9ORF72 gene. In a screen of 14 different epidrugs targeting bromodomains, chromodomains and histone-modifying enzymes, we found that several bromodomain and extra-terminal domain (BET) inhibitors (BETi), including PFI-1 and JQ1, increased luciferase reporter activity. Using primary cortical cultures from C9BAC mice, we further found that PFI-1 treatment increased the expression of V1-V3 transcripts of the human mutant C9ORF72 gene, reduced poly(GP)-DPR inclusions but enhanced intranuclear RNA foci. We also tested whether JQ1, an BETi previously shown to reach the mouse brain by intraperitoneal (i.p.) injection, can revert behavioral abnormalities in C9BAC mice. Interestingly, it was found that JQ1 administration (daily i.p. administration for 7 days) rescued hippocampal-dependent cognitive deficits in C9BAC mice. CONCLUSIONS Our findings place BET bromodomain inhibitors as a potential therapy for C9ALS/FTD by ameliorating C9ORF72-associated pathological and behavioral abnormalities. Our finding that PFI-1 increases accumulation of intranuclear RNA foci is in agreement with recent data in flies suggesting that nuclear RNA foci can be neuroprotective by sequestering repeat transcripts that result in toxic DPRs.
Collapse
Affiliation(s)
- Esteban Quezada
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Claudio Cappelli
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Iván Diaz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nur Jury
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicholas Wightman
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA
| | - Martín Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
- FONDAP Center for Genome Regulation, Santiago, Chile.
| | - Brigitte van Zundert
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA.
- CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
18
|
Fare CM, Shorter J. Open Access: A Role for p53 in c9ALS/FTD? Trends Genet 2021; 37:404-406. [PMID: 33551183 DOI: 10.1016/j.tig.2021.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
Poly(PR), a toxic dipeptide-repeat protein, translated from the pathogenic G4C2 repeat expansion in C9orf72, contributes to c9 amyotrophic lateral sclerosis/frontotemporal dementia (c9ALS/FTD). However, precisely how poly(PR) elicits neurodegeneration has remained unclear. Maor-Nof et al. now establish that poly(PR) remodels the neuronal epigenome to promote proapoptotic p53 activity involving PUMA, which drives neurodegeneration in several models.
Collapse
Affiliation(s)
- Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
19
|
Maor-Nof M, Shipony Z, Lopez-Gonzalez R, Nakayama L, Zhang YJ, Couthouis J, Blum JA, Castruita PA, Linares GR, Ruan K, Ramaswami G, Simon DJ, Nof A, Santana M, Han K, Sinnott-Armstrong N, Bassik MC, Geschwind DH, Tessier-Lavigne M, Attardi LD, Lloyd TE, Ichida JK, Gao FB, Greenleaf WJ, Yokoyama JS, Petrucelli L, Gitler AD. p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR). Cell 2021; 184:689-708.e20. [PMID: 33482083 PMCID: PMC7886018 DOI: 10.1016/j.cell.2020.12.025] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/07/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a GGGGCC repeat expansion in the C9orf72 gene. We developed a platform to interrogate the chromatin accessibility landscape and transcriptional program within neurons during degeneration. We provide evidence that neurons expressing the dipeptide repeat protein poly(proline-arginine), translated from the C9orf72 repeat expansion, activate a highly specific transcriptional program, exemplified by a single transcription factor, p53. Ablating p53 in mice completely rescued neurons from degeneration and markedly increased survival in a C9orf72 mouse model. p53 reduction also rescued axonal degeneration caused by poly(glycine-arginine), increased survival of C9orf72 ALS/FTD-patient-induced pluripotent stem cell (iPSC)-derived motor neurons, and mitigated neurodegeneration in a C9orf72 fly model. We show that p53 activates a downstream transcriptional program, including Puma, which drives neurodegeneration. These data demonstrate a neurodegenerative mechanism dynamically regulated through transcription-factor-binding events and provide a framework to apply chromatin accessibility and transcription program profiles to neurodegeneration.
Collapse
Affiliation(s)
- Maya Maor-Nof
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Zohar Shipony
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Lisa Nakayama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia A Castruita
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel R Linares
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Kai Ruan
- Department of Neurology, Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Gokul Ramaswami
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David J Simon
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Aviv Nof
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel Santana
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Laura D Attardi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Lloyd
- Department of Neurology, Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
20
|
The Role of Exosomal microRNAs and Oxidative Stress in Neurodegenerative Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3232869. [PMID: 33193999 PMCID: PMC7641266 DOI: 10.1155/2020/3232869] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases including Alzheimer's disease and Parkinson's disease are aging-associated diseases with irreversible damage of brain tissue. Oxidative stress is commonly detected in neurodegenerative diseases and related to neuronal injury and pathological progress. Exosome, one of the extracellular vesicles, is demonstrated to carry microRNAs (miRNAs) and build up a cell-cell communication in neurons. Recent research has found that exosomal miRNAs regulate the activity of multiple physiological pathways, including the oxidative stress response, in neurodegenerative diseases. Here, we review the role of exosomal miRNAs and oxidative stress in neurodegenerative diseases. Firstly, we explore the relationship between oxidative stress and neurodegenerative diseases. Secondly, we introduce the characteristics of exosomes and roles of exosome-related miRNAs. Thirdly, we summarized the crosstalk between exosomal miRNAs and oxidative stress in neurodegenerative diseases. Fourthly, we discuss the potential of exosomes to be a biomarker in neurodegenerative diseases. Finally, we summarize the advantages of exosome-based delivery and present situation of research on exosome-based delivery of therapeutic miRNA. Our work is aimed at probing and reinforcing the recognition of the pathomechanism of neurodegenerative diseases and providing the basis for novel strategies of clinical diagnosis and treatment.
Collapse
|
21
|
Lowry JL, Ryan ÉB, Esengul YT, Siddique N, Siddique T. Intricacies of aetiology in intrafamilial degenerative disease. Brain Commun 2020; 2:fcaa120. [PMID: 33134917 PMCID: PMC7585693 DOI: 10.1093/braincomms/fcaa120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/23/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
The genetic underpinnings of late-onset degenerative disease have typically been determined by screening families for the segregation of genetic variants with the disease trait in affected, but not unaffected, individuals. However, instances of intrafamilial etiological heterogeneity, where pathogenic variants in a culprit gene are not shared among all affected family members, continue to emerge and confound gene-discovery and genetic counselling efforts. Discordant intrafamilial cases lacking a mutation shared by other affected family members are described as disease phenocopies. This description often results in an over-simplified acceptance of an environmental cause of disease in the phenocopy cases, while the role of intrafamilial genetic heterogeneity, shared de novo mutations or epigenetic aberrations in such families is often ignored. On a related note, it is now evident that the same disease-associated variant can be present in individuals exhibiting clinically distinct phenotypes, thereby genetically uniting seemingly unrelated syndromes to form a spectrum of disease. Herein, we discuss the intricacies of determining complex degenerative disease aetiology and suggest alternative mechanisms of disease transmission that may account for the apparent missing heritability of disease.
Collapse
Affiliation(s)
- Jessica L Lowry
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Éanna B Ryan
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Northwestern University Interdepartmental Neuroscience Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Y Taylan Esengul
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nailah Siddique
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Teepu Siddique
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Northwestern University Interdepartmental Neuroscience Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Department of Pathology Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
22
|
Ghemrawi R, Khair M. Endoplasmic Reticulum Stress and Unfolded Protein Response in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:E6127. [PMID: 32854418 PMCID: PMC7503386 DOI: 10.3390/ijms21176127] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum (ER) is an important organelle involved in protein quality control and cellular homeostasis. The accumulation of unfolded proteins leads to an ER stress, followed by an adaptive response via the activation of the unfolded protein response (UPR), PKR-like ER kinase (PERK), inositol-requiring transmembrane kinase/endoribonuclease 1α (IRE1α) and activating transcription factor 6 (ATF6) pathways. However, prolonged cell stress activates apoptosis signaling leading to cell death. Neuronal cells are particularly sensitive to protein misfolding, consequently ER and UPR dysfunctions were found to be involved in many neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and prions diseases, among others characterized by the accumulation and aggregation of misfolded proteins. Pharmacological UPR modulation in affected tissues may contribute to the treatment and prevention of neurodegeneration. The association between ER stress, UPR and neuropathology is well established. In this review, we provide up-to-date evidence of UPR activation in neurodegenerative disorders followed by therapeutic strategies targeting the UPR and ameliorating the toxic effects of protein unfolding and aggregation.
Collapse
Affiliation(s)
- Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi 112612, UAE
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi 129188, UAE;
| |
Collapse
|
23
|
Bendotti C, Bonetto V, Pupillo E, Logroscino G, Al-Chalabi A, Lunetta C, Riva N, Mora G, Lauria G, Weishaupt JH, Agosta F, Malaspina A, Basso M, Greensmith L, Van Den Bosch L, Ratti A, Corbo M, Hardiman O, Chiò A, Silani V, Beghi E. Focus on the heterogeneity of amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2020; 21:485-495. [PMID: 32583689 DOI: 10.1080/21678421.2020.1779298] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The clinical manifestations of amyotrophic lateral sclerosis (ALS) are variable in terms of age at disease onset, site of onset, progression of symptoms, motor neuron involvement, and the occurrence of cognitive and behavioral changes. Genetic background is a key determinant of the ALS phenotype. The mortality of the disease also varies with the ancestral origin of the affected population and environmental factors are likely to be associated with ALS at least within some cohorts. Disease heterogeneity is likely underpinned by the presence of different pathogenic mechanisms. A variety of ALS animal models can be informative about the heterogeneity of the neuropathological or genetic aspects of the disease and can support the development of new therapeutic intervention. Evolving biomarkers can contribute to the identification of differing genotypes and phenotypes, and can be used to explore whether genotypic and phenotypic differences in animal models might help to provide a better definition of the heterogeneity of ALS in humans. These include neurofilaments, peripheral blood mononuclear cells, extracellular vesicles, microRNA and imaging findings. These biomarkers might predict not only the development of the disease, but also the variability in progression, although robust validation is required. A promising area of progress in modeling the heterogeneity of human ALS is represented by the use of human induced pluripotent stem cell (iPSCs)-derived motor neurons. Although the translational value of iPSCs remains unclear, this model is attractive in the perspective of replicating the heterogeneity of sporadic ALS as a first step toward a personalized medicine strategy.
Collapse
Affiliation(s)
- Caterina Bendotti
- Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Valentina Bonetto
- Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Elisabetta Pupillo
- Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Giancarlo Logroscino
- Department of Neurosciences and Sense Organs, Center for Neurodegenerative Diseases and the Aging Brain Università degli Studi di Bari, Bari; Fondazione Giovanni Panico Tricase, Lecce, Italy
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Serena Onlus Foundation, Milano, Italy
| | - Nilo Riva
- Neuroimaging Research Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milano, Italy
| | - Gabriela Mora
- Department of Neurorehabilitation, ICS Maugeri IRCCS, Milano, Italy
| | - Giuseppe Lauria
- Unit of Neurology, Motor Neuron Disease Center, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy.,Department of Biomedical and Clinical Sciences "Lduigi Sacco", University of Milan, Milan, Italy
| | | | - Federica Agosta
- Neuroimaging Research Unit, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milano, Italy
| | | | - Manuela Basso
- Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), Università degli Studi di Trento, Trento, Italy
| | - Linda Greensmith
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ludo Van Den Bosch
- Center for Brain & Disease Research (VIB) and Laboratory of Neurobiology (KU Leuven), Leuven, Belgium
| | - Antonia Ratti
- Department of Neurology - Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milano, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano, Italy
| | - Massimo Corbo
- Department of Neurorehabilitation Sciences, Casa Cura Policlinico (CCP), Milano, Italy
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, Università degli Studi di Torino, Torino, Italy
| | - Vincenzo Silani
- Department of Neurology - Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milano, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milano, Italy
| | - Ettore Beghi
- Mario Negri-ALS Study Group, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| |
Collapse
|
24
|
MicroRNA-5572 Is a Novel MicroRNA-Regulating SLC30A3 in Sporadic Amyotrophic Lateral Sclerosis. Int J Mol Sci 2020; 21:ijms21124482. [PMID: 32599739 PMCID: PMC7350020 DOI: 10.3390/ijms21124482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive degenerative disease caused by the loss of motor neurons. Although the pathogenesis of sporadic ALS (sALS) remains unclear, it has recently been suggested that disorders of microRNA (miRNA) may be involved in neurodegenerative conditions. The purpose of this study was to investigate miRNA levels in sALS and the target genes of miRNA. Microarray and real-time RT-PCR analyses revealed significantly-decreased levels of miR-139-5p and significantly increased levels of miR-5572 in the spinal cords of sALS patients compared with those in controls. We then focused on miR-5572, which has not been reported in ALS, and determined its target gene. By using TargetScan, we predicted SLC30A3 as the candidate target gene of miR-5572. In a previous study, we found decreased SLC30A3 levels in the spinal cords of sALS patients. We revealed that SLC30A3 was regulated by miR-5572. Taken together, these results demonstrate that the level of novel miRNA miR-5572 is increased in sALS and that SLC30A3 is one of the target genes regulated by miR-5572.
Collapse
|
25
|
Poeta L, Drongitis D, Verrillo L, Miano MG. DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms. Genes (Basel) 2020; 11:E684. [PMID: 32580525 PMCID: PMC7348995 DOI: 10.3390/genes11060684] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Unstable repeat disorders comprise a variable group of incurable human neurological and neuromuscular diseases caused by an increase in the copy number of tandem repeats located in various regions of their resident genes. It has become clear that dense DNA methylation in hyperexpanded non-coding repeats induces transcriptional silencing and, subsequently, insufficient protein synthesis. However, the ramifications of this paradigm reveal a far more profound role in disease pathogenesis. This review will summarize the significant progress made in a subset of non-coding repeat diseases demonstrating the role of dense landscapes of 5-methylcytosine (5mC) as a common disease modifier. However, the emerging findings suggest context-dependent models of 5mC-mediated silencing with distinct effects of excessive DNA methylation. An in-depth understanding of the molecular mechanisms underlying this peculiar group of human diseases constitutes a prerequisite that could help to discover novel pathogenic repeat loci, as well as to determine potential therapeutic targets. In this regard, we report on a brief description of advanced strategies in DNA methylation profiling for the identification of unstable Guanine-Cytosine (GC)-rich regions and on promising examples of molecular targeted therapies for Fragile X disease (FXS) and Friedrich ataxia (FRDA) that could pave the way for the application of this technique in other hypermethylated expansion disorders.
Collapse
Affiliation(s)
- Loredana Poeta
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy; (L.P.); (D.D.); (L.V.)
| | - Denise Drongitis
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy; (L.P.); (D.D.); (L.V.)
| | - Lucia Verrillo
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy; (L.P.); (D.D.); (L.V.)
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, CNR, 80131 Naples, Italy; (L.P.); (D.D.); (L.V.)
| |
Collapse
|
26
|
Liscic RM, Alberici A, Cairns NJ, Romano M, Buratti E. From basic research to the clinic: innovative therapies for ALS and FTD in the pipeline. Mol Neurodegener 2020; 15:31. [PMID: 32487123 PMCID: PMC7268618 DOI: 10.1186/s13024-020-00373-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and Frontotemporal Degeneration (FTD) are neurodegenerative disorders, related by deterioration of motor and cognitive functions and short survival. Aside from cases with an inherited pathogenic mutation, the causes of the disorders are still largely unknown and no effective treatment currently exists. It has been shown that FTD may coexist with ALS and this overlap occurs at clinical, genetic, and molecular levels. In this work, we review the main pathological aspects of these complex diseases and discuss how the integration of the novel pathogenic molecular insights and the analysis of molecular interaction networks among all the genetic players represents a critical step to shed light on discovering novel therapeutic strategies and possibly tailoring personalized medicine approaches to specific ALS and FTD patients.
Collapse
Affiliation(s)
- Rajka Maria Liscic
- Department of Neurology, Johannes Kepler University, Linz, Austria
- School of Medicine, University of Osijek, Osijek, Croatia
| | - Antonella Alberici
- Neurology Unit, Department of Neurological Sciences and Vision, ASST-Spedali Civili-University of Brescia, Brescia, Italy
| | - Nigel John Cairns
- College of Medicine and Health and Living Systems Institute, University of Exeter, Exeter, UK
| | - Maurizio Romano
- Department of Life Sciences, Via Valerio 28, University of Trieste, 34127, Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149, Trieste, Italy.
| |
Collapse
|
27
|
Abstract
DNA methylation at CpG sites is an essential epigenetic mark that regulates gene expression during mammalian development and diseases. Methylome refers to the entire set of methylation modifications present in the whole genome. Over the last several years, an increasing number of reports on brain DNA methylome reported the association between aberrant methylation and the abnormalities in the expression of critical genes known to have critical roles during aging and neurodegenerative diseases. Consequently, the role of methylation in understanding neurodegenerative diseases has been under focus. This review outlines the current knowledge of the human brain DNA methylomes during aging and neurodegenerative diseases. We describe the differentially methylated genes from fetal stage to old age and their biological functions. Additionally, we summarize the key aspects and methylated genes identified from brain methylome studies on neurodegenerative diseases. The brain methylome studies could provide a basis for studying the functional aspects of neurodegenerative diseases.
Collapse
Affiliation(s)
- Renuka Prasad
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Eek-Hoon Jho
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| |
Collapse
|
28
|
Jury N, Abarzua S, Diaz I, Guerra MV, Ampuero E, Cubillos P, Martinez P, Herrera-Soto A, Arredondo C, Rojas F, Manterola M, Rojas A, Montecino M, Varela-Nallar L, van Zundert B. Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice. Clin Epigenetics 2020; 12:32. [PMID: 32070418 PMCID: PMC7029485 DOI: 10.1186/s13148-020-0816-9] [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: 10/31/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background Hexanucleotide repeat expansions of the G4C2 motif in a non-coding region of the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Tissues from C9ALS/FTD patients and from mouse models of ALS show RNA foci, dipeptide-repeat proteins, and notably, widespread alterations in the transcriptome. Epigenetic processes regulate gene expression without changing DNA sequences and therefore could account for the altered transcriptome profiles in C9ALS/FTD; here, we explore whether the critical repressive marks H3K9me2 and H3K9me3 are altered in a recently developed C9ALS/FTD BAC mouse model (C9BAC). Results Chromocenters that constitute pericentric constitutive heterochromatin were visualized as DAPI- or Nucblue-dense foci in nuclei. Cultured C9BAC astrocytes exhibited a reduced staining signal for H3K9me3 (but not for H3K9me2) at chromocenters that was accompanied by a marked decline in the global nuclear level of this mark. Similar depletion of H3K9me3 at chromocenters was detected in astrocytes and neurons of the spinal cord, motor cortex, and hippocampus of C9BAC mice. The alterations of H3K9me3 in the hippocampus of C9BAC mice led us to identify previously undetected neuronal loss in CA1, CA3, and dentate gyrus, as well as hippocampal-dependent cognitive deficits. Conclusions Our data indicate that a loss of the repressive mark H3K9me3 in astrocytes and neurons in the central nervous system of C9BAC mice represents a signature during neurodegeneration and memory deficit of C9ALS/FTD.
Collapse
Affiliation(s)
- Nur Jury
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastian Abarzua
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ivan Diaz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Miguel V Guerra
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Estibaliz Ampuero
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,Current address: Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago, Chile
| | - Paula Cubillos
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Martinez
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Herrera-Soto
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Cristian Arredondo
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fabiola Rojas
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Manterola
- Program of Human Genetics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Adriana Rojas
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Martín Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Lorena Varela-Nallar
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
| | - Brigitte van Zundert
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile. .,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
29
|
Bisagno V, Bernardi MA, Sanz Blasco S, Urbano FJ, Garcia-Rill E. Differential effects of HDAC inhibitors on PPN oscillatory activity in vivo. Neuropharmacology 2019; 165:107922. [PMID: 31923766 DOI: 10.1016/j.neuropharm.2019.107922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/28/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023]
Abstract
The pedunculopontine nucleus (PPN) has long been known to be part of the reticular activating system (RAS) in charge of arousal and REM sleep. We previously showed that in vitro exposure to a HDAC Class I and II mixed inhibitor (TSA), or a specific HDAC class IIa inhibitor (MC 1568), decreased PPN gamma oscillations. Given the lack of information on systemic in vivo treatments on neuronal synaptic properties, the present study was designed to investigate the systemic effect of HDAC inhibitors (HDACi) on PPN rhythmicity. Rat pups were injected (acute, single dose) with TSA (4 or 20 mg/kg), MC1568 (4 or 20 mg/kg), or MS275 (20 or 100 mg/kg). Our results show that MC1568 (20 mg/kg) reduced mean frequency of PPN oscillations at gamma band, while increasing mean input resistance (Rm) of PPN neurons. For TSA (4 and 20 mg/kg), we observed reduced mean frequency of oscillations at gamma band and increased mean Rm of PPN neurons. Systemic administration of 20 mg/kg MC1568 and TSA effects on Rm were washed out after 60 min of in vitro incubation of PPN slices, suggesting an underlying functional recovery of PPN calcium-mediated gamma band oscillations over time. In addition, at a lower dose, 4 mg/kg, MC1568 and TSA induced higher mean amplitude gamma oscillations. Blocking HDAC class I might not have deleterious effects on gamma activity, but, more importantly, the inhibition of HDAC class I (at 100 mg/kg) increased gamma band oscillations. In conclusion, the present results in vivo validate our previous findings in vitro and further expand information on the effects of HDAC inhibition on PPN rhythmicity. PPN neurons require normal activity of HDAC class IIa in order to oscillate at gamma band.
Collapse
Affiliation(s)
| | | | | | - Francisco J Urbano
- IFIBYNE, DFBMC-CONICET, FCEN, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Edgar Garcia-Rill
- Center for Translational Neuroscience, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
30
|
Konovalova J, Gerasymchuk D, Parkkinen I, Chmielarz P, Domanskyi A. Interplay between MicroRNAs and Oxidative Stress in Neurodegenerative Diseases. Int J Mol Sci 2019; 20:ijms20236055. [PMID: 31801298 PMCID: PMC6929013 DOI: 10.3390/ijms20236055] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs are post-transcriptional regulators of gene expression, crucial for neuronal differentiation, survival, and activity. Age-related dysregulation of microRNA biogenesis increases neuronal vulnerability to cellular stress and may contribute to the development and progression of neurodegenerative diseases. All major neurodegenerative disorders are also associated with oxidative stress, which is widely recognized as a potential target for protective therapies. Albeit often considered separately, microRNA networks and oxidative stress are inextricably entwined in neurodegenerative processes. Oxidative stress affects expression levels of multiple microRNAs and, conversely, microRNAs regulate many genes involved in an oxidative stress response. Both oxidative stress and microRNA regulatory networks also influence other processes linked to neurodegeneration, such as mitochondrial dysfunction, deregulation of proteostasis, and increased neuroinflammation, which ultimately lead to neuronal death. Modulating the levels of a relatively small number of microRNAs may therefore alleviate pathological oxidative damage and have neuroprotective activity. Here, we review the role of individual microRNAs in oxidative stress and related pathways in four neurodegenerative conditions: Alzheimer’s (AD), Parkinson’s (PD), Huntington’s (HD) disease, and amyotrophic lateral sclerosis (ALS). We also discuss the problems associated with the use of oversimplified cellular models and highlight perspectives of studying microRNA regulation and oxidative stress in human stem cell-derived neurons.
Collapse
Affiliation(s)
- Julia Konovalova
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; (J.K.); (D.G.); (I.P.)
| | - Dmytro Gerasymchuk
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; (J.K.); (D.G.); (I.P.)
- Institute of Molecular Biology and Genetics, NASU, Kyiv 03143, Ukraine
| | - Ilmari Parkkinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; (J.K.); (D.G.); (I.P.)
| | - Piotr Chmielarz
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Andrii Domanskyi
- Institute of Biotechnology, HiLIFE, University of Helsinki, 00014 Helsinki, Finland; (J.K.); (D.G.); (I.P.)
- Correspondence: ; Tel.: +358-50-448-4545
| |
Collapse
|
31
|
Dios AM, Babu S, Granucci EJ, Mueller KA, Mills AN, Alshikho MJ, Zürcher NR, Cernasov P, Gilbert TM, Glass JD, Berry JD, Atassi N, Hooker JM, Sadri-Vakili G. Class I and II histone deacetylase expression is not altered in human amyotrophic lateral sclerosis: Neuropathological and positron emission tomography molecular neuroimaging evidence. Muscle Nerve 2019; 60:443-452. [PMID: 31241177 DOI: 10.1002/mus.26620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 02/06/2023]
Abstract
INTRODUCTION There is an unmet need for mechanism-based biomarkers and effective disease modifying treatments in amyotrophic lateral sclerosis (ALS). Previous findings have provided evidence that histone deacetylases (HDAC) are altered in ALS, providing a rationale for testing HDAC inhibitors as a therapeutic option. METHODS We measured class I and II HDAC protein and transcript levels together with acetylation levels of downstream substrates by using Western blotting in postmortem tissue of ALS and controls. [11 C]Martinostat, a novel HDAC positron emission tomography ligand, was also used to assess in vivo brain HDAC alterations in patients with ALS and healthy controls (HC). RESULTS There was no significant difference in HDAC levels between patients with ALS and controls as measured by Western blotting and reverse-transcription quantitative polymerase chain reaction. Similarly, no differences were detected in [11 C]Martinostat-positron emission tomography uptake in ALS participants compared with HCs. DISCUSSION These findings provide evidence that alterations in HDAC isoforms are not a dominant pathological feature at the bulk tissue level in ALS.
Collapse
Affiliation(s)
- Amanda M Dios
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Suma Babu
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Eric J Granucci
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kaly A Mueller
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexandra N Mills
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mohamad J Alshikho
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Nicole R Zürcher
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Paul Cernasov
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tonya M Gilbert
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - James D Berry
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nazem Atassi
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA.,Sanofi-Genzyme, Cambridge, Massachusetts, USA
| | - Jacob M Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Ghazaleh Sadri-Vakili
- Sean M Healey & AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
32
|
Cobos SN, Bennett SA, Torrente MP. The impact of histone post-translational modifications in neurodegenerative diseases. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1982-1991. [PMID: 30352259 PMCID: PMC6475498 DOI: 10.1016/j.bbadis.2018.10.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/05/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023]
Abstract
Every year, neurodegenerative disorders take more than 5000 lives in the US alone. Cures have not yet been found for many of the multitude of neuropathies. The majority of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD) cases have no known genetic basis. Thus, it is evident that contemporary genetic approaches have failed to explain the etiology or etiologies of ALS/FTD and PD. Recent investigations have explored the potential role of epigenetic mechanisms in disease development. Epigenetics comprises heritable changes in gene utilization that are not derived from changes in the genome. A main epigenetic mechanism involves the post-translational modification of histones. Increased knowledge of the epigenomic landscape of neurodegenerative diseases would not only further our understanding of the disease pathologies, but also lead to the development of treatments able to halt their progress. Here, we review recent advances on the association of histone post-translational modifications with ALS, FTD, PD and several ataxias.
Collapse
Affiliation(s)
- Samantha N Cobos
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Seth A Bennett
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Mariana P Torrente
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York 10016, United States.
| |
Collapse
|
33
|
|
34
|
Bennett SA, Tanaz R, Cobos SN, Torrente MP. Epigenetics in amyotrophic lateral sclerosis: a role for histone post-translational modifications in neurodegenerative disease. Transl Res 2019; 204:19-30. [PMID: 30391475 PMCID: PMC6331271 DOI: 10.1016/j.trsl.2018.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the third most common adult onset neurodegenerative disorder worldwide. It is generally characterized by progressive paralysis starting at the limbs ultimately leading to death caused by respiratory failure. There is no cure and current treatments fail to slow the progression of the disease. As such, new treatment options are desperately needed. Epigenetic targets are an attractive possibility because they are reversible. Epigenetics refers to heritable changes in gene expression unrelated to changes in DNA sequence. Three main epigenetic mechanisms include the methylation of DNA, microRNAs and the post-translational modification of histone proteins. Histone modifications occur in many amino acid residues and include phosphorylation, acetylation, methylation as well as other chemical moieties. Recent evidence points to a possible role for epigenetic mechanisms in the etiology of ALS. Here, we review recent advances linking ALS and epigenetics, with a strong focus on histone modifications. Both local and global changes in histone modification profiles are associated with ALS drawing attention to potential targets for future diagnostic and treatment approaches.
Collapse
Affiliation(s)
- Seth A Bennett
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York
| | - Royena Tanaz
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork
| | - Samantha N Cobos
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016
| | - Mariana P Torrente
- Department of Chemistry, Brooklyn College, Brooklyn, NewYork; Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, New York.
| |
Collapse
|
35
|
The Role of MicroRNAs in Patients with Amyotrophic Lateral Sclerosis. J Mol Neurosci 2018; 66:617-628. [PMID: 30415446 DOI: 10.1007/s12031-018-1204-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a serious neurodegenerative disease that affects motor neurons and leads to death within 2 to 3 years after the first symptoms manifest. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression in fundamental cellular processes and, post-transcriptionally, the translation levels of target mRNA transcripts. We searched PubMed for studies that examined miRNAs in ALS patients and attempted to group the results in order to find the strongest miRNA candidate for servings as an ALS biomarker. The studies on humans so far have been diverse, yielding considerably heterogeneous results, as they were performed on a wide variety of tissues and subjects. Among the miRNAs that were found consistently deregulated are miR-206, miR-133, miR-149, and miR-338-3p. Additively, the deregulation of some specific miRNAs seems to compose a miRNA expression profile that is specific for ALS. More research is required in order for the scientific community to reach a consensus.
Collapse
|
36
|
Masala A, Sanna S, Esposito S, Rassu M, Galioto M, Zinellu A, Carru C, Carrì MT, Iaccarino C, Crosio C. Epigenetic Changes Associated with the Expression of Amyotrophic Lateral Sclerosis (ALS) Causing Genes. Neuroscience 2018; 390:1-11. [DOI: 10.1016/j.neuroscience.2018.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/11/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
|
37
|
Validation of a Long-Read PCR Assay for Sensitive Detection and Sizing of C9orf72 Hexanucleotide Repeat Expansions. J Mol Diagn 2018; 20:871-882. [PMID: 30138726 DOI: 10.1016/j.jmoldx.2018.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/09/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal degeneration. Accurate determination and quantitation of the repeat length is critical in both clinical and research settings. However, because of the complexity of the C9orf72 expansion with high GC content, large size of repeats, and high rate of insertions/deletions (indels) and sequence variations in the flanking regions, molecular genetic analysis of the locus is challenging. To improve the performance characteristics for clinical testing, we evaluated a commercially available long-read C9orf72 PCR assay for research use only, AmplideX PCR/CE C9orf72 assay (AmplideX-C9), and compared its performance with our existing laboratory-developed C9orf72 expansion procedure. Overall, in comparison to the laboratory-developed C9orf72 expansion procedure, AmplideX-C9 demonstrated a more efficient workflow, greater PCR efficiency for sizing of repeat expansions, and improved peak amplitude with lower DNA input and higher analytic sensitivity. This, in turn, permitted detection of indels in the 3' downstream of the repeat expansion region in expanded alleles, showed a higher success rate with formalin-fixed, paraffin-embedded tissue specimens, and facilitated the assessment of repeat mosaicism. In summary, AmplideX-C9 will not only help to improve clinical testing for C9orf72-associated amyotrophic lateral sclerosis and frontotemporal degeneration but will also be a valuable research tool to better characterize the complexity of expansions and study the effects of indels/sequence variations in the flanking region.
Collapse
|
38
|
Poesen K. The Chromosomal Conformation Signature: A New Kid on the Block in ALS Biomarker Research? EBioMedicine 2018; 33:6-7. [PMID: 30049388 PMCID: PMC6085542 DOI: 10.1016/j.ebiom.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Koen Poesen
- Laboratory for Molecular Neurobiomarker Research (LAMON), Department of Neurosciences, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory Medicine, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium.
| |
Collapse
|
39
|
MicroRNA expression analysis identifies a subset of downregulated miRNAs in ALS motor neuron progenitors. Sci Rep 2018; 8:10105. [PMID: 29973608 PMCID: PMC6031650 DOI: 10.1038/s41598-018-28366-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/18/2018] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurological disorder that is characterized by a progressive degeneration of motor neurons (MNs). The pathomechanism underlying the disease is largely unknown, even though increasing evidence suggests that RNA metabolism, including microRNAs (miRNAs) may play an important role. In this study, human ALS induced pluripotent stem cells were differentiated into MN progenitors and their miRNA expression profiles were compared to those of healthy control cells. We identified 15 downregulated miRNAs in patients’ cells. Gene ontology and molecular pathway enrichment analysis indicated that the predicted target genes of the differentially expressed miRNAs were involved in neurodegeneration-related pathways. Among the 15 examined miRNAs, miR-34a and miR504 appeared particularly relevant due to their involvement in the p53 pathway, synaptic vesicle regulation and general involvement in neurodegenerative diseases. Taken together our results demonstrate that the neurodegenerative phenotype in ALS can be associated with a dysregulation of miRNAs involved in the control of disease-relevant genetic pathways, suggesting that targeting entire gene networks can be a potential strategy to treat complex diseases such as ALS.
Collapse
|
40
|
Buonvicino D, Felici R, Ranieri G, Caramelli R, Lapucci A, Cavone L, Muzzi M, Di Pietro L, Bernardini C, Zwergel C, Valente S, Mai A, Chiarugi A. Effects of Class II-Selective Histone Deacetylase Inhibitor on Neuromuscular Function and Disease Progression in SOD1-ALS Mice. Neuroscience 2018; 379:228-238. [PMID: 29588251 DOI: 10.1016/j.neuroscience.2018.03.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates that transcriptome alterations due to epigenetic deregulation concur to ALS pathogenesis. Accordingly, pan-histone deacetylase (HDAC) inhibitors delay ALS development in mice, but these compounds failed when tested in ALS patients. Possibly, lack of selectivity toward specific classes of HDACs weakens the therapeutic effects of pan-HDAC inhibitors. Here, we tested the effects of the HDAC Class II selective inhibitor MC1568 on disease evolution, motor neuron survival as well as skeletal muscle function in SOD1G93A mice. We report that HDACs did not undergo expression changes during disease evolution in isolated motor neurons of adult mice. Conversely, increase in specific Class II HDACs (-4, -5 and -6) occurs in skeletal muscle of mice with severe neuromuscular impairment. Importantly, treatment with MC1568 causes early improvement of motor performances that vanishes at later stages of disease. Notably, motor improvement is not paralleled by reduced motor neuron degeneration but by increased skeletal muscle electrical potentials, reduced activation of mir206/FGFBP1-dependent muscle reinnervation signaling, and increased muscle expression of myogenic genes.
Collapse
Affiliation(s)
- Daniela Buonvicino
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy.
| | - Roberta Felici
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Giuseppe Ranieri
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Riccardo Caramelli
- Neurophysiology Unit, Department of Neurology and Psychiatry, Azienda Ospedaliera Careggi, Florence, Italy
| | - Andrea Lapucci
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Leonardo Cavone
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Mirko Muzzi
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Lorena Di Pietro
- Institute of Anatomy and Cell Biology, University Cattolica del Sacro Cuore, Rome, Italy
| | - Camilla Bernardini
- Institute of Anatomy and Cell Biology, University Cattolica del Sacro Cuore, Rome, Italy
| | - Clemens Zwergel
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Italy
| | - Sergio Valente
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Italy
| | - Antonello Mai
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Italy
| | - Alberto Chiarugi
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| |
Collapse
|
41
|
Chen K, Bennett SA, Rana N, Yousuf H, Said M, Taaseen S, Mendo N, Meltser SM, Torrente MP. Neurodegenerative Disease Proteinopathies Are Connected to Distinct Histone Post-translational Modification Landscapes. ACS Chem Neurosci 2018; 9:838-848. [PMID: 29243911 DOI: 10.1021/acschemneuro.7b00297] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are devastating neurodegenerative diseases involving the progressive degeneration of neurons. No cure is available for patients diagnosed with these diseases. A prominent feature of both ALS and PD is the accumulation of protein inclusions in the cytoplasm of degenerating neurons; however, the particular proteins constituting these inclusions vary: the RNA-binding proteins TDP-43 and FUS are most notable in ALS, while α-synuclein aggregates into Lewy bodies in PD. In both diseases, genetic causes fail to explain the occurrence of a large proportion of cases, and thus, both are considered mostly sporadic. Despite mounting evidence for a possible role of epigenetics in the occurrence and progression of ALS and PD, epigenetic mechanisms in the context of these diseases remain mostly unexplored. Here we comprehensively delineate histone post-translational modification (PTM) profiles in ALS and PD yeast proteinopathy models. Remarkably, we find distinct changes in histone modification profiles for each. We detect the most striking changes in the context of FUS aggregation: changes in several histone marks support a global decrease in gene transcription. We also detect more modest changes in histone modifications in cells overexpressing TDP-43 or α-synuclein. Our results highlight a great need for the inclusion of epigenetic mechanisms in the study of neurodegeneration. We hope our work will pave the way for the discovery of more effective therapies to treat patients suffering from ALS, PD, and other neurodegenerative diseases.
Collapse
Affiliation(s)
- Karen Chen
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Seth A. Bennett
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
- Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Navin Rana
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Huda Yousuf
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Mohamed Said
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Sadiqa Taaseen
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Natalie Mendo
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Steven M. Meltser
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
| | - Mariana P. Torrente
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States
- Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, New York 10016, United States
| |
Collapse
|
42
|
Mendioroz M, Martínez-Merino L, Blanco-Luquin I, Urdánoz A, Roldán M, Jericó I. Liquid biopsy: a new source of candidate biomarkers in amyotrophic lateral sclerosis. Ann Clin Transl Neurol 2018; 5:763-768. [PMID: 29928659 PMCID: PMC5989775 DOI: 10.1002/acn3.565] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 12/26/2022] Open
Abstract
Noninvasive tests to diagnose and monitor the progression of neurodegenerative disorders have been a challenge for decades. The aim of this study was to explore the feasibility of applying liquid biopsy procedures to patients with a neurodegenerative disease such as amyotrophic lateral sclerosis (ALS). We isolated plasma cell‐free DNA (cfDNA) in 20 ALS patients and 20 controls and used cfDNA to identify a novel differentially methylated mark in RHBDF2 gene in ALS patients compared to controls. Our findings support the notion that liquid biopsy may be applied to living patients as a source of potential epigenetic biomarkers for neurodegenerative disorders.
Collapse
Affiliation(s)
- Maite Mendioroz
- Department of Neurology Complejo Hospitalario de Navarra IdiSNA (Navarra Institute for Health Research) Pamplona Spain.,Neuroepigenetics Laboratory- Navarrabiomed Complejo Hospitalario de Navarra (CHN) Public University of Navarre (UPNA) IdiSNA (Navarra Institute for Health Research Pamplona Spain
| | - Leyre Martínez-Merino
- Department of Neurology Complejo Hospitalario de Navarra IdiSNA (Navarra Institute for Health Research) Pamplona Spain
| | - Idoia Blanco-Luquin
- Neuroepigenetics Laboratory- Navarrabiomed Complejo Hospitalario de Navarra (CHN) Public University of Navarre (UPNA) IdiSNA (Navarra Institute for Health Research Pamplona Spain
| | - Amaya Urdánoz
- Neuroepigenetics Laboratory- Navarrabiomed Complejo Hospitalario de Navarra (CHN) Public University of Navarre (UPNA) IdiSNA (Navarra Institute for Health Research Pamplona Spain
| | - Miren Roldán
- Neuroepigenetics Laboratory- Navarrabiomed Complejo Hospitalario de Navarra (CHN) Public University of Navarre (UPNA) IdiSNA (Navarra Institute for Health Research Pamplona Spain
| | - Ivonne Jericó
- Department of Neurology Complejo Hospitalario de Navarra IdiSNA (Navarra Institute for Health Research) Pamplona Spain
| |
Collapse
|
43
|
Lehmer C, Oeckl P, Weishaupt JH, Volk AE, Diehl-Schmid J, Schroeter ML, Lauer M, Kornhuber J, Levin J, Fassbender K, Landwehrmeyer B, Schludi MH, Arzberger T, Kremmer E, Flatley A, Feederle R, Steinacker P, Weydt P, Ludolph AC, Edbauer D, Otto M. Poly-GP in cerebrospinal fluid links C9orf72-associated dipeptide repeat expression to the asymptomatic phase of ALS/FTD. EMBO Mol Med 2018; 9:859-868. [PMID: 28408402 PMCID: PMC5494528 DOI: 10.15252/emmm.201607486] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The C9orf72 GGGGCC repeat expansion is a major cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). Non‐conventional repeat translation results in five dipeptide repeat proteins (DPRs), but their clinical utility, overall significance, and temporal course in the pathogenesis of c9ALS/FTD are unclear, although animal models support a gain‐of‐function mechanism. Here, we established a poly‐GP immunoassay from cerebrospinal fluid (CSF) to identify and characterize C9orf72 patients. Significant poly‐GP levels were already detectable in asymptomatic C9orf72 mutation carriers compared to healthy controls and patients with other neurodegenerative diseases. The poly‐GP levels in asymptomatic carriers were similar to symptomatic c9ALS/FTD cases. Poly‐GP levels were not correlated with disease onset, clinical scores, and CSF levels of neurofilaments as a marker for axonal damage. Poly‐GP determination in CSF revealed a C9orf72 mutation carrier in our cohort and may thus be used as a diagnostic marker in addition to genetic testing to screen patients. Presymptomatic expression of poly‐GP and likely other DPR species may contribute to disease onset and thus represents an alluring therapeutic target.
Collapse
Affiliation(s)
- Carina Lehmer
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany
| | - Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| | | | - Alexander E Volk
- Institute of Human Genetics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, Technical University of Munich, München, Germany
| | - Matthias L Schroeter
- Clinic for Cognitive Neurology, University Clinic Leipzig, Leipzig, Germany.,Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Martin Lauer
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Johannes Levin
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany.,Department of Neurology, Ludwig-Maximilians-University Universität München, Munich, Germany
| | | | | | | | - Martin H Schludi
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany
| | - Thomas Arzberger
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany.,Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Regina Feederle
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany.,Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich, Germany
| | | | - Patrick Weydt
- Department of Neurology, Ulm University Hospital, Ulm, Germany.,Department of Neurodegenerative Diseases and Gerontopsychiatry, Bonn University Hospital, Bonn, Germany
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), Munich, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Ulm, Germany
| |
Collapse
|
44
|
Starr A, Sattler R. Synaptic dysfunction and altered excitability in C9ORF72 ALS/FTD. Brain Res 2018; 1693:98-108. [PMID: 29453960 DOI: 10.1016/j.brainres.2018.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 02/08/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by a progressive degeneration of upper and lower motor neurons, resulting in fatal paralysis due to denervation of the muscle. Due to genetic, pathological and symptomatic overlap, ALS is now considered a spectrum disease together with frontotemporal dementia (FTD), the second most common cause of dementia in individuals under the age of 65. Interestingly, in both diseases, there is a large prevalence of RNA binding proteins (RBPs) that are mutated and considered disease-causing, or whose dysfunction contribute to disease pathogenesis. The most common shared genetic mutation in ALS/FTD is a hexanucleuotide repeat expansion within intron 1 of C9ORF72 (C9). Three potentially overlapping, putative toxic mechanisms have been proposed: loss of function due to haploinsufficient expression of the C9ORF72 mRNA, gain of function of the repeat RNA aggregates, or RNA foci, and repeat-associated non-ATG-initiated translation (RAN) of the repeat RNA into toxic dipeptide repeats (DPRs). Regardless of the causative mechanism, disease symptoms are ultimately caused by a failure of neurotransmission in three regions: the brain, the spinal cord, and the neuromuscular junction. Here, we review C9 ALS/FTD-associated synaptic dysfunction and aberrant neuronal excitability in these three key regions, focusing on changes in morphology and synapse formation, excitability, and excitotoxicity in patients, animal models, and in vitro models. We compare these deficits to those seen in other forms of ALS and FTD in search of shared pathways, and discuss the potential targeting of synaptic dysfunctions for therapeutic intervention in ALS and FTD patients.
Collapse
Affiliation(s)
- Alexander Starr
- Division of Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, United States
| | - Rita Sattler
- Division of Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, United States.
| |
Collapse
|
45
|
Ebbert MTW, Ross CA, Pregent LJ, Lank RJ, Zhang C, Katzman RB, Jansen-West K, Song Y, da Rocha EL, Palmucci C, Desaro P, Robertson AE, Caputo AM, Dickson DW, Boylan KB, Rademakers R, Ordog T, Li H, Belzil VV. Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease. Acta Neuropathol 2017; 134:715-728. [PMID: 28808785 DOI: 10.1007/s00401-017-1760-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/20/2017] [Accepted: 08/02/2017] [Indexed: 12/13/2022]
Abstract
We previously found C9orf72-associated (c9ALS) and sporadic amyotrophic lateral sclerosis (sALS) brain transcriptomes comprise thousands of defects, among which, some are likely key contributors to ALS pathogenesis. We have now generated complementary methylome data and combine these two data sets to perform a comprehensive "multi-omic" analysis to clarify the molecular mechanisms initiating RNA misregulation in ALS. We found that c9ALS and sALS patients have generally distinct but overlapping methylome profiles, and that the c9ALS- and sALS-affected genes and pathways have similar biological functions, indicating conserved pathobiology in disease. Our results strongly implicate SERPINA1 in both C9orf72 repeat expansion carriers and non-carriers, where expression levels are greatly increased in both patient groups across the frontal cortex and cerebellum. SERPINA1 expression is particularly pronounced in C9orf72 repeat expansion carriers for both brain regions, where SERPINA1 levels are strictly down regulated across most human tissues, including the brain, except liver and blood, and are not measurable in E18 mouse brain. The altered biological networks we identified contain critical molecular players known to contribute to ALS pathology, which also interact with SERPINA1. Our comprehensive combined methylation and transcription study identifies new genes and highlights that direct genetic and epigenetic changes contribute to c9ALS and sALS pathogenesis.
Collapse
Affiliation(s)
- Mark T W Ebbert
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Christian A Ross
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Luc J Pregent
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Rebecca J Lank
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Rebecca B Katzman
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Yuping Song
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Edroaldo Lummertz da Rocha
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Stem Cell Transplantation Program, Department of Pediatric Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carla Palmucci
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Pamela Desaro
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Amelia E Robertson
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Ana M Caputo
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Physiology and Medical Engineering, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Veronique V Belzil
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| |
Collapse
|
46
|
Coppedè F, Stoccoro A, Mosca L, Gallo R, Tarlarini C, Lunetta C, Marocchi A, Migliore L, Penco S. Increase in DNA methylation in patients with amyotrophic lateral sclerosis carriers of not fully penetrant SOD1 mutations. Amyotroph Lateral Scler Frontotemporal Degener 2017; 19:93-101. [PMID: 28859526 DOI: 10.1080/21678421.2017.1367401] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE More than 180 different superoxide dismutase 1 (SOD1) mutations have been described to date in amyotrophic lateral sclerosis (ALS) patients, including not completely penetrant ones leading to phenotypic heterogeneity among carriers. We collected DNA samples from five ALS families with not fully penetrant SOD1 mutations (p.Asn65Ser, p.Gly72Ser, p.Gly93Asp, and p.Gly130_Glu133del) searching for epigenetic differences among ALS patients, asymptomatic/paucisymptomatic carriers and non-carrier family members. METHODS Global DNA methylation levels (5-methylcytosine levels) were determined in blood DNA samples with an enzyme-linked immunosorbent assay (ELISA), and the methylation analysis of SOD1, FUS, TARDBP and C9orf72 genes was performed using Methylation-Sensitive High-Resolution Melting (MS-HRM) technique. RESULTS Global DNA methylation levels were significantly higher in blood DNA of ALS patients than in asymptomatic/paucisymptomatic carriers or family members non-carriers of SOD1 mutations, and a positive correlation between global DNA methylation levels and disease duration (months) was observed. SOD1, FUS, TARDBP and C9orf72 gene promoters were demethylated in all subjects. CONCLUSIONS The present study suggests that global changes in DNA methylation might contribute to the ALS phenotype in carriers of not fully penetrant SOD1 mutations, thus reinforcing the role of epigenetic factors in modulating the phenotypic expression of the disease.
Collapse
Affiliation(s)
- Fabio Coppedè
- a Department of Translational Research and New Technologies in Medicine and Surgery , Section of Medical Genetics, University of Pisa , Pisa , Italy
| | - Andrea Stoccoro
- a Department of Translational Research and New Technologies in Medicine and Surgery , Section of Medical Genetics, University of Pisa , Pisa , Italy.,b Doctoral School in Genetics Oncology and Clinical Medicine, Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Lorena Mosca
- c Medical Genetics Unit, Department of Laboratory Medicine , ASST Grande Ospedale Metropolitano Niguarda , Milan , Italy , and
| | - Roberta Gallo
- a Department of Translational Research and New Technologies in Medicine and Surgery , Section of Medical Genetics, University of Pisa , Pisa , Italy
| | - Claudia Tarlarini
- c Medical Genetics Unit, Department of Laboratory Medicine , ASST Grande Ospedale Metropolitano Niguarda , Milan , Italy , and
| | - Christian Lunetta
- d NEuroMuscular Omnicentre (NEMO) , ASST Grande Ospedale Metropolitano Niguarda , Milan , Italy
| | - Alessandro Marocchi
- c Medical Genetics Unit, Department of Laboratory Medicine , ASST Grande Ospedale Metropolitano Niguarda , Milan , Italy , and
| | - Lucia Migliore
- a Department of Translational Research and New Technologies in Medicine and Surgery , Section of Medical Genetics, University of Pisa , Pisa , Italy
| | - Silvana Penco
- c Medical Genetics Unit, Department of Laboratory Medicine , ASST Grande Ospedale Metropolitano Niguarda , Milan , Italy , and
| |
Collapse
|
47
|
Taskesen E, Mishra A, van der Sluis S, Ferrari R, Veldink JH, van Es MA, Smit AB, Posthuma D, Pijnenburg Y. Susceptible genes and disease mechanisms identified in frontotemporal dementia and frontotemporal dementia with Amyotrophic Lateral Sclerosis by DNA-methylation and GWAS. Sci Rep 2017; 7:8899. [PMID: 28827549 PMCID: PMC5567187 DOI: 10.1038/s41598-017-09320-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Frontotemporal dementia (FTD) is a neurodegenerative disorder predominantly affecting the frontal and temporal lobes. Genome-wide association studies (GWAS) on FTD identified only a few risk loci. One of the possible explanations is that FTD is clinically, pathologically, and genetically heterogeneous. An important open question is to what extent epigenetic factors contribute to FTD and whether these factors vary between FTD clinical subgroup. We compared the DNA-methylation levels of FTD cases (n = 128), and of FTD cases with Amyotrophic Lateral Sclerosis (FTD-ALS; n = 7) to those of unaffected controls (n = 193), which resulted in 14 and 224 candidate genes, respectively. Cluster analysis revealed significant class separation of FTD-ALS from controls. We could further specify genes with increased susceptibility for abnormal gene-transcript behavior by jointly analyzing DNA-methylation levels with the presence of mutations in a GWAS FTD-cohort. For FTD-ALS, this resulted in 9 potential candidate genes, whereas for FTD we detected 1 candidate gene (ELP2). Independent validation-sets confirmed the genes DLG1, METTL7A, KIAA1147, IGHMBP2, PCNX, UBTD2, WDR35, and ELP2/SLC39A6 among others. We could furthermore demonstrate that genes harboring mutations and/or displaying differential DNA-methylation, are involved in common pathways, and may therefore be critical for neurodegeneration in both FTD and FTD-ALS.
Collapse
Affiliation(s)
- E Taskesen
- VU University Amsterdam, Center for Neurogenomics and Cognitive Research, Complex Trait Genetics (CTG), Amsterdam Neuroscience, Amsterdam, The Netherlands.,VU University Medical Center (VUMC), Alzheimer Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - A Mishra
- VU University Amsterdam, Center for Neurogenomics and Cognitive Research, Complex Trait Genetics (CTG), Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - S van der Sluis
- VU University Amsterdam, Center for Neurogenomics and Cognitive Research, Complex Trait Genetics (CTG), Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - R Ferrari
- UCL London, Institute of Neurology, Department of Molecular Neuroscience, London, UK
| | | | - J H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M A van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A B Smit
- VU University Amsterdam, Center for Neurogenomics and Cognitive Research, Department of Molecular and Cellular Neurobiology (MCN), Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - D Posthuma
- VU University Amsterdam, Center for Neurogenomics and Cognitive Research, Complex Trait Genetics (CTG), Amsterdam Neuroscience, Amsterdam, The Netherlands.,VU University Medical Center (VUMC), Alzheimer Center, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Y Pijnenburg
- VU University Medical Center (VUMC), Alzheimer Center, Amsterdam Neuroscience, Amsterdam, The Netherlands.
| |
Collapse
|
48
|
Young PE, Kum Jew S, Buckland ME, Pamphlett R, Suter CM. Epigenetic differences between monozygotic twins discordant for amyotrophic lateral sclerosis (ALS) provide clues to disease pathogenesis. PLoS One 2017; 12:e0182638. [PMID: 28797086 PMCID: PMC5552194 DOI: 10.1371/journal.pone.0182638] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/22/2017] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating late-onset neurodegenerative disorder in which only a small proportion of patients carry an identifiable causative genetic lesion. Despite high heritability estimates, a genetic etiology for most sporadic ALS remains elusive. Here we report the epigenetic profiling of five monozygotic twin pairs discordant for ALS, four with classic ALS and one with the progressive muscular atrophy ALS variant, in whom previous whole genome sequencing failed to uncover a genetic basis for their disease discordance. By studying cytosine methylation patterns in peripheral blood DNA we identified thousands of large between-twin differences at individual CpGs. While the specific sites of differences were mostly idiosyncratic to a twin pair, a proportion involving GABA signalling were common to all ALS individuals. For both idiosyncratic and common sites the differences occurred within genes and pathways related to neurobiological functions or dysfunctions, some of particular relevance to ALS such as glutamate metabolism and the Golgi apparatus. All four classic ALS patients were epigenetically older than their unaffected co-twins, suggesting accelerated aging in multiple tissues in this disease. In conclusion, widespread changes in methylation patterns were found in ALS-affected co-twins, consistent with an epigenetic contribution to disease. These DNA methylation findings could be used to develop blood-based ALS biomarkers, gain insights into disease pathogenesis, and provide a reference for future large-scale ALS epigenetic studies.
Collapse
Affiliation(s)
- Paul E. Young
- Division of Molecular Structural and Computational Biology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Stephen Kum Jew
- Discipline of Pathology, Sydney Medical School, Brain and Mind Research Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Michael E. Buckland
- Discipline of Pathology, Sydney Medical School, Brain and Mind Research Institute, The University of Sydney, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Roger Pamphlett
- Discipline of Pathology, Sydney Medical School, Brain and Mind Research Institute, The University of Sydney, Camperdown, NSW, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- * E-mail: (CMS); (RP)
| | - Catherine M. Suter
- Division of Molecular Structural and Computational Biology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia
- * E-mail: (CMS); (RP)
| |
Collapse
|
49
|
Lapucci A, Cavone L, Buonvicino D, Felici R, Gerace E, Zwergel C, Valente S, Mai A, Chiarugi A. Effect of Class II HDAC inhibition on glutamate transporter expression and survival in SOD1-ALS mice. Neurosci Lett 2017; 656:120-125. [PMID: 28732762 DOI: 10.1016/j.neulet.2017.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/13/2022]
Abstract
Transcriptional deregulation emerges as a key pathogenetic mechanism in ALS pathogenesis, and non-class-specific histone deacetylase (HDACs) inhibitors proved of therapeutic efficacy in preclinical models of ALS. When tested in patients, however, these drugs failed, probably because of a lack of selectivity toward pathogenetic HDACs. Here, we studied the effects of MC1568, an inhibitor of Class-II HDACs which have been reported to contribute to ALS pathogenesis. We focused on transcriptional regulation of glutamate transporter EAAT2, whose reduced expression may contribute to motor neuron degeneration in ALS. We report that MC1568 highly increased EAAT2 transcripts in primary cultures of mouse glia, but these increases did not correlate with increased glutamate uptake capacity. Accordingly, we found that MC1568 augmented protein expression of EAAT2 together with its sumoylation, a post-translational modification typically altering protein function and localization. When tested in SOD1G93A mice, however, MC1568 fully restored the reduced spinal cord expression of EAAT2 and glutamate uptake up to control levels. A prolonged treatment with MC1568 (from onset to end stage) was unable to prolong survival of mice. Data reveal a key role of Class-II HDACs in expression and function of glutamate transporter, further corroborating preclinical and clinical evidence that the sole restoration of glutamate uptake is not of therapeutic relevance to ALS therapy.
Collapse
Affiliation(s)
- Andrea Lapucci
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Leonardo Cavone
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Daniela Buonvicino
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy.
| | - Roberta Felici
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Elisabetta Gerace
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Italy
| | - Antonello Mai
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Italy
| | - Alberto Chiarugi
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Italy
| |
Collapse
|
50
|
Giannoccaro MP, Bartoletti-Stella A, Piras S, Pession A, De Massis P, Oppi F, Stanzani-Maserati M, Pasini E, Baiardi S, Avoni P, Parchi P, Liguori R, Capellari S. Multiple variants in families with amyotrophic lateral sclerosis and frontotemporal dementia related to C9orf72 repeat expansion: further observations on their oligogenic nature. J Neurol 2017. [PMID: 28620717 DOI: 10.1007/s00415-017-8540-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The C9orf72 repeat expansion (RE) is one of the most frequent causative mutations of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, it is still unclear how the C9orf72 RE can lead to a heterogeneous phenotype. Several reports have shown the coexistence of mutations in multiple ALS/FTD causative genes in the same family, suggesting an oligogenic etiology for ALS and FTD. Our aim was to investigate this phenomenon in an Italian group of ALS/FTD pedigrees carrying the C9orf72 RE. We included 11 subjects from 11 pedigrees with ALS/FTD and the C9orf72 RE. Mutation screening of FUS, SOD1 and TARDBP genes was performed by direct sequencing. A dementia-specific custom-designed targeted next-generation sequencing panel was used for screening dementia-associated genes mutations. We found genetic variants in additional ALS or dementia-related genes in four pedigrees, including the p.V47A variant in the TYROBP gene. As a group, double mutation carriers displayed a tendency toward a younger age at onset and a higher frequency of positive familiar history and of parkinsonism. Our observation supports the hypothesis that the co-presence of mutations in different genes may be relevant for the clinical expression of ALS/FTD and of their oligogenic nature.
Collapse
Affiliation(s)
- Maria Pia Giannoccaro
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.
| | - Anna Bartoletti-Stella
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,Dipartimento Neuroscienze, psicologia, area del farmaco e salute del bambino, Università di Firenze, Firenze, Italy
| | - Silvia Piras
- IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | - Annalisa Pession
- UOC Anatomia patologica, Dipartimento di Scienze Oncologiche, via Altura, 3, 40136, Bologna, Italy
| | | | - Federico Oppi
- IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | | | - Elena Pasini
- IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | - Simone Baiardi
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Patrizia Avoni
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | - Piero Parchi
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | - Rocco Liguori
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy
| | - Sabina Capellari
- UOC Clinica Neurologica, Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy. .,IRCCS Istituto delle Scienze Neurologiche, UOC Clinica Neurologica, Ospedale Bellaria, via Altura, 3, Bologna, Italy.
| |
Collapse
|