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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] [MESH Headings] [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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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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Kumari D, Lokanga RA, McCann C, Ried T, Usdin K. The fragile X locus is prone to spontaneous DNA damage that is preferentially repaired by nonhomologous end-joining to preserve genome integrity. iScience 2024; 27:108814. [PMID: 38303711 PMCID: PMC10831274 DOI: 10.1016/j.isci.2024.108814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
A long CGG-repeat tract in the FMR1 gene induces the epigenetic silencing that causes fragile X syndrome (FXS). Epigenetic changes include H4K20 trimethylation, a heterochromatic modification frequently implicated in transcriptional silencing. Here, we report that treatment with A-196, an inhibitor of SUV420H1/H2, the enzymes responsible for H4K20 di-/trimethylation, does not affect FMR1 transcription, but does result in increased chromosomal duplications. Increased duplications were also seen in FXS cells treated with SCR7, an inhibitor of Lig4, a ligase essential for NHEJ. Our study suggests that the fragile X (FX) locus is prone to spontaneous DNA damage that is normally repaired by NHEJ. We suggest that heterochromatinization of the FX allele may be triggered, at least in part, in response to this DNA damage.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachel Adihe Lokanga
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cai McCann
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK. METTL17 is an Fe-S cluster checkpoint for mitochondrial translation. Mol Cell 2024; 84:359-374.e8. [PMID: 38199006 PMCID: PMC11046306 DOI: 10.1016/j.molcel.2023.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe4S4]2+ cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.
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Affiliation(s)
- Tslil Ast
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Shayan Sadre
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason G McCoy
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gil Namkoong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jordan C Wengrod
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Chicherin
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pallavi R Joshi
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Kamenski
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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Pellerin D, Danzi MC, Renaud M, Houlden H, Synofzik M, Zuchner S, Brais B. Spinocerebellar ataxia 27B: A novel, frequent and potentially treatable ataxia. Clin Transl Med 2024; 14:e1504. [PMID: 38279833 PMCID: PMC10819088 DOI: 10.1002/ctm2.1504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 01/29/2024] Open
Abstract
Hereditary ataxias, especially when presenting sporadically in adulthood, present a particular diagnostic challenge owing to their great clinical and genetic heterogeneity. Currently, up to 75% of such patients remain without a genetic diagnosis. In an era of emerging disease-modifying gene-stratified therapies, the identification of causative alleles has become increasingly important. Over the past few years, the implementation of advanced bioinformatics tools and long-read sequencing has allowed the identification of a number of novel repeat expansion disorders, such as the recently described spinocerebellar ataxia 27B (SCA27B) caused by a (GAA)•(TTC) repeat expansion in intron 1 of the fibroblast growth factor 14 (FGF14) gene. SCA27B is rapidly gaining recognition as one of the most common forms of adult-onset hereditary ataxia, with several studies showing that it accounts for a substantial number (9-61%) of previously undiagnosed cases from different cohorts. First natural history studies and multiple reports have already outlined the progression and core phenotype of this novel disease, which consists of a late-onset slowly progressive pan-cerebellar syndrome that is frequently associated with cerebellar oculomotor signs, such as downbeat nystagmus, and episodic symptoms. Furthermore, preliminary studies in patients with SCA27B have shown promising symptomatic benefits of 4-aminopyridine, an already marketed drug. This review describes the current knowledge of the genetic and molecular basis, epidemiology, clinical features and prospective treatment strategies in SCA27B.
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Affiliation(s)
- David Pellerin
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and InstituteMcGill UniversityMontrealQuebecCanada
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and NeurosurgeryUniversity College LondonLondonUK
| | - Matt C. Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human GenomicsUniversity of Miami Miller School of MedicineMiamiFloridaUSA
| | - Mathilde Renaud
- INSERM‐U1256 NGEREUniversité de LorraineNancyFrance
- Service de Neurologie, CHRU de NancyNancyFrance
- Service de Génétique Clinique, CHRU de NancyNancyFrance
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and NeurosurgeryUniversity College LondonLondonUK
| | - Matthis Synofzik
- Division of Translational Genomics of Neurodegenerative DiseasesHertie‐Institute for Clinical Brain Research and Center of Neurology, University of TübingenTübingenGermany
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human GenomicsUniversity of Miami Miller School of MedicineMiamiFloridaUSA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and InstituteMcGill UniversityMontrealQuebecCanada
- Department of Human GeneticsMcGill UniversityMontrealQuebecCanada
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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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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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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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Yaméogo P, Gérard C, Majeau N, Tremblay JP. Removal of the GAA repeat in the heart of a Friedreich's ataxia mouse model using CjCas9. Gene Ther 2023; 30:612-619. [PMID: 36781946 DOI: 10.1038/s41434-023-00387-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
Most Friedreich ataxia (FRDA) cases are caused by the elongation of the GAA repeat (GAAr) sequence in the first intron of the FXN gene, leading to a decrease of the frataxin protein expression. Deletion of this GAAr with CRISPR/Cas9 technology leads to an increase in frataxin expression in vitro. We are therefore aiming to develop FRDA treatment based on the deletion of GAAr with CRISPR/Cas9 technology using a single AAV expressing a small Cas9 (CjCas9) and two single guide RNAs (sgRNAs) targeting the FXN gene. This AAV was intraperitoneally administrated to YG8sR (250-300 GAAr) and to YG8-800 (800 GAAr) mice. DNA and RNA were extracted from different organs a month later. PCR amplification of part of intron 1 of the FXN gene detected some GAAr deletion in some cells in heart and liver of both mouse models, but the editing rate was not sufficient to cause an increase in frataxin mRNA in the heart. However, the correlation observed between the editing rate and the distribution of AAV suggests a possible therapy based on the removal of the GAAr with a better delivery tool of the CRISPR/Cas9 system.
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Affiliation(s)
- Pouiré Yaméogo
- Centre de Recherche du CHU de Québec-Université Laval, Québec city, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Québec city, QC, Canada
| | - Catherine Gérard
- Centre de Recherche du CHU de Québec-Université Laval, Québec city, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Québec city, QC, Canada
| | - Nathalie Majeau
- Centre de Recherche du CHU de Québec-Université Laval, Québec city, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Québec city, QC, Canada
| | - Jacques P Tremblay
- Centre de Recherche du CHU de Québec-Université Laval, Québec city, QC, Canada.
- Département de Médecine Moléculaire, Université Laval, Québec city, QC, Canada.
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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11
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Phenotype and management of neurologic intronic repeat disorders (NIRDs). Rev Neurol (Paris) 2023; 179:173-182. [PMID: 36371266 DOI: 10.1016/j.neurol.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/11/2022]
Abstract
During recent years an increasing number of neurologic disorders due to expanded tri-, tetra-, penta-, or hexa-nucleotide repeat motifs in introns of various genes have been described (neurologic intronic repeat disorders (NIRDs)). The repeat may be pathogenic in the heterozygous or homozygous form. Repeat lengths vary considerably and can be stable or unstable during transmission to the next generation. The most well-known NIRDs are Friedreich ataxia, spinocerebellar ataxia types-10, -31, and -36, CANVAS, C9Orf72 familial amyotrophic lateral sclerosis (fALS), and myotonic dystrophy-2 (MD2). Phenotypically, NIRDs manifest as mono-organ (e.g. spinocerebellar ataxia type 31) or multi-organ disease (e.g. Friedreich ataxia, myotonic dystrophy-2). A number of other more rare NIRDs have been recently detected. This review aims at summarising and discussing previous findings and recent advances concerning the etiology, pathophysiology, clinical presentation, and therapeutic management of the most common NIRDs.
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Kalef-Ezra E, Edzeamey FJ, Valle A, Khonsari H, Kleine P, Oggianu C, Al-Mahdawi S, Pook MA, Anjomani Virmouni S. A new FRDA mouse model [ Fxn null:YG8s(GAA) > 800] with more than 800 GAA repeats. Front Neurosci 2023; 17:930422. [PMID: 36777637 PMCID: PMC9909538 DOI: 10.3389/fnins.2023.930422] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction Friedreich's ataxia (FRDA) is an inherited recessive neurodegenerative disorder caused by a homozygous guanine-adenine-adenine (GAA) repeat expansion within intron 1 of the FXN gene, which encodes the essential mitochondrial protein frataxin. There is still no effective therapy for FRDA, therefore the development of optimal cell and animal models of the disease is one of the priorities for preclinical therapeutic testing. Methods We obtained the latest FRDA humanized mouse model that was generated on the basis of our previous YG8sR, by Jackson laboratory [YG8JR, Fxn null:YG8s(GAA) > 800]. We characterized the behavioral, cellular, molecular and epigenetics properties of the YG8JR model, which has the largest GAA repeat sizes compared to all the current FRDA mouse models. Results We found statistically significant behavioral deficits, together with reduced levels of frataxin mRNA and protein, and aconitase activity in YG8JR mice compared with control Y47JR mice. YG8JR mice exhibit intergenerational GAA repeat instability by the analysis of parent and offspring tissue samples. Somatic GAA repeat instability was also detected in individual brain and cerebellum tissue samples. In addition, increased DNA methylation of CpG U13 was identified in FXN GAA repeat region in the brain, cerebellum, and heart tissues. Furthermore, we show decreased histone H3K9 acetylation and increased H3K9 methylation of YG8JR cerebellum tissues within the FXN gene, upstream and downstream of the GAA repeat region compared to Y47JR controls. Discussion These studies provide a detailed characterization of the GAA repeat expansion-based YG8JR transgenic mouse models that will help investigations of FRDA disease mechanisms and therapy.
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Affiliation(s)
- Ester Kalef-Ezra
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Fred Jonathan Edzeamey
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Adamo Valle
- Energy Metabolism and Nutrition, Research Institute of Health Sciences (IUNICS), University of Balearic Islands, Palma, Spain,Health Research Institute of Balearic Islands (IdISBa), Palma, Spain,Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBERobn CB06/03/0043), Instituto de Salud Carlos III, Madrid, Spain
| | - Hassan Khonsari
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Paula Kleine
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Carlo Oggianu
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark A. Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sara Anjomani Virmouni
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom,*Correspondence: Sara Anjomani Virmouni,
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13
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Basri R, Awan FM, Yang BB, Awan UA, Obaid A, Naz A, Ikram A, Khan S, Haq IU, Khan SN, Aqeel MB. Brain-protective mechanisms of autophagy associated circRNAs: Kick starting self-cleaning mode in brain cells via circRNAs as a potential therapeutic approach for neurodegenerative diseases. Front Mol Neurosci 2023; 15:1078441. [PMID: 36727091 PMCID: PMC9885805 DOI: 10.3389/fnmol.2022.1078441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Altered autophagy is a hallmark of neurodegeneration but how autophagy is regulated in the brain and dysfunctional autophagy leads to neuronal death has remained cryptic. Being a key cellular waste-recycling and housekeeping system, autophagy is implicated in a range of brain disorders and altering autophagy flux could be an effective therapeutic strategy and has the potential for clinical applications down the road. Tight regulation of proteins and organelles in order to meet the needs of complex neuronal physiology suggests that there is distinct regulatory pattern of neuronal autophagy as compared to non-neuronal cells and nervous system might have its own separate regulator of autophagy. Evidence has shown that circRNAs participates in the biological processes of autophagosome assembly. The regulatory networks between circRNAs, autophagy, and neurodegeneration remains unknown and warrants further investigation. Understanding the interplay between autophagy, circRNAs and neurodegeneration requires a knowledge of the multiple steps and regulatory interactions involved in the autophagy pathway which might provide a valuable resource for the diagnosis and therapy of neurodegenerative diseases. In this review, we aimed to summarize the latest studies on the role of brain-protective mechanisms of autophagy associated circRNAs in neurodegenerative diseases (including Alzheimer's disease, Parkinson's disease, Huntington's disease, Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, and Friedreich's ataxia) and how this knowledge can be leveraged for the development of novel therapeutics against them. Autophagy stimulation might be potential one-size-fits-all therapy for neurodegenerative disease as per considerable body of evidence, therefore future research on brain-protective mechanisms of autophagy associated circRNAs will illuminate an important feature of nervous system biology and will open the door to new approaches for treating neurodegenerative diseases.
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Affiliation(s)
- Rabea Basri
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan,*Correspondence: Faryal Mehwish Awan, ✉ ;
| | - Burton B. Yang
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Usman Ayub Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Ayesha Obaid
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Aqsa Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Ijaz ul Haq
- Department of Public Health and Nutrition, The University of Haripur (UOH), Haripur, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Muslim Bin Aqeel
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
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14
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Keita M, McIntyre K, Rodden LN, Schadt K, Lynch DR. Friedreich ataxia: clinical features and new developments. Neurodegener Dis Manag 2022; 12:267-283. [PMID: 35766110 PMCID: PMC9517959 DOI: 10.2217/nmt-2022-0011] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Friedreich's ataxia (FRDA), a neurodegenerative disease characterized by ataxia and other neurological features, affects 1 in 50,000-100,000 individuals in the USA. However, FRDA also includes cardiac, orthopedic and endocrine dysfunction, giving rise to many secondary disease characteristics. The multifaceted approach for clinical care has necessitated the development of disease-specific clinical care guidelines. New developments in FRDA include the advancement of clinical drug trials targeting the NRF2 pathway and frataxin restoration. Additionally, a novel understanding of gene silencing in FRDA, reflecting a variegated silencing pattern, will have applications to current and future therapeutic interventions. Finally, new perspectives on the neuroanatomy of FRDA and its developmental features will refine the time course and anatomical targeting of novel approaches.
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Affiliation(s)
- Medina Keita
- Departments of Pediatrics & Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kellie McIntyre
- Departments of Pediatrics & Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Layne N Rodden
- Departments of Pediatrics & Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kim Schadt
- Departments of Pediatrics & Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David R Lynch
- Departments of Pediatrics & Neurology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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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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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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18
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Rodden LN, Gilliam KM, Lam C, Lynch DR, Bidichandani SI. Epigenetic Heterogeneity in Friedreich Ataxia Underlies Variable FXN Reactivation. Front Neurosci 2021; 15:752921. [PMID: 34899161 PMCID: PMC8655727 DOI: 10.3389/fnins.2021.752921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat in intron 1 of the FXN gene. The expanded repeat induces repressive histone changes and DNA hypermethylation, which result in epigenetic silencing and FXN transcriptional deficiency. A class I histone deacetylase inhibitor (HDACi-109) reactivates the silenced FXN gene, although with considerable inter-individual variability, which remains etiologically unexplained. Because HDAC inhibitors work by reversing epigenetic silencing, we reasoned that epigenetic heterogeneity among patients may help to explain this inter-individual variability. As a surrogate measure for epigenetic heterogeneity, a highly quantitative measurement of DNA hypermethylation via bisulfite deep sequencing, with single molecule resolution, was used to assess the prevalence of unmethylated, partially methylated, and fully methylated somatic FXN molecules in PBMCs from a prospective cohort of 50 FRDA patients. Treatment of the same PBMCs from this cohort with HDACi-109 significantly increased FXN transcript to levels seen in asymptomatic heterozygous carriers, albeit with the expected inter-individual variability. Response to HDACi-109 correlated significantly with the prevalence of unmethylated and partially methylated FXN molecules, supporting the model that FXN reactivation involves a proportion of genes that are amenable to correction in non-dividing somatic cells, and that heavily methylated FXN molecules are relatively resistant to reactivation. FXN reactivation is a promising therapeutic strategy in FRDA, and inter-individual variability is explained, at least in part, by somatic epigenetic heterogeneity.
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Affiliation(s)
- Layne N Rodden
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Oklahoma Center for Neuroscience, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kaitlyn M Gilliam
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Christina Lam
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - David R Lynch
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sanjay I Bidichandani
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Oklahoma Center for Neuroscience, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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19
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Yang W, Thompson B, Kwa FAA. Molecular approaches for the treatment and prevention of Friedreich's ataxia. Drug Discov Today 2021; 27:866-880. [PMID: 34763067 DOI: 10.1016/j.drudis.2021.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/01/2021] [Accepted: 11/01/2021] [Indexed: 12/11/2022]
Abstract
Friedreich's ataxia (FRDA) is caused by an intronic guanine-adenine-adenine (GAA) trinucleotide expansion in the gene encoding the frataxin protein (FXN). This triggers the transcriptional silencing of the fratxin gene (FXN) and subsequent FXN deficiency in affected cells, which accounts for the multisystemic symptoms of this condition. Current management strategies aim for symptomatic relief and no treatments can prevent disease onset or progression. Thus, research efforts have focused on targeting the molecular pathways that silence FXN and downstream pathological processes. However, progression of potential therapies into clinical use has been hindered by inconclusive clinical trials because of the small patient sample size associated with the low prevalence of this condition. Here, we discuss various molecular approaches and explore their therapeutic potential to alter the course of this progressive condition.
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Affiliation(s)
- Wenyao Yang
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Bruce Thompson
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Faith A A Kwa
- School of Health Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
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20
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Morales F, Corrales E, Zhang B, Vásquez M, Santamaría-Ulloa C, Quesada H, Sirito M, Estecio MR, Monckton DG, Krahe R. Myotonic dystrophy type 1 (DM1) clinical sub-types and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent. Hum Mol Genet 2021; 31:262-274. [PMID: 34432028 DOI: 10.1093/hmg/ddab243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a complex disease with a wide spectrum of symptoms. The exact relationship between mutant CTG repeat expansion size and clinical outcome remains unclear. DM1 congenital patients (CDM) inherit the largest expanded alleles, which are associated with abnormal and increased DNA methylation flanking the CTG repeat. However, DNA methylation at the DMPK locus remains understudied. Its relationship to DM1 clinical subtypes, expansion size and age-at-onset is not yet completely understood. Using pyrosequencing-based methylation analysis on 225 blood DNA samples from Costa Rican DM1 patients, we determined that the size of the estimated progenitor allele length (ePAL) is not only a good discriminator between CDM and non-CDM cases (with an estimated threshold at 653 CTG repeats), but also for all DM1 clinical subtypes. Secondly, increased methylation at both CTCF sites upstream and downstream of the expansion was almost exclusively present in CDM cases. Thirdly, levels of abnormal methylation were associated with clinical subtype, age and ePAL, with strong correlations between these variables. Fourthly, both ePAL and the intergenerational expansion size were significantly associated with methylation status. Finally, methylation status was associated with ePAL and maternal inheritance, with almost exclusively maternal transmission of CDM. In conclusion, increased DNA methylation at the CTCF sites flanking the DM1 expansion could be linked to ePAL, and both increased methylation and the ePAL could be considered biomarkers for the CDM phenotype.
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Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Eyleen Corrales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Baili Zhang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Melissa Vásquez
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Carolina Santamaría-Ulloa
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Hazel Quesada
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Mario Sirito
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Marcos R Estecio
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Ralf Krahe
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA.,Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, Texas, 77030-4009, USA
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21
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Napierala JS, Rajapakshe K, Clark A, Chen YY, Huang S, Mesaros C, Xu P, Blair IA, Hauser LA, Farmer J, Lynch DR, Edwards DP, Coarfa C, Napierala M. Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia. Mol Cell Proteomics 2021; 20:100094. [PMID: 33991687 PMCID: PMC8214145 DOI: 10.1016/j.mcpro.2021.100094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
Identifying biomarkers is important for assessment of disease progression, prediction of symptom development, and determination of treatment effectiveness. While unbiased analyses of differential gene expression using next-generation sequencing methods are now routinely conducted, proteomics studies are more challenging because of traditional methods predominantly being low throughput and offering a limited dynamic range for simultaneous detection of hundreds of proteins that drastically differ in their intracellular abundance. We utilized a sensitive and high-throughput proteomic technique, reverse phase protein array (RPPA), to attain protein expression profiles of primary fibroblasts obtained from patients with Friedreich's ataxia (FRDA) and unaffected controls (CTRLs). The RPPA was designed to detect 217 proteins or phosphorylated proteins by individual antibody, and the specificity of each antibody was validated prior to the experiment. Among 62 fibroblast samples (44 FRDA and 18 CTRLs) analyzed, 30 proteins/phosphoproteins were significantly changed in FRDA fibroblasts compared with CTRL cells (p < 0.05), mostly representing signaling molecules and metabolic enzymes. As expected, frataxin was significantly downregulated in FRDA samples, thus serving as an internal CTRL for assay integrity. Extensive bioinformatics analyses were conducted to correlate differentially expressed proteins with critical disease parameters (e.g., selected symptoms, age of onset, guanine-adenine-adenine sizes, frataxin levels, and Functional Assessment Rating Scale scores). Members of the integrin family of proteins specifically associated with hearing loss in FRDA. Also, RPPA data, combined with results of transcriptome profiling, uncovered defects in the retinoic acid metabolism pathway in FRDA samples. Moreover, expression of aldehyde dehydrogenase family 1 member A3 differed significantly between cardiomyopathy-positive and cardiomyopathy-negative FRDA cohorts, demonstrating that metabolites such as retinol, retinal, or retinoic acid could become potential predictive biomarkers of cardiac presentation in FRDA.
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Affiliation(s)
- Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Amanda Clark
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yu-Yun Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peining Xu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren A Hauser
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer Farmer
- Friedreich's Ataxia Research Alliance, Downingtown, Pennsylvania, USA
| | - David R Lynch
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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22
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Handal T, Eiges R. Correction of Heritable Epigenetic Defects Using Editing Tools. Int J Mol Sci 2021; 22:ijms22083966. [PMID: 33921346 PMCID: PMC8070094 DOI: 10.3390/ijms22083966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 11/21/2022] Open
Abstract
Epimutations refer to mistakes in the setting or maintenance of epigenetic marks in the chromatin. They lead to mis-expression of genes and are often secondary to germline transmitted mutations. As such, they are the cause for a considerable number of genetically inherited conditions in humans. The correction of these types of epigenetic defects constitutes a good paradigm to probe the fundamental mechanisms underlying the development of these diseases, and the molecular basis for the establishment, maintenance and regulation of epigenetic modifications in general. Here, we review the data to date, which is limited to repetitive elements, that relates to the applications of key editing tools for addressing the epigenetic aspects of various epigenetically regulated diseases. For each approach we summarize the efforts conducted to date, highlight their contribution to a better understanding of the molecular basis of epigenetic mechanisms, describe the limitations of each approach and suggest perspectives for further exploration in this field.
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Affiliation(s)
- Tayma Handal
- Stem Cell Research Laboratory, Medical Genetics Institute Shaare Zedek Medical Center, Jerusalem 91031, Israel;
- School of Medicine, The Hebrew University, Campus Ein Kerem, Jerusalem 91120, Israel
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute Shaare Zedek Medical Center, Jerusalem 91031, Israel;
- School of Medicine, The Hebrew University, Campus Ein Kerem, Jerusalem 91120, Israel
- Correspondence:
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23
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Bhattacharyya B, Mitra U, Bhattacharyya R. Tandem repeat interval pattern identifies animal taxa. Bioinformatics 2021; 37:2250-2258. [PMID: 33677492 DOI: 10.1093/bioinformatics/btab124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/11/2020] [Accepted: 02/22/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION We discover that maximality of information content among intervals of Tandem Repeats (TRs) in animal genome segregates over taxa such that taxa identification becomes swift and accurate. Successive TRs of a motif occur at intervals over the sequence, forming a trail of TRs of the motif across the genome. We present a method, Tandem Repeat Information Mining (TRIM), that mines 4k number of TR trails of all k length motifs from a whole genome sequence and extracts the information content within intervals of the trails. TRIM vector formed from the ordered set of interval entropies becomes instrumental for genome segregation. RESULTS Reconstruction of correct phylogeny for animals from whole genome sequences proves precision of TRIM. Identification of animal taxa by TRIM vector upon feature selection is the most significant achievement. These suggest Tandem Repeat Interval Pattern (TRIP) is a taxa-specific constitutional characteristic in animal genome. AVAILABILITY Source and executable code of TRIM along with usage manual are made available at https://github.com/BB-BiG/TRIM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Balaram Bhattacharyya
- Department of Computer and System Sciences, Visva-Bharati University, Santiniketan, 731235
| | - Uddalak Mitra
- Department of Computer and System Sciences, Visva-Bharati University, Santiniketan, 731235
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24
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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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25
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Fink JK. Hereditary Myelopathies. ACTA ACUST UNITED AC 2021; 27:185-204. [PMID: 33522742 DOI: 10.1212/con.0000000000000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE OF REVIEW This article guides clinicians in the clinical recognition and differential diagnosis of hereditary myelopathies. RECENT FINDINGS Rather than a disease, a disease process, or relating to specific cellular vulnerability, the term hereditary myelopathy refers to diverse inherited disorders in which major aspects of the clinical syndrome reflect disturbance of elements within the spinal cord (specifically, the dorsal columns and dorsal root ganglia, corticospinal tracts, and anterior horn cells). It is important to note that the clinical features of almost all hereditary myelopathies reflect not only disturbance of elements within the spinal cord but also disturbance of extraspinal structures (particularly, but not limited to, peripheral nerves and the cerebellum) and that these extraspinal clinical features can be very helpful in recognizing specific myelopathy syndromes. The value of classifying disorders as inherited myelopathies lies primarily in facilitating their clinical recognition and differential diagnosis. It is useful to recognize that many hereditary myelopathies conform to one of four clinical paradigms: (1) spinocerebellar ataxia, (2) motor neuron disorder, (3) leukodystrophy, or (4) distal motor-sensory axonopathy predominantly affecting the central nervous system. Although they are myelopathies, spinal dysraphisms such as spina bifida and myelomeningocele are not included in this context because they are not usually due to single-gene mutation and have low hereditability. SUMMARY This article illustrates clinical paradigms of hereditary myelopathy with clinical examples emphasizing the spectrum, clinical recognition, and differential diagnosis of hereditary myelopathies.
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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: 9] [Impact Index Per Article: 2.3] [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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27
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Castro AF, Loureiro JR, Bessa J, Silveira I. Antisense Transcription across Nucleotide Repeat Expansions in Neurodegenerative and Neuromuscular Diseases: Progress and Mysteries. Genes (Basel) 2020; 11:E1418. [PMID: 33261024 PMCID: PMC7760973 DOI: 10.3390/genes11121418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Unstable repeat expansions and insertions cause more than 30 neurodegenerative and neuromuscular diseases. Remarkably, bidirectional transcription of repeat expansions has been identified in at least 14 of these diseases. More remarkably, a growing number of studies has been showing that both sense and antisense repeat RNAs are able to dysregulate important cellular pathways, contributing together to the observed clinical phenotype. Notably, antisense repeat RNAs from spinocerebellar ataxia type 7, myotonic dystrophy type 1, Huntington's disease and frontotemporal dementia/amyotrophic lateral sclerosis associated genes have been implicated in transcriptional regulation of sense gene expression, acting either at a transcriptional or posttranscriptional level. The recent evidence that antisense repeat RNAs could modulate gene expression broadens our understanding of the pathogenic pathways and adds more complexity to the development of therapeutic strategies for these disorders. In this review, we cover the amazing progress made in the understanding of the pathogenic mechanisms associated with repeat expansion neurodegenerative and neuromuscular diseases with a focus on the impact of antisense repeat transcription in the development of efficient therapies.
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Affiliation(s)
- Ana F. Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.F.C.); (J.R.L.)
- IBMC-Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal;
- ICBAS, Universidade do Porto, 4050-313 Porto, Portugal
| | - Joana R. Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.F.C.); (J.R.L.)
- IBMC-Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal;
| | - José Bessa
- IBMC-Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal;
- Vertebrate Development and Regeneration Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (A.F.C.); (J.R.L.)
- IBMC-Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal;
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28
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Santoro M, Perna A, La Rosa P, Petrillo S, Piemonte F, Rossi S, Riso V, Nicoletti TF, Modoni A, Pomponi MG, Chiurazzi P, Silvestri G. Compound heterozygosity for an expanded (GAA) and a (GAAGGA) repeat at FXN locus: from a diagnostic pitfall to potential clues to the pathogenesis of Friedreich ataxia. Neurogenetics 2020; 21:279-287. [PMID: 32638185 DOI: 10.1007/s10048-020-00620-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/14/2020] [Indexed: 12/23/2022]
Abstract
Friedreich's ataxia (FRDA) is usually due to a homozygous GAA expansion in intron 1 of the frataxin (FXN) gene. Rarely, uncommon molecular rearrangements at the FXN locus can cause pitfalls in the molecular diagnosis of FRDA. Here we describe a family whose proband was affected by late-onset Friedreich's ataxia (LOFA); long-range PCR (LR-PCR) documented two small expanded GAA alleles both in the proband and in her unaffected younger sister, who therefore received a diagnosis of pre-symptomatic LOFA. Later studies, however, revealed that the proband's unaffected sister, as well as their healthy mother, were both carriers of an expanded GAA allele and an uncommon (GAAGGA)66-67 repeat mimicking a GAA expansion at the LR-PCR that was the cause of the wrong initial diagnosis of pre-symptomatic LOFA. Extensive studies in tissues from all the family members, including LR-PCR, assessment of methylation status of FXN locus, MboII restriction analysis and direct sequencing of LR-PCR products, analysis of FXN mRNA, and frataxin protein expression, support the virtual lack of pathogenicity of the rare (GAAGGA)66-67 repeat, also providing significant data about the modulation of epigenetic modifications at the FXN locus. Overall, this report highlights a rare but possible pitfall in FRDA molecular diagnosis, emphasizing the need of further analysis in case of discrepancy between clinical and molecular data.
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Affiliation(s)
- Massimo Santoro
- IRCCS Fondazione Don Carlo Gnocchi, Piazzale Morandi, 6, 20121, Milan, Italy
| | - Alessia Perna
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
| | - Piergiorgio La Rosa
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Sara Petrillo
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Fiorella Piemonte
- Unit of Muscular and Neurodegenerative Diseases, Ospedale Pediatrico Bambino Gesù, IRCCS, Viale San Paolo, 15, 00146, Rome, Italy
| | - Salvatore Rossi
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
| | - Vittorio Riso
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Tommaso Filippo Nicoletti
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Anna Modoni
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Maria Grazia Pomponi
- Institute of Genomic Medicine, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Pietro Chiurazzi
- Institute of Genomic Medicine, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy
| | - Gabriella Silvestri
- Dept of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Scaro Cuore, L.go F. Vito 1, 000168, Rome, Italy.
- Institute of Neurology, Neuroscience Area, Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00168, Rome, Italy.
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Mazzara PG, Muggeo S, Luoni M, Massimino L, Zaghi M, Valverde PTT, Brusco S, Marzi MJ, Palma C, Colasante G, Iannielli A, Paulis M, Cordiglieri C, Giannelli SG, Podini P, Gellera C, Taroni F, Nicassio F, Rasponi M, Broccoli V. Frataxin gene editing rescues Friedreich's ataxia pathology in dorsal root ganglia organoid-derived sensory neurons. Nat Commun 2020; 11:4178. [PMID: 32826895 PMCID: PMC7442818 DOI: 10.1038/s41467-020-17954-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 07/28/2020] [Indexed: 12/31/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal-recessive neurodegenerative and cardiac disorder which occurs when transcription of the FXN gene is silenced due to an excessive expansion of GAA repeats into its first intron. Herein, we generate dorsal root ganglia organoids (DRG organoids) by in vitro differentiation of human iPSCs. Bulk and single-cell RNA sequencing show that DRG organoids present a transcriptional signature similar to native DRGs and display the main peripheral sensory neuronal and glial cell subtypes. Furthermore, when co-cultured with human intrafusal muscle fibers, DRG organoid sensory neurons contact their peripheral targets and reconstitute the muscle spindle proprioceptive receptors. FRDA DRG organoids model some molecular and cellular deficits of the disease that are rescued when the entire FXN intron 1 is removed, and not with the excision of the expanded GAA tract. These results strongly suggest that removal of the repressed chromatin flanking the GAA tract might contribute to rescue FXN total expression and fully revert the pathological hallmarks of FRDA DRG neurons.
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Affiliation(s)
- Pietro Giuseppe Mazzara
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- Department of Neuroscience, The Scripps Research Institute, 92037, La Jolla, CA, USA
| | - Sharon Muggeo
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luca Massimino
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Mattia Zaghi
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | | | - Simone Brusco
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Cecilia Palma
- Department of Electronics, Information & Bioengineering, Politecnico di Milano, 20133, Milan, Italy
| | - Gaia Colasante
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Angelo Iannielli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy
| | - Marianna Paulis
- Humanitas Clinical and Research Center, 20089, Rozzano, Milano, Italy
| | - Chiara Cordiglieri
- National Institute of Molecular Genetics "Romeo e Enrica Invernizzi" - INGM, 20122, Milan, Italy
| | - Serena Gea Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy
| | - Marco Rasponi
- Department of Electronics, Information & Bioengineering, Politecnico di Milano, 20133, Milan, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132, Milan, Italy.
- National Research Council (CNR), Institute of Neuroscience, 20129, Milan, Italy.
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30
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Li J, Li Y, Wang J, Gonzalez TJ, Asokan A, Napierala JS, Napierala M. Defining Transcription Regulatory Elements in the Human Frataxin Gene: Implications for Gene Therapy. Hum Gene Ther 2020; 31:839-851. [PMID: 32527155 PMCID: PMC7462031 DOI: 10.1089/hum.2020.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
Friedreich's ataxia (FRDA) is the most common inherited form of ataxia in humans. It is caused by severe downregulation of frataxin (FXN) expression instigated by hyperexpansion of the GAA repeats located in intron 1 of the FXN gene. Despite numerous studies focused on identifying compounds capable of stimulating FXN expression, current knowledge regarding cis-regulatory elements involved in FXN gene expression is lacking. Using a combination of episomal and genome-integrated constructs, we defined a minimal endogenous promoter sequence required to efficiently drive FXN expression in human cells. We generated 19 constructs varying in length of the DNA sequences upstream and downstream of the ATG start codon. Using transient transfection, we evaluated the capability of these constructs to drive FXN expression. These analyses allowed us to identify a region of the gene indispensable for FXN expression. Subsequently, selected constructs containing the FXN expression control regions of varying lengths were site specifically integrated into the genome of HEK293T and human-induced pluripotent stem cells (iPSCs). FXN expression was detected in iPSCs and persisted after differentiation to neuronal and cardiac cells, indicating lineage independent function of defined regulatory DNA sequences. Finally, based on these results, we generated AAV encoding miniFXN genes and demonstrated in vivo FXN expression in mice. Results of these studies identified FXN sequences necessary to express FXN in human and mouse cells and provided rationale for potential use of endogenous FXN sequence in gene therapy strategies for FRDA.
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Affiliation(s)
- Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trevor J. Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jill S. Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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31
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Ruiz Buendía GA, Leleu M, Marzetta F, Vanzan L, Tan JY, Ythier V, Randall EL, Marques AC, Baubec T, Murr R, Xenarios I, Dion V. Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. SCIENCE ADVANCES 2020; 6:eaaz4012. [PMID: 32656337 PMCID: PMC7334000 DOI: 10.1126/sciadv.aaz4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.
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Affiliation(s)
- Gustavo A. Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Flavia Marzetta
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Jennifer Y. Tan
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Victor Ythier
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Emma L. Randall
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
| | - Ana C. Marques
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Rabih Murr
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
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Sherzai M, Valle A, Perry N, Kalef-Ezra E, Al-Mahdawi S, Pook M, Anjomani Virmouni S. HMTase Inhibitors as a Potential Epigenetic-Based Therapeutic Approach for Friedreich's Ataxia. Front Genet 2020; 11:584. [PMID: 32582297 PMCID: PMC7291394 DOI: 10.3389/fgene.2020.00584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/17/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disorder caused by a homozygous GAA repeat expansion mutation in intron 1 of the frataxin gene (FXN), which instigates reduced transcription. As a consequence, reduced levels of frataxin protein lead to mitochondrial iron accumulation, oxidative stress, and ultimately cell death; particularly in dorsal root ganglia (DRG) sensory neurons and the dentate nucleus of the cerebellum. In addition to neurological disability, FRDA is associated with cardiomyopathy, diabetes mellitus, and skeletal deformities. Currently there is no effective treatment for FRDA and patients die prematurely. Recent findings suggest that abnormal GAA expansion plays a role in histone modification, subjecting the FXN gene to heterochromatin silencing. Therefore, as an epigenetic-based therapy, we investigated the efficacy and tolerability of two histone methyltransferase (HMTase) inhibitor compounds, BIX0194 (G9a-inhibitor) and GSK126 (EZH2-inhibitor), to specifically target and reduce H3K9me2/3 and H3K27me3 levels, respectively, in FRDA fibroblasts. We show that a combination treatment of BIX0194 and GSK126, significantly increased FXN gene expression levels and reduced the repressive histone marks. However, no increase in frataxin protein levels was observed. Nevertheless, our results are still promising and may encourage to investigate HMTase inhibitors with other synergistic epigenetic-based therapies for further preliminary studies.
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Affiliation(s)
- Mursal Sherzai
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Adamo Valle
- Energy Metabolism and Nutrition, Research Institute of Health Sciences (IUNICS) and Health Research Institute of Balearic Islands (IdISBa), University of Balearic Islands, Palma de Mallorca, Spain.,Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Nicholas Perry
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Ester Kalef-Ezra
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sara Anjomani Virmouni
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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Rocca CJ, Rainaldi JN, Sharma J, Shi Y, Haquang JH, Luebeck J, Mali P, Cherqui S. CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia. Mol Ther Methods Clin Dev 2020; 17:1026-1036. [PMID: 32462051 PMCID: PMC7240056 DOI: 10.1016/j.omtm.2020.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/26/2022]
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by expansion of GAA repeats in intron 1 of the frataxin (FXN) gene, leading to significant decreased expression of frataxin, a mitochondrial iron-binding protein. We previously reported that syngeneic hematopoietic stem and progenitor cell (HSPC) transplantation prevented neurodegeneration in the FRDA mouse model YG8R. We showed that the mechanism of rescue was mediated by the transfer of the functional frataxin from HSPC-derived microglia/macrophage cells to neurons/myocytes. In this study, we report the first step toward an autologous HSPC transplantation using the CRISPR-Cas9 system for FRDA. We first identified a pair of CRISPR RNAs (crRNAs) that efficiently removes the GAA expansions in human FRDA lymphoblasts, restoring the non-pathologic level of frataxin expression and normalizing mitochondrial activity. We also optimized the gene-editing approach in HSPCs isolated from healthy and FRDA patients' peripheral blood and demonstrated normal hematopoiesis of gene-edited cells in vitro and in vivo. The procedure did not induce cellular toxic effect or major off-target events, but a p53-mediated cell proliferation delay was observed in the gene-edited cells. This study provides the foundation for the clinical translation of autologous transplantation of gene-corrected HSPCs for FRDA.
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Affiliation(s)
- Celine J. Rocca
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph N. Rainaldi
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jay Sharma
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yanmeng Shi
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph H. Haquang
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jens Luebeck
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Cherqui
- Division of Genetics, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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Fernández-Frías I, Pérez-Luz S, Díaz-Nido J. Analysis of Putative Epigenetic Regulatory Elements in the FXN Genomic Locus. Int J Mol Sci 2020; 21:E3410. [PMID: 32408537 PMCID: PMC7279236 DOI: 10.3390/ijms21103410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/05/2020] [Accepted: 05/09/2020] [Indexed: 12/22/2022] Open
Abstract
Friedreich´s ataxia (FRDA) is an autosomal recessive disease caused by an abnormally expanded Guanine-Adenine-Adenine (GAA) repeat sequence within the first intron of the frataxin gene (FXN). The molecular mechanisms associated with FRDA are still poorly understood and most studies on FXN gene regulation have been focused on the region around the minimal promoter and the region in which triplet expansion occurs. Nevertheless, since there could be more epigenetic changes involved in the reduced levels of FXN transcripts, the aim of this study was to obtain a more detailed view of the possible regulatory elements by analyzing data from ENCODE and Roadmap consortia databases. This bioinformatic analysis indicated new putative regulatory regions within the FXN genomic locus, including exons, introns, and upstream and downstream regions. Moreover, the region next to the end of intron 4 is of special interest, since the enhancer signals in FRDA-affected tissues are weak or absent in this region, whilst they are strong in the rest of the analyzed tissues. Therefore, these results suggest that there could be a direct relationship between the absence of enhancer sequences in this specific region and their predisposition to be affected in this pathology.
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Affiliation(s)
- Iván Fernández-Frías
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
| | - Sara Pérez-Luz
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
| | - Javier Díaz-Nido
- Departamento Biología Molecular and Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (I.F.-F.); (J.D.-N.)
- Instituto Investigación Sanitaria Puerta de Hierro-Majadahonda, 28222 Madrid, Spain
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Armstrong MJ, Jin Y, Allen EG, Jin P. Diverse and dynamic DNA modifications in brain and diseases. Hum Mol Genet 2019; 28:R241-R253. [PMID: 31348493 PMCID: PMC6872432 DOI: 10.1093/hmg/ddz179] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is a class of epigenetic modification essential for coordinating gene expression timing and magnitude throughout normal brain development and for proper brain function following development. Aberrant methylation changes are associated with changes in chromatin architecture, transcriptional alterations and a host of neurological disorders and diseases. This review highlights recent advances in our understanding of the methylome's functionality and covers potential new roles for DNA methylation, their readers, writers, and erasers. Additionally, we examine novel insights into the relationship between the methylome, DNA-protein interactions, and their contribution to neurodegenerative diseases. Lastly, we outline the gaps in our knowledge that will likely be filled through the widespread use of newer technologies that provide greater resolution into how individual cell types are affected by disease and the contribution of each individual modification site to disease pathogenicity.
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Affiliation(s)
- Matthew J Armstrong
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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Weng L, Wang Q, Yu S, Yang X, Lynch DR, Mesaros C, Blair IA. Evaluation of antibodies for western blot analysis of frataxin protein isoforms. J Immunol Methods 2019; 474:112629. [PMID: 31279523 PMCID: PMC6829029 DOI: 10.1016/j.jim.2019.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/21/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022]
Abstract
Frataxin is the protein that is down-regulated in Friedreich ataxia (FRDA), an autosomal recessive genetic disease caused by an intronic GAA repeat expansion in intron-1 of the FXN gene. The GAA repeats result in epigenetic silencing of the FXN gene and reduced expression of the cytosolic full-length frataxin (1-210) protein. Full length frataxin translocates to the mitochondria, leading to formation of mature frataxin (81-210) formed by cleavage of the mitochondrial targeting sequence at K-80 of the full-length protein. There are currently no approved treatments for FRDA, although experimental approaches involving up-regulation or replacement of mature frataxin protein through numerous approaches are being tested. Many of the pre-clinical studies of these experimental approaches are conducted in mouse and monkey models as well as in human cell lines. Consequently, well-validated antibodies are required for use in western blot analysis to determine whether levels of various forms of frataxin have been increased. Here we examined the specificity of five commercially available anti-frataxin antibodies and determined whether they detect mature frataxin in mouse heart tissue. Four protein standards of monkey, human, and mouse frataxin as well as mouse heart tissue were examined using polyacrylamide gel electrophoresis (PAGE) in combination with western blot analysis. One antibody failed to detect any of the frataxin standards or endogenous frataxin in mouse heart tissue. Three of the antibodies detected a protein in mouse heart tissue that ran slightly faster on PAGE (at 23.4 kDa) to that predicted for full-length frataxin (23.9 kDa). One antibody detected all four frataxin standards as well as endogenous mouse mature frataxin in mouse tissue. Significantly, this antibody, which will be useful for monitoring mature frataxin levels in monkey, human, and mouse tissues, did not detect a protein in mouse heart tissue at 23.4 kDa. Therefore, antibodies detecting the immunoreactive protein at 23.4 kDa could be misleading when testing for the up-regulation of frataxin in animal models.
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Affiliation(s)
- Liwei Weng
- Penn/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Wang
- Penn/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixiang Yu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaolu Yang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David R Lynch
- Penn/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics and Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Clementina Mesaros
- Penn/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Blair
- Penn/CHOP Center of Excellence in Friedreich's Ataxia, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Fedotova E, Abramycheva N, Nuzhny E, Ershova M, Klyushnikov S, Illarioshkin S. Friedreich ataxia: FXN gene expression and its relationship with DNA methylation pattern. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Friedreich ataxia (FRDA) is the most common autosomal recessive ataxia associated with the non-coding GAA tandem repeats expansion in the FXN gene. Transcription impairment and frataxin protein deficiency are the key features of the disease pathogenesis. Our research was aimed to study the FXN gene mRNA expression as well as to carry out the clinical, genetic and epigenetic correlation analysis in a group of patients with homozygous expansion, in a group of their relatives with heterozygous expansion and in a control group. The FXN mRNA level was determined using the real-time polymerase chain reaction. Methylation pattern of CpG sites was evaluated by direct bisulfite sequencing. As a result of the study, the threshold values were obtained between the FRDA patients group, the group of heterozygous carriers and the control group (15 and 79%, respectively). The clinical and genetic features comparison with the FXN expression level revealed no significant correlation. When comparing gene expression with an epigenetic profile, it was found that hypermethylation of a number of CpG sites upstream of the trinucleotide repeats and some non-CpG sites downstream of the region of repeats inhibited expression. Thus, the identified methylated sites may be considered as a target for epigenome editing to increase the FXN transcription and, consequently, for target therapy of the disease.
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Affiliation(s)
| | | | - E.P. Nuzhny
- Research Center of Neurology, Moscow, Russia
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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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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: 74] [Impact Index Per Article: 14.8] [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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Jasoliya M, Sacca F, Sahdeo S, Chedin F, Pane C, Brescia Morra V, Filla A, Pook M, Cortopassi G. Dimethyl fumarate dosing in humans increases frataxin expression: A potential therapy for Friedreich's Ataxia. PLoS One 2019; 14:e0217776. [PMID: 31158268 PMCID: PMC6546270 DOI: 10.1371/journal.pone.0217776] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/18/2019] [Indexed: 11/19/2022] Open
Abstract
Friedreich's Ataxia (FA) is an inherited neurodegenerative disorder resulting from decreased expression of the mitochondrial protein frataxin, for which there is no approved therapy. High throughput screening of clinically used drugs identified Dimethyl fumarate (DMF) as protective in FA patient cells. Here we demonstrate that DMF significantly increases frataxin gene (FXN) expression in FA cell model, FA mouse model and in DMF treated humans. DMF also rescues mitochondrial biogenesis deficiency in FA-patient derived cell model. We further examined the mechanism of DMF's frataxin induction in FA patient cells. It has been shown that transcription-inhibitory R-loops form at GAA expansion mutations, thus decreasing FXN expression. In FA patient cells, we demonstrate that DMF significantly increases transcription initiation. As a potential consequence, we observe significant reduction in both R-loop formation and transcriptional pausing thereby significantly increasing FXN expression. Lastly, DMF dosed Multiple Sclerosis (MS) patients showed significant increase in FXN expression by ~85%. Since inherited deficiency in FXN is the primary cause of FA, and DMF is demonstrated to increase FXN expression in humans, DMF could be considered for Friedreich's therapy.
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Affiliation(s)
- Mittal Jasoliya
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Francesco Sacca
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Sunil Sahdeo
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California, United States of America
| | - Chiara Pane
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Vincenzo Brescia Morra
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Alessandro Filla
- Department of Neurosciences, Odontostomatological and Reproductive Sciences, University Federico II, Naples, Italy
| | - Mark Pook
- Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Gino Cortopassi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California, United States of America
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Srivastava S, Avvaru AK, Sowpati DT, Mishra RK. Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 2019; 20:153. [PMID: 30795733 PMCID: PMC6387519 DOI: 10.1186/s12864-019-5516-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/07/2019] [Indexed: 11/28/2022] Open
Abstract
Background Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite the huge resource of genomic information currently available, SSRs have been studied in a limited context and compared across relatively few species. Results We have identified ~ 685 million eukaryotic microsatellites and analyzed their genomic trends across 15 taxonomic subgroups from protists to mammals. The distribution of SSRs reveals taxon-specific variations in their exonic, intronic and intergenic densities. Our analysis reveals the differences among non-related species and novel patterns uniquely demarcating closely related species. We document several repeats common across subgroups as well as rare SSRs that are excluded almost throughout evolution. We further identify species-specific signatures in pathogens like Leishmania as well as in cereal crops, Drosophila, birds and primates. We also find that distinct SSRs preferentially exist as long repeating units in different subgroups; most unicellular organisms show no length preference for any SSR class, while many SSR motifs accumulate as long repeats in complex organisms, especially in mammals. Conclusions We present a comprehensive analysis of SSRs across taxa at an unprecedented scale. Our analysis indicates that the SSR composition of organisms with heterogeneous cell types is highly constrained, while simpler organisms such as protists, green algae and fungi show greater diversity in motif abundance, density and GC content. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and for studying their roles across the evolutionary landscape. Electronic supplementary material The online version of this article (10.1186/s12864-019-5516-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Surabhi Srivastava
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Akshay Kumar Avvaru
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Divya Tej Sowpati
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| | - Rakesh K Mishra
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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Abstract
Friedreich's ataxia (FRDA) is a degenerative disease that affects both the central and the peripheral nervous systems and non-neural tissues including, mainly, heart, and endocrine pancreas. It is an autosomal recessive disease caused by a GAA triplet-repeat localized within an Alu sequence element in intron 1 of frataxin (FXN) gene, which encodes a mitochondrial protein FXN. This protein is essential for mitochondrial function by the involvement of iron-sulfur cluster biogenesis. The effects of its deficiency also include disruption of cellular, particularly mitochondrial, iron homeostasis, i.e., relatively more iron accumulated in mitochondria and less iron presented in cytosol. Though iron toxicity is commonly thought to be mediated via Fenton reaction, oxidative stress seems not to be the main problem to result in detrimental effects on cell survival, particularly neuron survival. Therefore, the basic research on FXN function is urgently demanded to understand the disease. This chapter focuses on the outcome of FXN expression, regulation, and function in cellular or animal models of FRDA and on iron pathophysiology in the affected tissues. Finally, therapeutic strategies based on the control of iron toxicity and iron cellular redistribution are considered. The combination of multiple therapeutic targets including iron, oxidative stress, mitochondrial function, and FXN regulation is also proposed.
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Affiliation(s)
- Kuanyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210093, People's Republic of China.
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43
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Mikaeili H, Sandi M, Bayot A, Al-Mahdawi S, Pook MA. FAST-1 antisense RNA epigenetically alters FXN expression. Sci Rep 2018; 8:17217. [PMID: 30464193 PMCID: PMC6249312 DOI: 10.1038/s41598-018-35639-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022] Open
Abstract
Friedreich ataxia (FRDA) is a multisystem genetic disorder caused by GAA repeat expansion mutations within the FXN gene, resulting in heterochromatin formation and deficiency of frataxin protein. Elevated levels of the FXN antisense transcript (FAST-1) have previously been detected in FRDA. To investigate the effects of FAST-1 on the FXN gene expression, we first stably overexpressed FAST-1 in non-FRDA cell lines and then we knocked down FAST-1 in FRDA fibroblast cells. We observed decreased FXN expression in each FAST-1 overexpressing cell type compared to control cells. We also found that FAST-1 overexpression is associated with both CCCTC-Binding Factor (CTCF) depletion and heterochromatin formation at the 5'UTR of the FXN gene. We further showed that knocking down FAST-1 in FRDA fibroblast cells significantly increased FXN expression. Our results indicate that FAST-1 can act in trans in a similar manner to the cis-acting FAST-1 overexpression that has previously been identified in FRDA fibroblasts. The effects of stably transfected FAST-1 expression on CTCF occupancy and heterochromatin formation at the FXN locus suggest a direct role for FAST-1 in the FRDA molecular disease mechanism. Our findings also support the hypothesis that inhibition of FAST-1 may be a potential approach for FRDA therapy.
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Affiliation(s)
- Hajar Mikaeili
- Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, and Synthetic Biology Theme, Institute of Environment, Health & Societies, Brunel University London, Uxbridge, United Kingdom
| | - Madhavi Sandi
- Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, and Synthetic Biology Theme, Institute of Environment, Health & Societies, Brunel University London, Uxbridge, United Kingdom
| | - Aurélien Bayot
- Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, and Synthetic Biology Theme, Institute of Environment, Health & Societies, Brunel University London, Uxbridge, United Kingdom
- Mitochondrial Biology Group, CNRS UMR 3691, Departement of Cell Biology and Infection, Institut Pasteur, Paris, France
| | - Sahar Al-Mahdawi
- Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, and Synthetic Biology Theme, Institute of Environment, Health & Societies, Brunel University London, Uxbridge, United Kingdom
| | - Mark A Pook
- Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, and Synthetic Biology Theme, Institute of Environment, Health & Societies, Brunel University London, Uxbridge, United Kingdom.
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Role of frataxin protein deficiency and metabolic dysfunction in Friedreich ataxia, an autosomal recessive mitochondrial disease. Neuronal Signal 2018; 2:NS20180060. [PMID: 32714592 PMCID: PMC7373238 DOI: 10.1042/ns20180060] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/04/2023] Open
Abstract
Friedreich ataxia (FRDA) is a progressive neurodegenerative disease with developmental features caused by a genetic deficiency of frataxin, a small, nuclear-encoded mitochondrial protein. Frataxin deficiency leads to impairment of iron–sulphur cluster synthesis, and consequently, ATP production abnormalities. Based on the involvement of such processes in FRDA, initial pathophysiological hypotheses focused on reactive oxygen species (ROS) production as a key component of the mechanism. With further study, a variety of other events appear to be involved, including abnormalities of mitochondrially related metabolism and dysfunction in mitochondrial biogenesis. Consequently, present therapies focus not only on free radical damage, but also on control of metabolic abnormalities and correction of mitochondrial biogenesis. Understanding the multitude of abnormalities in FRDA thus offers possibilities for treatment of this disorder.
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Salman OF, El-Rayess HM, Abi Khalil C, Nemer G, Refaat MM. Inherited Cardiomyopathies and the Role of Mutations in Non-coding Regions of the Genome. Front Cardiovasc Med 2018; 5:77. [PMID: 29998127 PMCID: PMC6028572 DOI: 10.3389/fcvm.2018.00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023] Open
Abstract
Cardiomyopathies (CMs) are a group of cardiac pathologies caused by an intrinsic defect within the myocardium. The relative contribution of genetic mutations in the pathogenesis of certain CMs, such as hypertrophic cardiomyopathy (HCM), arrythmogenic right/left ventricular cardiomyopathy (ARVC) and left ventricular non-compacted cardiomyopathy (LVNC) has been established in comparison to dilated cardiomyopathy (DCM) and restrictive cardiomyopathy (RCM). The aim of this article is to review mutations in the non-coding parts of the genome, namely, microRNA, promoter elements, enhancer/silencer elements, 3′/5′UTRs and introns, that are involved in the pathogenesis CMs. Additionally, we will explore the role of some long non-coding RNAs in the pathogenesis of CMs.
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Affiliation(s)
- Oday F Salman
- Division of Cardiology, Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hebah M El-Rayess
- Division of Cardiology, Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Marwan M Refaat
- Division of Cardiology, Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Gendron TF, Petrucelli L. Disease Mechanisms of C9ORF72 Repeat Expansions. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a024224. [PMID: 28130314 DOI: 10.1101/cshperspect.a024224] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
G4C2 repeat expansions within the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These bidirectionally transcribed expansions lead to (1) the accumulation of sense G4C2 and antisense G2C4 repeat-containing RNA, (2) the production of proteins of repeating dipeptides through unconventional translation of these transcripts, and (3) decreased C9ORF72 mRNA and protein expression. Consequently, there is ample opportunity for the C9ORF72 mutation to give rise to a spectrum of clinical manifestations, ranging from muscle weakness and atrophy to changes in behavior and cognition. It is thus somewhat surprising that investigations of these three seemingly disparate events often converge on similar putative pathological mechanisms. This review aims to summarize the findings and questions emerging from the field's quest to decipher how C9ORF72 repeat expansions cause the devastating diseases collectively referred to as "c9ALS/FTD."
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Affiliation(s)
- Tania F Gendron
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224
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Santoro M, Fontana L, Maiorca F, Centofanti F, Massa R, Silvestri G, Novelli G, Botta A. Expanded [CCTG]n repetitions are not associated with abnormal methylation at the CNBP locus in myotonic dystrophy type 2 (DM2) patients. Biochim Biophys Acta Mol Basis Dis 2018; 1864:917-924. [DOI: 10.1016/j.bbadis.2017.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/21/2017] [Accepted: 12/28/2017] [Indexed: 01/10/2023]
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48
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Esanov R, Andrade NS, Bennison S, Wahlestedt C, Zeier Z. The FMR1 promoter is selectively hydroxymethylated in primary neurons of fragile X syndrome patients. Hum Mol Genet 2018; 25:4870-4880. [PMID: 28173181 DOI: 10.1093/hmg/ddw311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/17/2016] [Accepted: 09/02/2016] [Indexed: 12/13/2022] Open
Abstract
Fragile X syndrome (FXS) results from a repeat expansion mutation near the FMR1 gene promoter and is the most common form of heritable intellectual disability and autism. Full mutations larger than 200 CGG repeats trigger FMR1 heterochromatinization and loss of gene expression, which is primarily responsible for the pathological features of FXS . In contrast, smaller pre-mutations of 55–200 CGG are associated with FMR1 overexpression and Fragile X-associated tremor/ataxia syndrome (FXTAS), a late-onset neurodegenerative condition. While the role of 5-methylcytosine (5mC) in FMR1 gene silencing has been studied extensively, the role of 5-hydroxymethylation (5hmC), a newly discovered epigenetic mark produced through active DNA demethylation, has not been previously investigated in FXS neurons. Here, we used two complementary epigenetic assays, 5hmC sensitive restriction digest and ten-eleven translocation-assisted bisulfite pyrosequencing, to quantify FMR1 5mC and 5hmC levels. We observed increased levels of 5hmC at the FMR1 promoter in FXS patient brains with full-mutations relative to pre-mutation carriers and unaffected controls. In addition, we found that 5hmC enrichment at the FMR1 locus in FXS cells is specific to neurons by utilizing a nuclei sorting technique to separate neuronal and glial DNA fractions from post-mortem brain tissues. This FMR1 5hmC enrichment was not present in cellular models of FXS including fibroblasts, lymphocytes and reprogrammed neurons, indicating they do not fully recapitulate this epigenetic feature of disease. Future studies could investigate the potential to leverage this epigenetic pathway to restore FMR1 expression and discern whether levels of 5hmC correlate with phenotypic severity.
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Affiliation(s)
- Rustam Esanov
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Nadja S Andrade
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sarah Bennison
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Claes Wahlestedt
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Abstract
Accumulating evidence suggests that many classes of DNA repeats exhibit attributes that distinguish them from other genetic variants, including the fact that they are more liable to mutation; this enables them to mediate genetic plasticity. The expansion of tandem repeats, particularly of short tandem repeats, can cause a range of disorders (including Huntington disease, various ataxias, motor neuron disease, frontotemporal dementia, fragile X syndrome and other neurological disorders), and emerging data suggest that tandem repeat polymorphisms (TRPs) can also regulate gene expression in healthy individuals. TRPs in human genomes may also contribute to the missing heritability of polygenic disorders. A better understanding of tandem repeats and their associated repeatome, as well as their capacity for genetic plasticity via both germline and somatic mutations, is needed to transform our understanding of the role of TRPs in health and disease.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne.,Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria, Australia
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50
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Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 2017; 358:1617-1622. [PMID: 29192133 PMCID: PMC6037176 DOI: 10.1126/science.aan6414] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. Here we present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. The modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew P Grieshop
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepak Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Istaq Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Anna McNally
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Natalia Teider
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Katie Worringer
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Md Ashraf
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Jeffery
- Small Animal Imaging Facility, University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Mousheng Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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