1
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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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2
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Mosbach V, Puccio H. A multiple animal and cellular models approach to study frataxin deficiency in Friedreich Ataxia. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119809. [PMID: 39134123 DOI: 10.1016/j.bbamcr.2024.119809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Friedreich's ataxia (FA) is one of the most frequent inherited recessive ataxias characterized by a progressive sensory and spinocerebellar ataxia. The main causative mutation is a GAA repeat expansion in the first intron of the frataxin (FXN) gene which leads to a transcriptional silencing of the gene resulting in a deficit in FXN protein. The nature of the mutation (an unstable GAA expansion), as well as the multi-systemic nature of the disease (with neural and non-neural sites affected) make the generation of models for Friedreich's ataxia quite challenging. Over the years, several cellular and animal models for FA have been developed. These models are all complementary and possess their own strengths to investigate different aspects of the disease, such as the epigenetics of the locus or the pathophysiology of the disease, as well as being used to developed novel therapeutic approaches. This review will explore the recent advancements in the different mammalian models developed for FA.
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Affiliation(s)
- Valentine Mosbach
- Institut NeuroMyoGene-PGNM UCBL-CNRS UMR5261 INSERM U1315, Lyon, France
| | - Hélène Puccio
- Institut NeuroMyoGene-PGNM UCBL-CNRS UMR5261 INSERM U1315, Lyon, France.
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3
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Nishiyama M, Kalambogias J, Imai F, Yang E, Lang S, de Nooij JC, Yoshida Y. Anatomical and functional analysis of the corticospinal tract in an FRDA mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601178. [PMID: 39005321 PMCID: PMC11244874 DOI: 10.1101/2024.06.28.601178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Friedreich's ataxia (FRDA) is one of the most common hereditary ataxias. It is caused by a GAA repeat in the first intron of the FXN gene, which encodes an essential mitochondrial protein. Patients suffer from progressive motor dysfunction due to the degeneration of mechanoreceptive and proprioceptive neurons in dorsal root ganglia (DRG) and cerebellar dentate nucleus neurons, especially at early disease stages. Postmortem analyses of FRDA patients also indicate pathological changes in motor cortex including in the projection neurons that give rise to the cortical spinal tract (CST). Yet, it remains poorly understood how early in the disease cortical spinal neurons (CSNs) show these alterations, or whether CSN/CST pathology resembles the abnormalities observed in other tissues affected by FXN loss. To address these questions, we examined CSN driven motor behaviors and pathology in the YG8JR FRDA mouse model. We find that FRDA mice show impaired motor skills, exhibit significant reductions in CSN functional output, and, among other pathological changes, show abnormal mitochondrial distributions in CSN neurons and CST axonal tracts. Moreover, some of these alterations were observed as early as two months of age, suggesting that CSN/CST pathology may be an earlier event in FRDA disease than previously appreciated. These studies warrant a detailed mechanistic understanding of how FXN loss impacts CSN health and functionality.
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Affiliation(s)
- Misa Nishiyama
- Burke Neurological Institute, White Plains, New York, United States
| | - John Kalambogias
- Burke Neurological Institute, White Plains, New York, United States
- Department of Neurology, Columbia University, New York, NY, USA
| | - Fumiyasu Imai
- Burke Neurological Institute, White Plains, New York, United States
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
| | - Emily Yang
- Burke Neurological Institute, White Plains, New York, United States
| | - Sonia Lang
- Burke Neurological Institute, White Plains, New York, United States
| | | | - Yutaka Yoshida
- Burke Neurological Institute, White Plains, New York, United States
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
- Neural Circuit Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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4
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Dong YN, Mercado-Ayón E, Coulman J, Flatley L, Ngaba LV, Adeshina MW, Lynch DR. The Regulation of the Disease-Causing Gene FXN. Cells 2024; 13:1040. [PMID: 38920668 PMCID: PMC11202134 DOI: 10.3390/cells13121040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease caused in almost all patients by expanded guanine-adenine-adenine (GAA) trinucleotide repeats within intron 1 of the FXN gene. This results in a relative deficiency of frataxin, a small nucleus-encoded mitochondrial protein crucial for iron-sulfur cluster biogenesis. Currently, there is only one medication, omaveloxolone, available for FRDA patients, and it is limited to patients 16 years of age and older. This necessitates the development of new medications. Frataxin restoration is one of the main strategies in potential treatment options as it addresses the root cause of the disease. Comprehending the control of frataxin at the transcriptional, post-transcriptional, and post-translational stages could offer potential therapeutic approaches for addressing the illness. This review aims to provide a general overview of the regulation of frataxin and its implications for a possible therapeutic treatment of FRDA.
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Affiliation(s)
- Yi Na Dong
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Jennifer Coulman
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Liam Flatley
- The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lucie Vanessa Ngaba
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miniat W. Adeshina
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David R. Lynch
- Departments of Pediatrics and Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571345. [PMID: 38168171 PMCID: PMC10760133 DOI: 10.1101/2023.12.13.571345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.
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Affiliation(s)
- Connor J. Maltby
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yomira Palacios
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Muiños
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- UM SMART Undergraduate Summer Program, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Suárez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Asher
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vikram Khurana
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Anke A. Dijkstra
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
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6
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Krasilnikova MM, Humphries CL, Shinsky EM. Friedreich's ataxia: new insights. Emerg Top Life Sci 2023; 7:313-323. [PMID: 37698160 DOI: 10.1042/etls20230017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Friedreich ataxia (FRDA) is an inherited disease that is typically caused by GAA repeat expansion within the first intron of the FXN gene coding for frataxin. This results in the frataxin deficiency that affects mostly muscle, nervous, and cardiovascular systems with progressive worsening of the symptoms over the years. This review summarizes recent progress that was achieved in understanding of molecular mechanism of the disease over the last few years and latest treatment strategies focused on overcoming the frataxin deficiency.
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Affiliation(s)
- Maria M Krasilnikova
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
| | - Casey L Humphries
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
| | - Emily M Shinsky
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, U.S.A
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7
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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8
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Maheshwari S, Vilema-Enríquez G, Wade-Martins R. Patient-derived iPSC models of Friedreich ataxia: a new frontier for understanding disease mechanisms and therapeutic application. Transl Neurodegener 2023; 12:45. [PMID: 37726850 PMCID: PMC10510273 DOI: 10.1186/s40035-023-00376-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Friedreich ataxia (FRDA) is a rare genetic multisystem disorder caused by a pathological GAA trinucleotide repeat expansion in the FXN gene. The numerous drawbacks of historical cellular and rodent models of FRDA have caused difficulty in performing effective mechanistic and translational studies to investigate the disease. The recent discovery and subsequent development of induced pluripotent stem cell (iPSC) technology provides an exciting platform to enable enhanced disease modelling for studies of rare genetic diseases. Utilising iPSCs, researchers have created phenotypically relevant and previously inaccessible cellular models of FRDA. These models enable studies of the molecular mechanisms underlying GAA-induced pathology, as well as providing an exciting tool for the screening and testing of novel disease-modifying therapies. This review explores how the use of iPSCs to study FRDA has developed over the past decade, as well as discussing the enormous therapeutic potentials of iPSC-derived models, their current limitations and their future direction within the field of FRDA research.
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Affiliation(s)
- Saumya Maheshwari
- Department of Physiology, Anatomy and Genetics, Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Gabriela Vilema-Enríquez
- Department of Physiology, Anatomy and Genetics, Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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9
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Lam C, Gilliam KM, Rodden LN, Schadt KA, Lynch DR, Bidichandani S. FXN gene methylation determines carrier status in Friedreich ataxia. J Med Genet 2023; 60:797-800. [PMID: 36635061 PMCID: PMC10423546 DOI: 10.1136/jmg-2022-108742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
BACKGROUND Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat (GAA-TRE) in intron 1 of the FXN gene. Some patients are compound heterozygous for the GAA-TRE and another FXN pathogenic variant. Detection of the GAA-TRE in the heterozygous state, occasionally technically challenging, is essential for diagnosing compound heterozygotes and asymptomatic carriers. OBJECTIVE We explored if the FRDA differentially methylated region (FRDA-DMR) in intron 1, which is hypermethylated in cis with the GAA-TRE, effectively detects heterozygous GAA-TRE. METHODS FXN DNA methylation was assayed by targeted bisulfite deep sequencing using the Illumina platform. RESULTS FRDA-DMR methylation effectively identified a cohort of known heterozygous carriers of the GAA-TRE. In an individual with clinical features of FRDA, commercial testing showed a paternally inherited pathogenic FXN initiation codon variant but no GAA-TRE. Methylation in the FRDA-DMR effectively identified the proband, his mother and various maternal relatives as heterozygous carriers of the GAA-TRE, thus confirming the diagnosis of FRDA. CONCLUSION FXN DNA methylation reliably detects the GAA-TRE in the heterozygous state and offers a robust alternative strategy to diagnose FRDA due to compound heterozygosity and to identify asymptomatic heterozygous carriers of the GAA-TRE.
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Affiliation(s)
- Christina Lam
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Kaitlyn M Gilliam
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Layne N Rodden
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kimberly A Schadt
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David R Lynch
- Department of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sanjay Bidichandani
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Department of Biochemistry & Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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10
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Rafehi H, Read J, Szmulewicz DJ, Davies KC, Snell P, Fearnley LG, Scott L, Thomsen M, Gillies G, Pope K, Bennett MF, Munro JE, Ngo KJ, Chen L, Wallis MJ, Butler EG, Kumar KR, Wu KHC, Tomlinson SE, Tisch S, Malhotra A, Lee-Archer M, Dolzhenko E, Eberle MA, Roberts LJ, Fogel BL, Brüggemann N, Lohmann K, Delatycki MB, Bahlo M, Lockhart PJ. An intronic GAA repeat expansion in FGF14 causes the autosomal-dominant adult-onset ataxia SCA50/ATX-FGF14. Am J Hum Genet 2023; 110:105-119. [PMID: 36493768 PMCID: PMC9892775 DOI: 10.1016/j.ajhg.2022.11.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/19/2022] [Indexed: 12/13/2022] Open
Abstract
Adult-onset cerebellar ataxias are a group of neurodegenerative conditions that challenge both genetic discovery and molecular diagnosis. In this study, we identified an intronic (GAA) repeat expansion in fibroblast growth factor 14 (FGF14). Genetic analysis of 95 Australian individuals with adult-onset ataxia identified four (4.2%) with (GAA)>300 and a further nine individuals with (GAA)>250. PCR and long-read sequence analysis revealed these were pure (GAA) repeats. In comparison, no control subjects had (GAA)>300 and only 2/311 control individuals (0.6%) had a pure (GAA)>250. In a German validation cohort, 9/104 (8.7%) of affected individuals had (GAA)>335 and a further six had (GAA)>250, whereas 10/190 (5.3%) control subjects had (GAA)>250 but none were (GAA)>335. The combined data suggest (GAA)>335 are disease causing and fully penetrant (p = 6.0 × 10-8, OR = 72 [95% CI = 4.3-1,227]), while (GAA)>250 is likely pathogenic with reduced penetrance. Affected individuals had an adult-onset, slowly progressive cerebellar ataxia with variable features including vestibular impairment, hyper-reflexia, and autonomic dysfunction. A negative correlation between age at onset and repeat length was observed (R2 = 0.44, p = 0.00045, slope = -0.12) and identification of a shared haplotype in a minority of individuals suggests that the expansion can be inherited or generated de novo during meiotic division. This study demonstrates the power of genome sequencing and advanced bioinformatic tools to identify novel repeat expansions via model-free, genome-wide analysis and identifies SCA50/ATX-FGF14 as a frequent cause of adult-onset ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Read
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - David J. Szmulewicz
- Cerebellar Ataxia Clinic, Eye and Ear Hospital, Melbourne, VIC, Australia,The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Kayli C. Davies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam G. Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Liam Scott
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia
| | - Mark F. Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Kathie J. Ngo
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Luke Chen
- Alfred Hospital, Department of Neurology, Melbourne, VIC, Australia
| | - Mathew J. Wallis
- Clinical Genetics Service, Austin Health, Melbourne, VIC, Australia,Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | | | - Kishore R. Kumar
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord, NSW, Australia,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kathy HC. Wu
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Clinical Genomics, St Vincent’s Hospital, Darlinghurst, NSW, Australia,Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,School of Medicine, University of Notre Dame, Sydney, NSW, Australia
| | - Susan E. Tomlinson
- School of Medicine, University of Notre Dame, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Stephen Tisch
- School of Medicine, University of New South Wales, Sydney, NSW, Australia,Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
| | - Abhishek Malhotra
- Department of Neuroscience, University Hospital Geelong, Geelong, VIC, Australia
| | - Matthew Lee-Archer
- Launceston General Hospital, Tasmanian Health Service, Launceston, TAS, Australia
| | | | | | - Leslie J. Roberts
- Department of Neurology and Neurological Research, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Brent L. Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA,Departments of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Martin B. Delatycki
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Victorian Clinical Genetics Services, Melbourne, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Paul J. Lockhart
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, VIC, Australia,Corresponding author
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11
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Ye M, Chen EV, Pfeil SH, Martin KN, Atrafi T, Yun S, Martinez Z, Yatsunyk LA. Homopurine guanine-rich sequences in complex with N-methyl mesoporphyrin IX form parallel G-quadruplex dimers and display a unique symmetry tetrad. Bioorg Med Chem 2023; 77:117112. [PMID: 36508994 PMCID: PMC9812923 DOI: 10.1016/j.bmc.2022.117112] [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: 09/20/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by π-π stacking of G-tetrads. GQs are important in many biological processes, which makes them promising therapeutic targets. We identified a 42-nucleotide long, purine-only G-rich sequence from human genome, which contains eight G-stretches connected by A and AAAA loops. We divided this sequence into five unique segments, four guanine stretches each, named GA1-5. In order to investigate the role of adenines in GQ structure formation, we performed biophysical and X-ray crystallographic studies of GA1-5 and their complexes with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). Our data indicate that all variants form parallel GQs whose stability depends on the number of flexible AAAA loops. GA1-3 bind NMM with 1:1 stoichiometry. The Ka for GA1 and GA3 is modest, ∼0.3 μM -1, and that for GA2 is significantly higher, ∼1.2 μM -1. NMM stabilizes GA1-3 by 14.6, 13.1, and 7.0 °C, respectively, at 2 equivalents. We determined X-ray crystal structures of GA1-NMM (1.98 Å resolution) and GA3-NMM (2.01 Å). The structures confirm the parallel topology of GQs with all adenines forming loops and display NMM binding at the 3' G-tetrad. Both complexes dimerize through the 5' interface. We observe two novel structural features: 1) a 'symmetry tetrad' at the dimer interface, which is formed by two guanines from each GQ monomer and 2) a NMM dimer in GA1-NMM. Our structural work confirms great flexibility of adenines as structural elements in GQ formation and contributes greatly to our understanding of the structural diversity of GQs and their modes of interaction with small molecule ligands.
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Affiliation(s)
- Ming Ye
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Erin V Chen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Shawn H Pfeil
- Department of Physics, West Chester University, West Chester, PA 19383, United States
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Tamanaa Atrafi
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Sara Yun
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Zahara Martinez
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States.
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12
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Li Y, Li J, Wang J, Zhang S, Giles K, Prakash TP, Rigo F, Napierala JS, Napierala M. Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to the Frataxin transcriptional deficit in Friedreich's ataxia. Hum Mol Genet 2022; 31:3539-3557. [PMID: 35708503 PMCID: PMC9558844 DOI: 10.1093/hmg/ddac134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 06/05/2022] [Indexed: 11/18/2022] Open
Abstract
Frataxin deficiency in Friedreich's ataxia results from transcriptional downregulation of the FXN gene caused by expansion of the intronic trinucleotide guanine-adenine-adenine (GAA) repeats. We used multiple transcriptomic approaches to determine the molecular mechanism of transcription inhibition caused by long GAAs. We uncovered that transcription of FXN in patient cells is prematurely terminated upstream of the expanded repeats leading to the formation of a novel, truncated and stable RNA. This FXN early terminated transcript (FXN-ett) undergoes alternative, non-productive splicing and does not contribute to the synthesis of functional frataxin. The level the FXN-ett RNA directly correlates with the length of the longer of the two expanded GAA tracts. Targeting GAAs with antisense oligonucleotides or excision of the repeats eliminates the transcription impediment, diminishes expression of the aberrant FXN-ett, while increasing levels of FXN mRNA and frataxin. Non-productive transcription may represent a common phenomenon and attractive therapeutic target in diseases caused by repeat-mediated transcription aberrations.
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Affiliation(s)
- Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Siyuan Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Keith Giles
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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13
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Masnovo C, Lobo AF, Mirkin SM. Replication dependent and independent mechanisms of GAA repeat instability. DNA Repair (Amst) 2022; 118:103385. [PMID: 35952488 PMCID: PMC9675320 DOI: 10.1016/j.dnarep.2022.103385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/20/2022]
Abstract
Trinucleotide repeat instability is a driver of human disease. Large expansions of (GAA)n repeats in the first intron of the FXN gene are the cause Friedreich's ataxia (FRDA), a progressive degenerative disorder which cannot yet be prevented or treated. (GAA)n repeat instability arises during both replication-dependent processes, such as cell division and intergenerational transmission, as well as in terminally differentiated somatic tissues. Here, we provide a brief historical overview on the discovery of (GAA)n repeat expansions and their association to FRDA, followed by recent advances in the identification of triplex H-DNA formation and replication fork stalling. The main body of this review focuses on the last decade of progress in understanding the mechanism of (GAA)n repeat instability during DNA replication and/or DNA repair. We propose that the discovery of additional mechanisms of (GAA)n repeat instability can be achieved via both comparative approaches to other repeat expansion diseases and genome-wide association studies. Finally, we discuss the advances towards FRDA prevention or amelioration that specifically target (GAA)n repeat expansions.
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Affiliation(s)
- Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Ayesha F Lobo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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14
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Mandal AK. Mitochondrial targeting of potent nanoparticulated drugs in combating diseases. J Biomater Appl 2022; 37:614-633. [PMID: 35790487 DOI: 10.1177/08853282221111656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mitochondrial dysfunction, characterized by the electron transport chain (ETC) leakage and reduced adenosine tri-phosphate synthesis, occurs primarily due to free radicals -induced mutations in either the mitochondrial deoxyribonucleic acid (mtDNA) or nuclear (n) DNA caused by pathogenic infections, toxicant exposures, adverse drug-effects, or other environmental exposures, leading to secondary dysfunction affecting ischemic, diabetic, cancerous, and degenerative diseases. In these concerns, mitochondria-targeted remedies may include a significant role in the protection and treatment of mitochondrial function to enhance its activity. Coenzyme Q10 pyridinol and pyrimidinol antioxidant analogues and other potent drug-compounds for their multifunctional radical quencher and other anti-toxic activities may take a significant therapeutic effectivity for ameliorating mitochondrial dysfunction. Moreover, the encapsulation of these bioactive ligands-attached potent compounds in vesicular system may enable them a superb biological effective for the treatment of mitochondria-targeted dysfunction-related diseases with least side effects. This review depicts mainly on mitochondrial enzymatic dysfunction and their amelioration by potent drugs with the usages of nanoparticulated delivery system against mitochondria-affected diseases.
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15
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Vicente-Acosta A, Giménez-Cassina A, Díaz-Nido J, Loria F. The smoothened agonist SAG reduces mitochondrial dysfunction and neurotoxicity of frataxin-deficient astrocytes. J Neuroinflammation 2022; 19:93. [PMID: 35413853 PMCID: PMC9006607 DOI: 10.1186/s12974-022-02442-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Friedreich's ataxia is a rare hereditary neurodegenerative disease caused by decreased levels of the mitochondrial protein frataxin. Similar to other neurodegenerative pathologies, previous studies suggested that astrocytes might contribute to the progression of the disease. To fully understand the mechanisms underlying neurodegeneration in Friedreich's ataxia, we investigated the reactivity status and functioning of cultured human astrocytes after frataxin depletion using an RNA interference-based approach and tested the effect of pharmacologically modulating the SHH pathway as a novel neuroprotective strategy. RESULTS We observed loss of cell viability, mitochondrial alterations, increased autophagy and lipid accumulation in cultured astrocytes upon frataxin depletion. Besides, frataxin-deficient cells show higher expression of several A1-reactivity markers and release of pro-inflammatory cytokines. Interestingly, most of these defects were prevented by chronically treating the cells with the smoothened agonist SAG. Furthermore, in vitro culture of neurons with conditioned medium from frataxin-deficient astrocytes results in a reduction of neuronal survival, neurite length and synapse formation. However, when frataxin-deficient astrocytes were chronically treated with SAG, we did not observe these alterations in neurons. CONCLUSIONS Our results demonstrate that the pharmacological activation of the SHH pathway could be used as a target to modulate astrocyte reactivity and neuron-glia interactions to prevent neurodegeneration in Friedreich's ataxia.
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Affiliation(s)
- Andrés Vicente-Acosta
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Francisco Tomás y Valiente, 7, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria Puerta de Hierro, Segovia de Arana, Hospital Universitario Puerta de Hierro, Joaquín Rodrigo 1, Majadahonda, 28222 Madrid, Spain
- Program in Molecular Biosciences, Doctoral School, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alfredo Giménez-Cassina
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Francisco Tomás y Valiente, 7, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Javier Díaz-Nido
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Francisco Tomás y Valiente, 7, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria Puerta de Hierro, Segovia de Arana, Hospital Universitario Puerta de Hierro, Joaquín Rodrigo 1, Majadahonda, 28222 Madrid, Spain
| | - Frida Loria
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Francisco Tomás y Valiente, 7, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
- Laboratorio de Apoyo a la Investigación, Hospital Universitario Fundación Alcorcón, Budapest 1, Alcorcón, 28922 Madrid, Spain
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16
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Rodden LN, Gilliam KM, Lam C, Rojsajjakul T, Mesaros C, Dionisi C, Pook M, Pandolfo M, Lynch DR, Blair IA, Bidichandani SI. DNA methylation in Friedreich ataxia silences expression of frataxin isoform E. Sci Rep 2022; 12:5031. [PMID: 35322126 PMCID: PMC8943190 DOI: 10.1038/s41598-022-09002-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/14/2022] [Indexed: 11/15/2022] Open
Abstract
Epigenetic silencing in Friedreich ataxia (FRDA), induced by an expanded GAA triplet-repeat in intron 1 of the FXN gene, results in deficiency of the mitochondrial protein, frataxin. A lesser known extramitochondrial isoform of frataxin detected in erythrocytes, frataxin-E, is encoded via an alternate transcript (FXN-E) originating in intron 1 that lacks a mitochondrial targeting sequence. We show that FXN-E is deficient in FRDA, including in patient-derived cell lines, iPS-derived proprioceptive neurons, and tissues from a humanized mouse model. In a series of FRDA patients, deficiency of frataxin-E protein correlated with the length of the expanded GAA triplet-repeat, and with repeat-induced DNA hypermethylation that occurs in close proximity to the intronic origin of FXN-E. CRISPR-induced epimodification to mimic DNA hypermethylation seen in FRDA reproduced FXN-E transcriptional deficiency. Deficiency of frataxin E is a consequence of FRDA-specific epigenetic silencing, and therapeutic strategies may need to address this deficiency.
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Affiliation(s)
- Layne N Rodden
- Department of Pediatrics, University of Oklahoma Health Sciences Center, OU Children's Physician Building, Suite 12100, 1200 Children's Avenue, Oklahoma City, OK, 73104, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kaitlyn M Gilliam
- Department of Pediatrics, University of Oklahoma Health Sciences Center, OU Children's Physician Building, Suite 12100, 1200 Children's Avenue, Oklahoma City, OK, 73104, USA
| | - Christina Lam
- Department of Pediatrics, University of Oklahoma Health Sciences Center, OU Children's Physician Building, Suite 12100, 1200 Children's Avenue, Oklahoma City, OK, 73104, USA
| | - Teerapat Rojsajjakul
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Mark Pook
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Massimo Pandolfo
- Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - David R Lynch
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sanjay I Bidichandani
- Department of Pediatrics, University of Oklahoma Health Sciences Center, OU Children's Physician Building, Suite 12100, 1200 Children's Avenue, Oklahoma City, OK, 73104, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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17
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Fei J, Xu J, Li Z, Xu K, Wang D, Kassavetis GA, Kadonaga JT. NDF is a transcription factor that stimulates elongation by RNA polymerase II. Genes Dev 2022; 36:294-299. [PMID: 35273076 PMCID: PMC8973848 DOI: 10.1101/gad.349150.121] [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: 10/27/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022]
Abstract
Here, Fei et al. found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. Their findings demonstrate that NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans. RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than that used by transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.
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Affiliation(s)
- Jia Fei
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Ziwei Li
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Kevin Xu
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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18
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Schreiber AM, Li Y, Chen YH, Napierala JS, Napierala M. Selected Histone Deacetylase Inhibitors Reverse the Frataxin Transcriptional Defect in a Novel Friedreich's Ataxia Induced Pluripotent Stem Cell-Derived Neuronal Reporter System. Front Neurosci 2022; 16:836476. [PMID: 35281493 PMCID: PMC8904878 DOI: 10.3389/fnins.2022.836476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a neurodegenerative disorder caused by the expansion of guanine-adenine-adenine repeats within the first intron of the frataxin (FXN) gene. The location and nature of the expansion have been proven to contribute to transcriptional repression of FXN by decreasing the rate of polymerase II (RNA polymerase II) progression and increasing the presence of histone modifications associated with a heterochromatin-like state. Targeting impaired FXN transcription appears as a feasible option for therapeutic intervention, while no cure currently exists. We created a novel reporter cell line containing an FXN-Nanoluciferase (FXN-NLuc) fusion in induced pluripotent stem cells (iPSCs) reprogrammed from the fibroblasts of patients with FRDA, thus allowing quantification of endogenous FXN expression. The use of iPSCs provides the opportunity to differentiate these cells into disease-relevant neural progenitor cells (NPCs). NPCs derived from the FXN-NLuc line responded to treatments with a known FXN inducer, RG109. Results were validated by quantitative PCR and Western blot in multiple FRDA NPC lines. We then screened a commercially available library of compounds consisting of molecules targeting various enzymes and pathways critical for silencing or activation of gene expression. Only selected histone deacetylase inhibitors were capable of partial reactivation of FXN expression. This endogenous, FRDA iPSC-derived reporter can be utilized for high-throughput campaigns performed in cells most relevant to disease pathology in search of FXN transcription activators.
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Affiliation(s)
- Anna M. Schreiber
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yanjie Li
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yi-Hsien Chen
- Genome Engineering and iPSC Center, Washington University, St. Louis, MO, United States
| | - Jill S. Napierala
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL, United States
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19
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Abstract
INTRODUCTION Friedreich ataxia (FRDA) is an autosomal recessive disorder caused by deficiency of frataxin, an essential mitochondrial protein involved in iron sulfur cluster biogenesis, oxidative phosphorylation and other processes. FRDA most notably affects the heart, sensory neurons, spinal cord, cerebellum, and other brain regions, and manifests clinically as ataxia, sensory loss, dysarthria, spasticity, and hypertrophic cardiomyopathy. Therapeutic approaches in FRDA have consisted of two different approaches: (1) augmenting or restoring frataxin production and (2) modulating a variety of downstream processes related to mitochondrial dysfunction, including reactive oxygen species production, ferroptosis, or Nrf2 activation. AREAS COVERED In this review, we summarize data from major phase II clinical trials in FRDA published between 2015 and 2020, which includes A0001/EPI743, Omaveloxolone, RT001, and Actimmune. EXPERT OPINION A growing number of drug candidates are being tested in phase II clinical trials for FRDA; however, most have not met their primary endpoints, and none have received FDA approval. In this review, we aim to summarize completed phase II clinical trials in FRDA, outlining critical lessons that have been learned and that should be incorporated into future trial design to ultimately optimize drug development in FRDA.
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20
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Malik I, Kelley CP, Wang ET, Todd PK. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat Rev Mol Cell Biol 2021; 22:589-607. [PMID: 34140671 PMCID: PMC9612635 DOI: 10.1038/s41580-021-00382-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 02/05/2023]
Abstract
The human genome contains over one million short tandem repeats. Expansion of a subset of these repeat tracts underlies over fifty human disorders, including common genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72), polyglutamine-associated ataxias and Huntington disease, myotonic dystrophy, and intellectual disability disorders such as Fragile X syndrome. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.
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Affiliation(s)
- Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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21
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Rodden LN, Chutake YK, Gilliam K, Lam C, Soragni E, Hauser L, Gilliam M, Wiley G, Anderson MP, Gottesfeld JM, Lynch DR, Bidichandani SI. Methylated and unmethylated epialleles support variegated epigenetic silencing in Friedreich ataxia. Hum Mol Genet 2021; 29:3818-3829. [PMID: 33432325 PMCID: PMC7861014 DOI: 10.1093/hmg/ddaa267] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 12/20/2022] Open
Abstract
Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat in intron 1 of the FXN gene, which results in transcriptional deficiency via epigenetic silencing. Most patients are homozygous for alleles containing > 500 triplets, but a subset (~20%) have at least one expanded allele with < 500 triplets and a distinctly milder phenotype. We show that in FRDA DNA methylation spreads upstream from the expanded repeat, further than previously recognized, and establishes an FRDA-specific region of hypermethylation in intron 1 (~90% in FRDA versus < 10% in non-FRDA) as a novel epigenetic signature. The hypermethylation of this differentially methylated region (FRDA-DMR) was observed in a variety of patient-derived cells; it significantly correlated with FXN transcriptional deficiency and age of onset, and it reverted to the non-disease state in isogenically corrected induced pluripotent stem cell (iPSC)-derived neurons. Bisulfite deep sequencing of the FRDA-DMR in peripheral blood mononuclear cells from 73 FRDA patients revealed considerable intra-individual epiallelic variability, including fully methylated, partially methylated, and unmethylated epialleles. Although unmethylated epialleles were rare (median = 0.33%) in typical patients homozygous for long GAA alleles with > 500 triplets, a significantly higher prevalence of unmethylated epialleles (median = 9.8%) was observed in patients with at least one allele containing < 500 triplets, less severe FXN deficiency (>20%) and later onset (>15 years). The higher prevalence in mild FRDA of somatic FXN epialleles devoid of DNA methylation is consistent with variegated epigenetic silencing mediated by expanded triplet-repeats. The proportion of unsilenced somatic FXN genes is an unrecognized phenotypic determinant in FRDA and has implications for the deployment of effective therapies.
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Affiliation(s)
- Layne N Rodden
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yogesh K Chutake
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kaitlyn Gilliam
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Christina Lam
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Elisabetta Soragni
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Lauren Hauser
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew Gilliam
- Department of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, USA
| | - Graham Wiley
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael P Anderson
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Joel M Gottesfeld
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - David R Lynch
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sanjay I Bidichandani
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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22
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Vilema-Enríquez G, Quinlan R, Kilfeather P, Mazzone R, Saqlain S, Del Molino Del Barrio I, Donato A, Corda G, Li F, Vedadi M, Németh AH, Brennan PE, Wade-Martins R. Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich's ataxia patient cells. J Biol Chem 2020; 295:17973-17985. [PMID: 33028632 PMCID: PMC7939392 DOI: 10.1074/jbc.ra120.015533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression of FXN by ∼1.5-fold in the reporter cell line. In several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells, A-196 increased FXN expression by up to 2-fold, an effect not seen in WT cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4-7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogs were synthesized and shown to give a 20-fold increase in potency for increasing FXN expression. Overall, our results suggest that histone methylation is important in the regulation of FXN expression and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.
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Affiliation(s)
| | - Robert Quinlan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Kilfeather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Roberta Mazzone
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Saba Saqlain
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Annalidia Donato
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Gabriele Corda
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Trust, Oxford, United Kingdom
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Alzheimer's Research UK Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
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23
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Liu J, Bandyopadhyay I, Zheng L, Khdour OM, Hecht SM. Antiferroptotic Activity of Phenothiazine Analogues: A Novel Therapeutic Strategy for Oxidative Stress Related Disease. ACS Med Chem Lett 2020; 11:2165-2173. [PMID: 33214825 DOI: 10.1021/acsmedchemlett.0c00293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Ferroptosis is an iron-catalyzed, nonapoptotic form of regulated necrosis that has been implicated in the pathological cell death associated with various disorders including neurodegenerative diseases (e.g., Friedreich's ataxia (FRDA), Alzheimer's disease, and Parkinson's disease), stroke, and traumatic brain injury. Recently, we showed that lipophilic methylene blue (MB) and methylene violet (MV) analogues both promoted increased frataxin levels and mitochondrial biogenesis, in addition to their antioxidant activity in cultured FRDA cells. Presently, we report the synthesis of series of lipophilic phenothiazine analogues that potently inhibit ferroptosis. The most promising compounds (1b-5b) exhibited an improved protection compared to the parent phenothiazine against erastin- and RSL3-induced ferroptotic cell death. These analogues have equivalent or better potency than ferrostatin-1 (Fer-1) and liproxstatin-1 (Lip-1), that are among the most potent inhibitors of this regulated cell death described so far. They represent novel lead compounds with therapeutic potential in relevant ferroptosis-driven disease models such as FRDA.
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24
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Chiang S, Huang MLH, Park KC, Richardson DR. Antioxidant defense mechanisms and its dysfunctional regulation in the mitochondrial disease, Friedreich's ataxia. Free Radic Biol Med 2020; 159:177-188. [PMID: 32739593 DOI: 10.1016/j.freeradbiomed.2020.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Redox stress is associated with the pathogenesis of a wide variety of disease states. This can be amplified potentially through redox active iron deposits in oxidatively active organelles such as the mitochondrion. There are a number of disease states, including Friedreich's ataxia (FA) and sideroblastic anemia, where iron metabolism is dysregulated and leads to mitochondrial iron accumulation. Considering FA, which is due to the decreased expression of the mitochondrial protein, frataxin, this iron accumulation does not occur within protective storage proteins such as mitochondrial ferritin. Instead, it forms unbound biomineral aggregates composed of high spin iron(III), phosphorous and sulfur, which probably contributes to the observed redox stress. There is also a dysregulated response to the ensuing redox assault, as the master regulator of oxidative stress, nuclear factor erythroid 2-related factor-2 (Nrf2), demonstrates marked down-regulation. The dysfunctional response of Nrf2 in FA is due to multiple mechanisms including: (1) up-regulation of Keap1 that is involved in Nrf2 degradation; (2) activation of the nuclear Nrf2 export/degradation machinery via glycogen synthase kinase-3β (Gsk3β) signaling; and (3) inhibited nuclear translocation of Nrf2. More recently, increased microRNA (miRNA) 144 expression has been demonstrated to down-regulate Nrf2 in several disease states, including an animal model of FA. Other miRNAs have also demonstrated to be dysregulated upon frataxin depletion in vivo in humans and animal models of FA. Collectively, frataxin depletion results in multiple, complex responses that lead to detrimental redox effects that could contribute to the mechanisms involved in the pathogenesis of FA.
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Affiliation(s)
- S Chiang
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, Sydney, New South Wales, 2006, Australia
| | - M L H Huang
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, Sydney, New South Wales, 2006, Australia
| | - K C Park
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, Sydney, New South Wales, 2006, Australia
| | - D R Richardson
- Molecular Pharmacology and Pathology Program, Department of Pathology and Bosch Institute, Medical Foundation Building (K25), University of Sydney, Sydney, New South Wales, 2006, Australia; Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Centre for Cancer Cell Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, 4111, Australia.
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25
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Fautsch MP, Wieben ED, Baratz KH, Bhattacharyya N, Sadan AN, Hafford-Tear NJ, Tuft SJ, Davidson AE. TCF4-mediated Fuchs endothelial corneal dystrophy: Insights into a common trinucleotide repeat-associated disease. Prog Retin Eye Res 2020; 81:100883. [PMID: 32735996 PMCID: PMC7988464 DOI: 10.1016/j.preteyeres.2020.100883] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 (TCF4) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field. FECD is a common, age-related corneal dystrophy. The majority of cases are associated with expansion of a CTG repeat (CTG18.1). FECD is the most common trinucleotide repeat expansion disease in humans. Evidence supports multiple molecular mechanisms underlying the pathophysiology. Novel CTG18.1-targeted therapeutics are in development.
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Affiliation(s)
- Michael P Fautsch
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, 200 1st St SW, Mayo Clinic, Rochester, MN, USA.
| | - Keith H Baratz
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Amanda N Sadan
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| | | | - Stephen J Tuft
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
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26
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Therapeutic potential of stem cells for treatment of neurodegenerative diseases. Biotechnol Lett 2020; 42:1073-1101. [DOI: 10.1007/s10529-020-02886-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 04/05/2020] [Indexed: 12/13/2022]
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27
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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28
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The NRF2 Signaling Network Defines Clinical Biomarkers and Therapeutic Opportunity in Friedreich's Ataxia. Int J Mol Sci 2020; 21:ijms21030916. [PMID: 32019240 PMCID: PMC7037688 DOI: 10.3390/ijms21030916] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Friedreich’s ataxia (FA) is a trinucleotide repeats expansion neurodegenerative disorder, for which no cure or approved therapies are present. In most cases, GAA trinucleotide repetitions in the first intron of the FXN gene are the genetic trigger of FA, determining a strong reduction of frataxin, a mitochondrial protein involved in iron homeostasis. Frataxin depletion impairs iron–sulfur cluster biosynthesis and determines iron accumulation in the mitochondria. Mounting evidence suggests that these defects increase oxidative stress susceptibility and reactive oxygen species production in FA, where the pathologic picture is worsened by a defective regulation of the expression and signaling pathway modulation of the transcription factor NF-E2 p45-related factor 2 (NRF2), one of the fundamental mediators of the cellular antioxidant response. NRF2 protein downregulation and impairment of its nuclear translocation can compromise the adequate cellular response to the frataxin depletion-dependent redox imbalance. As NRF2 stability, expression, and activation can be modulated by diverse natural and synthetic compounds, efforts have been made in recent years to understand if regulating NRF2 signaling might ameliorate the pathologic defects in FA. Here we provide an analysis of the pharmaceutical interventions aimed at restoring the NRF2 signaling network in FA, elucidating specific biomarkers useful for monitoring therapeutic effectiveness, and developing new therapeutic tools.
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29
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Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability. Proc Natl Acad Sci U S A 2020; 117:1628-1637. [PMID: 31911468 PMCID: PMC6983365 DOI: 10.1073/pnas.1913416117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Expansions of GAA repeats cause a severe hereditary neurodegenerative disease, Friedreich’s ataxia. In this study, we characterized the mechanisms of GAA repeat contractions in a yeast experimental system. These mechanisms might, in the long run, aid development of a therapy for this currently incurable disease. We show that GAA repeats contract during DNA replication, which can explain the high level of somatic instability of this repeat in patient tissues. We also provided evidence that a triple-stranded DNA structure is at the heart of GAA repeat instability. This discovery highlights the role of triplex DNA in genome instability and human disease. Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.
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30
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Stepanova A, Magrané J. Mitochondrial dysfunction in neurons in Friedreich's ataxia. Mol Cell Neurosci 2020; 102:103419. [PMID: 31770591 DOI: 10.1016/j.mcn.2019.103419] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
Friedreich's ataxia is a multisystemic genetic disorder within the family of mitochondrial diseases that is characterized by reduced levels of the essential mitochondrial protein frataxin. Based on clinical evidence, the peripheral nervous system is affected early, neuronal dysfunction progresses towards the central nervous system, and other organs (such as heart and pancreas) are affected later. However, little attention has been given to the specific aspects of mitochondria function altered by frataxin depletion in the nervous system. For years, commonly accepted views on mitochondria dysfunction in Friedreich's ataxia stemmed from studies using non-neuronal systems and may not apply to neurons, which have their own bioenergetic needs and present a unique, extensive neurite network. Moreover, the basis of the selective neuronal vulnerability, which primarily affects large sensory neurons in the dorsal root ganglia, large principal neurons in the dentate nuclei of the cerebellum, and pyramidal neurons in the cerebral cortex, remains elusive. In order to identify potential misbeliefs in the field and highlight controversies, we reviewed current knowledge on frataxin expression in different tissues, discussed the molecular function of frataxin, and the consequences of its deficiency for mitochondria structural and functional properties, with a focus on the nervous system.
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Affiliation(s)
- Anna Stepanova
- Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America.
| | - Jordi Magrané
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States of America.
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31
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Gottesfeld JM. Molecular Mechanisms and Therapeutics for the GAA·TTC Expansion Disease Friedreich Ataxia. Neurotherapeutics 2019; 16:1032-1049. [PMID: 31317428 PMCID: PMC6985418 DOI: 10.1007/s13311-019-00764-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Friedreich ataxia (FRDA), the most common inherited ataxia, is caused by transcriptional silencing of the nuclear FXN gene, encoding the essential mitochondrial protein frataxin. Currently, there is no approved therapy for this fatal disorder. Gene silencing in FRDA is due to hyperexpansion of the triplet repeat sequence GAA·TTC in the first intron of the FXN gene, which results in chromatin histone modifications consistent with heterochromatin formation. Frataxin is involved in mitochondrial iron homeostasis and the assembly and transfer of iron-sulfur clusters to various mitochondrial enzymes and components of the electron transport chain. Frataxin insufficiency leads to progressive spinocerebellar neurodegeneration, causing symptoms of gait and limb ataxia, slurred speech, muscle weakness, sensory loss, and cardiomyopathy in many patients, resulting in death in early adulthood. Numerous approaches are being taken to find a treatment for FRDA, including excision or correction of the repeats by genome engineering methods, gene activation with small molecules or artificial transcription factors, delivery of frataxin to affected cells by protein replacement therapy, gene therapy, or small molecules to increase frataxin protein levels, and therapies aimed at countering the cellular consequences of reduced frataxin. This review will summarize the mechanisms involved in repeat-mediated gene silencing and recent efforts aimed at development of therapeutics.
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Affiliation(s)
- Joel M Gottesfeld
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA.
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32
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Delatycki MB, Bidichandani SI. Friedreich ataxia- pathogenesis and implications for therapies. Neurobiol Dis 2019; 132:104606. [PMID: 31494282 DOI: 10.1016/j.nbd.2019.104606] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/08/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Friedreich ataxia is the most common of the hereditary ataxias. It is due to homozygous/compound heterozygous mutations in FXN. This gene encodes frataxin, a protein largely localized to mitochondria. In about 96% of affected individuals there is homozygosity for a GAA repeat expansion in intron 1 of the FXN gene. Studies of people with Friedreich ataxia and of animal and cell models, have provided much insight into the pathogenesis of this disorder. The expanded GAA repeat leads to transcriptional deficiency of the FXN gene. The consequent deficiency of frataxin protein leads to reduced iron-sulfur cluster biogenesis and mitochondrial ATP production, elevated mitochondrial iron, and oxidative stress. More recently, a role for inflammation has emerged as being important in the pathogenesis of Friedreich ataxia. These findings have led to a number of potential therapies that have been subjected to clinical trials or are being developed toward human studies. Therapies that have been proposed include pharmaceuticals that increase frataxin levels, protein and gene replacement therapies, antioxidants, iron chelators and modulators of inflammation. Whilst no therapies have yet been approved for Friedreich ataxia, there is much optimism that the advances in the understanding of the pathogenesis of this disorder since the discovery its genetic basis, will result in approved disease modifying therapies in the near future.
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Affiliation(s)
- Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
| | - Sanjay I Bidichandani
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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33
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Clay A, Hearle P, Schadt K, Lynch DR. New developments in pharmacotherapy for Friedreich ataxia. Expert Opin Pharmacother 2019; 20:1855-1867. [PMID: 31311349 DOI: 10.1080/14656566.2019.1639671] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Friedreich ataxia (FRDA), a rare disease caused by the deficiency of the mitochondrial matrix protein frataxin, affects roughly 1 in 50,000 individuals worldwide. Current and emerging therapies focus on reversing the deleterious effects of such deficiency including mitochondrial augmentation and increasing frataxin levels, providing the possibility of treatment options for this physiologically complex, multisystem disorder. Areas covered: In this review article, the authors discuss the current and prior in vivo and in vitro research studies related to the treatment of FRDA, with a particular interest in future implications of each therapy. Expert opinion: Since the discovery of FXN in 1996, multiple clinical trials have occurred or are currently occurring; at a rapid pace for a rare disease. These trials have been directed at the augmentation of mitochondrial function and/or alleviation of symptoms and are not regarded as potential cures in FRDA. Either a combination of therapies or a drug that replaces or increases the pathologically low levels of frataxin better represent potential cures in FRDA.
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Affiliation(s)
- Alexandra Clay
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Patrick Hearle
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Kim Schadt
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - David R Lynch
- Division of Neurology, Children's Hospital of Philadelphia , Philadelphia , PA , USA
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34
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Lipshultz SE, Law YM, Asante-Korang A, Austin ED, Dipchand AI, Everitt MD, Hsu DT, Lin KY, Price JF, Wilkinson JD, Colan SD. Cardiomyopathy in Children: Classification and Diagnosis: A Scientific Statement From the American Heart Association. Circulation 2019; 140:e9-e68. [PMID: 31132865 DOI: 10.1161/cir.0000000000000682] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this scientific statement from the American Heart Association, experts in the field of cardiomyopathy (heart muscle disease) in children address 2 issues: the most current understanding of the causes of cardiomyopathy in children and the optimal approaches to diagnosis cardiomyopathy in children. Cardiomyopathies result in some of the worst pediatric cardiology outcomes; nearly 40% of children who present with symptomatic cardiomyopathy undergo a heart transplantation or die within the first 2 years after diagnosis. The percentage of children with cardiomyopathy who underwent a heart transplantation has not declined over the past 10 years, and cardiomyopathy remains the leading cause of transplantation for children >1 year of age. Studies from the National Heart, Lung, and Blood Institute-funded Pediatric Cardiomyopathy Registry have shown that causes are established in very few children with cardiomyopathy, yet genetic causes are likely to be present in most. The incidence of pediatric cardiomyopathy is ≈1 per 100 000 children. This is comparable to the incidence of such childhood cancers as lymphoma, Wilms tumor, and neuroblastoma. However, the published research and scientific conferences focused on pediatric cardiomyopathy are sparcer than for those cancers. The aim of the statement is to focus on the diagnosis and classification of cardiomyopathy. We anticipate that this report will help shape the future research priorities in this set of diseases to achieve earlier diagnosis, improved clinical outcomes, and better quality of life for these children and their families.
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35
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Nguyen L, Cleary JD, Ranum LPW. Repeat-Associated Non-ATG Translation: Molecular Mechanisms and Contribution to Neurological Disease. Annu Rev Neurosci 2019; 42:227-247. [PMID: 30909783 DOI: 10.1146/annurev-neuro-070918-050405] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microsatellite mutations involving the expansion of tri-, tetra-, penta-, or hexanucleotide repeats cause more than 40 different neurological disorders. Although, traditionally, the position of the repeat within or outside of an open reading frame has been used to focus research on disease mechanisms involving protein loss of function, protein gain of function, or RNA gain of function, the discoveries of bidirectional transcription and repeat-associated non-ATG (RAN) have blurred these distinctions. Here we review what is known about RAN proteins in disease, the mechanisms by which they are produced, and the novel therapeutic opportunities they provide.
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Affiliation(s)
- Lien Nguyen
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, and McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida 32610, USA;
| | - John Douglas Cleary
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, and McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida 32610, USA;
| | - Laura P W Ranum
- Center for NeuroGenetics, Department of Molecular Genetics and Microbiology, Genetics Institute, and McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida 32610, USA;
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36
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Šviković S, Crisp A, Tan-Wong SM, Guilliam TA, Doherty AJ, Proudfoot NJ, Guilbaud G, Sale JE. R-loop formation during S phase is restricted by PrimPol-mediated repriming. EMBO J 2018; 38:embj.201899793. [PMID: 30478192 PMCID: PMC6356060 DOI: 10.15252/embj.201899793] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/08/2018] [Accepted: 11/06/2018] [Indexed: 12/17/2022] Open
Abstract
During DNA replication, conflicts with ongoing transcription are frequent and require careful management to avoid genetic instability. R‐loops, three‐stranded nucleic acid structures comprising a DNA:RNA hybrid and displaced single‐stranded DNA, are important drivers of damage arising from such conflicts. How R‐loops stall replication and the mechanisms that restrain their formation during S phase are incompletely understood. Here, we show in vivo how R‐loop formation drives a short purine‐rich repeat, (GAA)10, to become a replication impediment that engages the repriming activity of the primase‐polymerase PrimPol. Further, the absence of PrimPol leads to significantly increased R‐loop formation around this repeat during S phase. We extend this observation by showing that PrimPol suppresses R‐loop formation in genes harbouring secondary structure‐forming sequences, exemplified by G quadruplex and H‐DNA motifs, across the genome in both avian and human cells. Thus, R‐loops promote the creation of replication blocks at susceptible structure‐forming sequences, while PrimPol‐dependent repriming limits the extent of unscheduled R‐loop formation at these sequences, mitigating their impact on replication.
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Affiliation(s)
| | | | | | - Thomas A Guilliam
- Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Aidan J Doherty
- Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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Abstract
SIGNIFICANCE The concepts of junk DNA and transcriptional noise are long gone as the existence of noncoding RNAs (ncRNAs) has been tested extensively in recent years. Given that the epigenetic status of cells affects many biological processes, how ncRNAs mechanistically contribute to these processes is of great interest. Recent Advances: Recent studies show that various ncRNAs interact with epigenetic and/or transcription factors to modulate the epigenetic status of cells directly and/or indirectly. There exists growing interest in the field of cardiovascular research to understand the roles of ncRNAs. Due to the large number of ncRNAs in the mammalian genome, only a handful of ncRNAs have been functionally elucidated, which makes it difficult to understand how ncRNAs interact with protein-coding genes and their encoded proteins. CRITICAL ISSUES Although the canonical function of microRNAs (miRNAs) to inhibit the translation of protein-coding genes is well established, the number of functionally annotated long noncoding RNAs (lncRNAs) is still small, which is especially true in the heart. FUTURE DIRECTIONS Future studies must connect the epigenetic controls of various cellular phenomena by incorporating both miRNAs and lncRNAs. Antioxid. Redox Signal. 29, 832-845.
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Affiliation(s)
- Shizuka Uchida
- 1 Cardiovascular Innovation Institute, University of Louisville , Louisville, Kentucky
| | - Roberto Bolli
- 1 Cardiovascular Innovation Institute, University of Louisville , Louisville, Kentucky.,2 Institute of Molecular Cardiology, University of Louisville , Louisville, Kentucky
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Van Ghelder C, Esmenjaud D, Callot C, Dubois E, Mazier M, Duval H. Ma Orthologous Genes in Prunus spp. Shed Light on a Noteworthy NBS-LRR Cluster Conferring Differential Resistance to Root-Knot Nematodes. FRONTIERS IN PLANT SCIENCE 2018; 9:1269. [PMID: 30254651 PMCID: PMC6141779 DOI: 10.3389/fpls.2018.01269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 06/01/2023]
Abstract
Root-knot nematodes (RKNs) are considerable polyphagous pests that severely challenge plants worldwide and especially perennials. The specific genetic resistance of plants mainly relies on the NBS-LRR genes that are pivotal factors for pathogens control. In Prunus spp., the Ma plum and RMja almond genes possess different spectra for resistance to RKNs. While previous works based on the Ma gene allowed to clone it and to decipher its peculiar TIR-NBS-LRR (TNL) structure, we only knew that the RMja gene mapped on the same chromosome as Ma. We carried out a high-resolution mapping using an almond segregating F2 progeny of 1448 seedlings from resistant (R) and susceptible (S) parental accessions, to locate precisely RMja on the peach genome, the reference sequence for Prunus species. We showed that the RMja gene maps in the Ma resistance cluster and that the Ma ortholog is the best candidate for RMja. This co-localization is a crucial step that opens the way to unravel the molecular determinants involved in the resistance to RKNs. Then we sequenced both almond parental NGS genomes and aligned them onto the RKN susceptible reference peach genome. We produced a BAC library of the R parental accession and, from two overlapping BAC clones, we obtained a 336-kb sequence encompassing the RMja candidate region. Thus, we could benefit from three Ma orthologous regions to investigate their sequence polymorphism, respectively, within plum (complete R spectrum), almond (incomplete R spectrum) and peach (null R spectrum). We showed that the Ma TNL cluster has evolved orthologs with a unique conserved structure comprised of five repeated post-LRR (PL) domains, which contain most polymorphism. In addition to support the Ma and RMja orthologous relationship, our results suggest that the polymorphism contained in the PL sequences might underlie differential resistance interactions with RKNs and an original immune mechanism in woody perennials. Besides, our study illustrates how PL exon duplications and losses shape TNL structure and give rise to atypical PL domain repeats of yet unknown role.
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Affiliation(s)
- Cyril Van Ghelder
- Institut Sophia Agrobiotech, INRA, CNRS, Université Côte d’Azur, Sophia Antipolis, France
| | - Daniel Esmenjaud
- Institut Sophia Agrobiotech, INRA, CNRS, Université Côte d’Azur, Sophia Antipolis, France
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Marianne Mazier
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRA, Montfavet, France
| | - Henri Duval
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRA, Montfavet, France
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Eimer H, Sureshkumar S, Singh Yadav A, Kraupner-Taylor C, Bandaranayake C, Seleznev A, Thomason T, Fletcher SJ, Gordon SF, Carroll BJ, Balasubramanian S. RNA-Dependent Epigenetic Silencing Directs Transcriptional Downregulation Caused by Intronic Repeat Expansions. Cell 2018; 174:1095-1105.e11. [PMID: 30057112 DOI: 10.1016/j.cell.2018.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 04/20/2018] [Accepted: 06/22/2018] [Indexed: 01/07/2023]
Abstract
Transcriptional downregulation caused by intronic triplet repeat expansions underlies diseases such as Friedreich's ataxia. This downregulation of gene expression is coupled with epigenetic changes, but the underlying mechanisms are unknown. Here, we show that an intronic GAA/TTC triplet expansion within the IIL1 gene of Arabidopsis thaliana results in accumulation of 24-nt short interfering RNAs (siRNAs) and repressive histone marks at the IIL1 locus, which in turn causes its transcriptional downregulation and an associated phenotype. Knocking down DICER LIKE-3 (DCL3), which produces 24-nt siRNAs, suppressed transcriptional downregulation of IIL1 and the triplet expansion-associated phenotype. Furthermore, knocking down additional components of the RNA-dependent DNA methylation (RdDM) pathway also suppressed both transcriptional downregulation of IIL1 and the repeat expansion-associated phenotype. Thus, our results show that triplet repeat expansions can lead to local siRNA biogenesis, which in turn downregulates transcription through an RdDM-dependent epigenetic modification.
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Affiliation(s)
- Hannes Eimer
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | | | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Andrei Seleznev
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Tamblyn Thomason
- School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia
| | - Stephen J Fletcher
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
| | | | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia QLD 4072, Australia
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Khdour OM, Bandyopadhyay I, Visavadiya NP, Roy Chowdhury S, Hecht SM. Phenothiazine antioxidants increase mitochondrial biogenesis and frataxin levels in Friedreich's ataxia cells. MEDCHEMCOMM 2018; 9:1491-1501. [PMID: 30288223 DOI: 10.1039/c8md00274f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022]
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease that is linked to transcriptional repression of the nuclear FXN gene encoding the essential mitochondrial protein frataxin (FXN). Compounds that increase frataxin levels may enable effective therapeutic intervention for blunting disease progression. Recently, we showed that lipophilic methylene violet (MV) and methylene blue (MB) analogues both conferred benefit to cultured FRDA cells in several regards, including ROS suppression, maintenance of mitochondrial membrane potential and increased ATP production. Some of the MB analogues were also shown to promote increased frataxin levels and mitochondrial biogenesis. Presently, we report that two of the MV analogues studied previously (1 and 2) also increased frataxin levels and mitochondrial biogenesis significantly. Because the substitution pattern in the two series of compounds was not the same, we also prepared new MV derivatives having the same substitution pattern as the original MB derivatives studied to enable a more direct comparison. Two of the new MV compounds, 4b and 6b, exhibited enhanced antioxidant capability, increased frataxin levels and mitochondrial biogenesis, and improved aconitase activity. These encouraging findings demonstrated that the MV analogues had better overall activity with less cytotoxicity.
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Affiliation(s)
- Omar M Khdour
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA .
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
| | - Nishant P Visavadiya
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA .
| | - Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics , Arizona State University , Tempe , AZ 85287 , USA . .,School of Molecular Sciences , Arizona State University , Tempe , AZ 85287 , USA
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41
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Khdour OM, Bandyopadhyay I, Chowdhury SR, Visavadiya NP, Hecht SM. Lipophilic methylene blue analogues enhance mitochondrial function and increase frataxin levels in a cellular model of Friedreich's ataxia. Bioorg Med Chem 2018; 26:3359-3369. [PMID: 29773347 DOI: 10.1016/j.bmc.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/25/2018] [Accepted: 05/03/2018] [Indexed: 01/31/2023]
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder resulting from reduced expression of the protein frataxin (FXN). Although its function is not fully understood, frataxin appears to help assemble iron sulfur clusters; these are critical for the function of many proteins, including those needed for mitochondrial energy production. Finding ways to increase FXN levels has been a major therapeutic strategy for this disease. Previously, we described a novel series of methylene violet analogues and their structural optimization as potential therapeutic agents for neurodegenerative and mitochondrial disorders. Presently, a series of methylene blue analogues has been synthesized and characterized for their in vitro biochemical and biological properties in cultured Friedreich's ataxia lymphocytes. Favorable methylene blue analogues were shown to increase frataxin levels and mitochondrial biogenesis, and to improve aconitase activity. The analogues were found to be good ROS scavengers, and able to protect cultured FRDA lymphocytes from oxidative stress resulting from inhibition of complex I and from glutathione depletion. The analogues also preserved mitochondrial membrane potential and augmented ATP production. Our results suggest that analogue 5, emerging from the initial structure of the parent compound methylene blue (MB), represents a promising lead structure and lacks the cytotoxicity associated with the parent compound MB.
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Affiliation(s)
- Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Indrajit Bandyopadhyay
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Nishant P Visavadiya
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
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Chiang S, Kalinowski DS, Jansson PJ, Richardson DR, Huang MLH. Mitochondrial dysfunction in the neuro-degenerative and cardio-degenerative disease, Friedreich's ataxia. Neurochem Int 2018; 117:35-48. [PMID: 28782591 DOI: 10.1016/j.neuint.2017.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/25/2017] [Accepted: 08/03/2017] [Indexed: 01/09/2023]
Abstract
Mitochondrial homeostasis is essential for maintaining healthy cellular function and survival. The detrimental involvement of mitochondrial dysfunction in neuro-degenerative diseases has recently been highlighted in human conditions, such as Parkinson's, Alzheimer's and Huntington's disease. Friedreich's ataxia (FA) is another neuro-degenerative, but also cardio-degenerative condition, where mitochondrial dysfunction plays a crucial role in disease progression. Deficient expression of the mitochondrial protein, frataxin, is the primary cause of FA, which leads to adverse alterations in whole cell and mitochondrial iron metabolism. Dys-regulation of iron metabolism in these compartments, results in the accumulation of inorganic iron deposits in the mitochondrial matrix that is thought to potentiate oxidative damage observed in FA. Therefore, the maintenance of mitochondrial homeostasis is crucial in the progression of neuro-degenerative conditions, particularly in FA. In this review, vital mitochondrial homeostatic processes and their roles in FA pathogenesis will be discussed. These include mitochondrial iron processing, mitochondrial dynamics (fusion and fission processes), mitophagy, mitochondrial biogenesis, mitochondrial energy production and calcium metabolism.
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Affiliation(s)
- Shannon Chiang
- Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Danuta S Kalinowski
- Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Patric J Jansson
- Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Des R Richardson
- Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Michael L-H Huang
- Department of Pathology and Bosch Institute, University of Sydney, Sydney, New South Wales, 2006, Australia.
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43
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Ueyama M, Nagai Y. Repeat Expansion Disease Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:63-78. [PMID: 29951815 DOI: 10.1007/978-981-13-0529-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Repeat expansion disorders are a group of inherited neuromuscular diseases, which are caused by expansion mutations of repeat sequences in the disease-causing genes. Repeat expansion disorders include a class of diseases caused by repeat expansions in the coding region of the genes, producing mutant proteins with amino acid repeats, mostly the polyglutamine (polyQ) diseases, and another class of diseases caused by repeat expansions in the noncoding regions, producing aberrant RNA with expanded repeats, which are called noncoding repeat expansion diseases. A variety of Drosophila disease models have been established for both types of diseases, and they have made significant contributions toward elucidating the molecular mechanisms of and developing therapies for these neuromuscular diseases.
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Affiliation(s)
- Morio Ueyama
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, Japan.
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Singh HN, Scheiber-Mojdehkar B, Rajeswari MR. DNA trinucleotide (GAA) repeats in human genome: hint for disease pathogenesis? J Biomol Struct Dyn 2018; 36:1958-1965. [PMID: 28605995 DOI: 10.1080/07391102.2017.1341336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Himanshu Narayan Singh
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Barbara Scheiber-Mojdehkar
- b Department of Medical Chemistry and Pathobiochemistry , Medical University of Vienna , Vienna , Austria
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
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45
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Weirick T, Militello G, Uchida S. Long Non-coding RNAs in Endothelial Biology. Front Physiol 2018; 9:522. [PMID: 29867565 PMCID: PMC5960726 DOI: 10.3389/fphys.2018.00522] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
In recent years, the role of RNA has expanded to the extent that protein-coding RNAs are now the minority with a variety of non-coding RNAs (ncRNAs) now comprising the majority of RNAs in higher organisms. A major contributor to this shift in understanding is RNA sequencing (RNA-seq), which allows a largely unconstrained method for monitoring the status of RNA from whole organisms down to a single cell. This observational power presents both challenges and new opportunities, which require specialized bioinformatics tools to extract knowledge from the data and the ability to reuse data for multiple studies. In this review, we summarize the current status of long non-coding RNA (lncRNA) research in endothelial biology. Then, we will cover computational methods for identifying, annotating, and characterizing lncRNAs in the heart, especially endothelial cells.
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Affiliation(s)
- Tyler Weirick
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY, United States
| | - Giuseppe Militello
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY, United States
| | - Shizuka Uchida
- Cardiovascular Innovation Institute, University of Louisville, Louisville, KY, United States
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Kemp KC, Hares K, Redondo J, Cook AJ, Haynes HR, Burton BR, Pook MA, Rice CM, Scolding NJ, Wilkins A. Bone marrow transplantation stimulates neural repair in Friedreich's ataxia mice. Ann Neurol 2018; 83:779-793. [PMID: 29534309 PMCID: PMC5947591 DOI: 10.1002/ana.25207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Friedreich's ataxia is an incurable inherited neurological disease caused by frataxin deficiency. Here, we report the neuroreparative effects of myeloablative allogeneic bone marrow transplantation in a humanized murine model of the disease. METHODS Mice received a transplant of fluorescently tagged sex-mismatched bone marrow cells expressing wild-type frataxin and were assessed at monthly intervals using a range of behavioral motor performance tests. At 6 months post-transplant, mice were euthanized for protein and histological analysis. In an attempt to augment numbers of bone marrow-derived cells integrating within the nervous system and improve therapeutic efficacy, a subgroup of transplanted mice also received monthly subcutaneous infusions of the cytokines granulocyte-colony stimulating factor and stem cell factor. RESULTS Transplantation caused improvements in several indicators of motor coordination and locomotor activity. Elevations in frataxin levels and antioxidant defenses were detected. Abrogation of disease pathology throughout the nervous system was apparent, together with extensive integration of bone marrow-derived cells in areas of nervous tissue injury that contributed genetic material to mature neurons, satellite-like cells, and myelinating Schwann cells by processes including cell fusion. Elevations in circulating bone marrow-derived cell numbers were detected after cytokine administration and were associated with increased frequencies of Purkinje cell fusion and bone marrow-derived dorsal root ganglion satellite-like cells. Further improvements in motor coordination and activity were evident. INTERPRETATION Our data provide proof of concept of gene replacement therapy, via allogeneic bone marrow transplantation, that reverses neurological features of Friedreich's ataxia with the potential for rapid clinical translation. Ann Neurol 2018;83:779-793.
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Affiliation(s)
- Kevin C. Kemp
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Kelly Hares
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Juliana Redondo
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Amelia J. Cook
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Harry R. Haynes
- Department of Cellular PathologyNorth Bristol National Health Service TrustBristolUnited Kingdom
| | - Bronwen R. Burton
- Infection and Immunity, School of Cellular and Molecular MedicineUniversity of BristolBristolUnited Kingdom
| | - Mark A. Pook
- Synthetic Biology Theme, Institute of Environment, Health and Societies, Biosciences, Department of Life Sciences, College of Health and Life SciencesBrunel University LondonLondonUnited Kingdom
| | - Claire M. Rice
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Neil J. Scolding
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
| | - Alastair Wilkins
- Multiple Sclerosis and Stem Cell Group, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUnited Kingdom
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Santoro A, Anjomani Virmouni S, Paradies E, Villalobos Coa VL, Al-Mahdawi S, Khoo M, Porcelli V, Vozza A, Perrone M, Denora N, Taroni F, Merla G, Palmieri L, Pook MA, Marobbio CMT. Effect of diazoxide on Friedreich ataxia models. Hum Mol Genet 2018; 27:992-1001. [PMID: 29325032 DOI: 10.1093/hmg/ddy016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/03/2018] [Indexed: 12/17/2023] Open
Abstract
Friedreich ataxia (FRDA) is an inherited recessive disorder caused by a deficiency in the mitochondrial protein frataxin. There is currently no effective treatment for FRDA available, especially for neurological deficits. In this study, we tested diazoxide, a drug commonly used as vasodilator in the treatment of acute hypertension, on cellular and animal models of FRDA. We first showed that diazoxide increases frataxin protein levels in FRDA lymphoblastoid cell lines, via the mammalian target of rapamycin (mTOR) pathway. We then explored the potential therapeutic effect of diazoxide in frataxin-deficient transgenic YG8sR mice and we found that prolonged oral administration of 3 mpk/d diazoxide was found to be safe, but produced variable effects concerning efficacy. YG8sR mice showed improved beam walk coordination abilities and footprint stride patterns, but a generally reduced locomotor activity. Moreover, they showed significantly increased frataxin expression, improved aconitase activity, and decreased protein oxidation in cerebellum and brain mitochondrial tissue extracts. Further studies are needed before this drug should be considered for FRDA clinical trials.
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Affiliation(s)
- Antonella Santoro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Sara Anjomani Virmouni
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Eleonora Paradies
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | | | - Sahar Al-Mahdawi
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Mee Khoo
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Vito Porcelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Angelo Vozza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Mara Perrone
- Department of Pharmacy - Drug Sciences, University of Bari, 70125 Bari, Italy
| | - Nunzio Denora
- Department of Pharmacy - Drug Sciences, University of Bari, 70125 Bari, Italy
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS-Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giuseppe Merla
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni, Rotondo, Italy
| | - Luigi Palmieri
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Mark A Pook
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Carlo M T Marobbio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
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Abstract
Epigenetics is a growing field of knowledge that is changing our understanding of pathologic processes. For many cerebellar disorders, recent discoveries of epigenetic mechanisms help us to understand their pathophysiology. In this chapter, a short explanation of each epigenetic mechanism (including methylation, histone modification, and miRNA) is followed by references to those cerebellar disorders in which relevant epigenetic advances have been made. The importance of normal timing and distribution of methylation during neurodevelopment is explained. Abnormal methylation and altered gene expression in the developing cerebellum have been related to neurodevelopmental disorders such as autism, Rett syndrome, and fragile X syndrome. DNA packaging by histones is another important epigenetic mechanism in cerebellar functioning. Current knowledge of histone abnormalities in cerebellar diseases such as Friedreich ataxia and spinocerebellar ataxias is reviewed, including implications for new therapeutic approaches to these degenerative diseases. Finally, micro RNAs, the third mechanism to modulate DNA expression, and their role in normal cerebellar development and disease are described. Understanding how genetic and epigenetic mechanisms interact not only in normal cerebellar development but also in disease is a great challenge. However, such understanding will lead to promising new therapeutic possibilities as is already occurring in other areas of medicine.
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Affiliation(s)
- Mercedes Serrano
- Pediatric Neurology Department and Pediatric Institute for Genetic Medicine and Rare Diseases, Hospital Sant Joan de Déu; and Centre for Biomedical Research on Rare Diseases, Instituto de Salud Carlos III, Barcelona, Spain.
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49
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Abstract
More than 40 diseases, most of which primarily affect the nervous system, are caused by expansions of simple sequence repeats dispersed throughout the human genome. Expanded trinucleotide repeat diseases were discovered first and remain the most frequent. More recently tetra-, penta-, hexa-, and even dodeca-nucleotide repeat expansions have been identified as the cause of human disease, including some of the most common genetic disorders seen by neurologists. Repeat expansion diseases include both causes of myotonic dystrophy (DM1 and DM2), the most common genetic cause of amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72), Huntington disease, and eight other polyglutamine disorders, including the most common forms of dominantly inherited ataxia, the most common recessive ataxia (Friedreich ataxia), and the most common heritable mental retardation (fragile X syndrome). Here I review distinctive features of this group of diseases that stem from the unusual, dynamic nature of the underlying mutations. These features include marked clinical heterogeneity and the phenomenon of clinical anticipation. I then discuss the diverse molecular mechanisms driving disease pathogenesis, which vary depending on the repeat sequence, size, and location within the disease gene, and whether the repeat is translated into protein. I conclude with a brief clinical and genetic description of individual repeat expansion diseases that are most relevant to neurologists.
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Affiliation(s)
- Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States.
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Lin H, Magrane J, Clark EM, Halawani SM, Warren N, Rattelle A, Lynch DR. Early VGLUT1-specific parallel fiber synaptic deficits and dysregulated cerebellar circuit in the KIKO mouse model of Friedreich ataxia. Dis Model Mech 2017; 10:1529-1538. [PMID: 29259026 PMCID: PMC5769605 DOI: 10.1242/dmm.030049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/30/2017] [Indexed: 01/01/2023] Open
Abstract
Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder with progressive ataxia that affects both the peripheral and central nervous system (CNS). While later CNS neuropathology involves loss of large principal neurons and glutamatergic and GABAergic synaptic terminals in the cerebellar dentate nucleus, early pathological changes in FRDA cerebellum remain largely uncharacterized. Here, we report early cerebellar VGLUT1 (SLC17A7)-specific parallel fiber (PF) synaptic deficits and dysregulated cerebellar circuit in the frataxin knock-in/knockout (KIKO) FRDA mouse model. At asymptomatic ages, VGLUT1 levels in cerebellar homogenates are significantly decreased, whereas VGLUT2 (SLC17A6) levels are significantly increased, in KIKO mice compared with age-matched controls. Additionally, GAD65 (GAD2) levels are significantly increased, while GAD67 (GAD1) levels remain unaltered. This suggests early VGLUT1-specific synaptic input deficits, and dysregulation of VGLUT2 and GAD65 synaptic inputs, in the cerebellum of asymptomatic KIKO mice. Immunohistochemistry and electron microscopy further show specific reductions of VGLUT1-containing PF presynaptic terminals in the cerebellar molecular layer, demonstrating PF synaptic input deficiency in asymptomatic and symptomatic KIKO mice. Moreover, the parvalbumin levels in cerebellar homogenates and Purkinje neurons are significantly reduced, but preserved in other interneurons of the cerebellar molecular layer, suggesting specific parvalbumin dysregulation in Purkinje neurons of these mice. Furthermore, a moderate loss of large principal neurons is observed in the dentate nucleus of asymptomatic KIKO mice, mimicking that of FRDA patients. Our findings thus identify early VGLUT1-specific PF synaptic input deficits and dysregulated cerebellar circuit as potential mediators of cerebellar dysfunction in KIKO mice, reflecting developmental features of FRDA in this mouse model.
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Affiliation(s)
- Hong Lin
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jordi Magrane
- Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065, USA
| | - Elisia M Clark
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah M Halawani
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Warren
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Amy Rattelle
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David R Lynch
- Departments of Pediatrics and Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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