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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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2
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Quatrana A, Morini E, Tiano F, Vancheri C, Panarello L, Romano S, Marcotulli C, Casali C, Mariotti C, Mongelli A, Fichera M, Rufini A, Condò I, Novelli G, Testi R, Amati F, Malisan F. Hsa-miR223-3p circulating level is upregulated in Friedreich's ataxia and inversely associated with HCLS1 associated protein X-1, HAX-1. Hum Mol Genet 2022; 31:2010-2022. [PMID: 35015850 DOI: 10.1093/hmg/ddac005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/15/2021] [Accepted: 01/04/2022] [Indexed: 11/12/2022] Open
Abstract
Frataxin (FXN) deficiency is responsible for Friedreich's ataxia (FRDA) in which, besides the characteristic features of spinocerebellar ataxia, two thirds of patients develop hypertrophic cardiomyopathy that often progresses to heart failure and premature death. Different mechanisms might underlie FRDA pathogenesis. Among them, the role of miRNAs deserves investigations. We carried out a miRNA PCR-array analysis of plasma samples of early-, intermediate- and late-onset FRDA groups, defining a set of 30 differentially expressed miRNAs. Hsa-miR223-3p is the only miRNA shared between the three patient groups and appears upregulated in all of them. The upregulation of hsa-miR223-3p was further validated in all enrolled patients (n = 37, Fc = +2.3; p < 0.0001). Using a Receiver Operating Characteristic (ROC) curve analysis, we quantified the predictive value of circulating hsa-miR223-3p for FRDA, obtaining an AUC (Area Under the ROC Curve) value of 0.835 (p < 0.0001) for all patients. Interestingly, we found a significant positive correlation between hsa-miR223-3p expression and cardiac parameters in typical FRDA patients (onset < 25 years). Moreover, a significant negative correlation between hsa-miR223-3p expression and HAX-1 (HCLS1 associated protein X-1) at mRNA and protein level was observed in all FRDA patients. In silico analyses suggested HAX-1 as a target gene of hsa-miR223-3p. Accordingly, we report that HAX-1 is negatively regulated by hsa-miR223-3p in cardiomyocytes (AC16) and neurons (SH-SY5Y), which are critically affected cell types in FRDA. This study describes for the first time the association between hsa-miR223-3p and HAX-1 expression in FRDA, thus supporting a potential role of this microRNA as non-invasive epigenetic biomarker for FRDA.
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Affiliation(s)
- Andrea Quatrana
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Elena Morini
- Section of Medical Genetics, Dept. of Biomedicine and Prevention, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Francesca Tiano
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy.,Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Chiara Vancheri
- Section of Medical Genetics, Dept. of Biomedicine and Prevention, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Luca Panarello
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Silvia Romano
- Neurosciences, Mental Health and Sensory Organs (NESMOS) Department, Faculty of Medicine and Psychology, Sapienza University, 00189 Rome, Italy
| | | | - Carlo Casali
- Dept. of Medical Surgical Sciences and Biotechnologies, Polo Pontino-Sapienza University of Rome, 04100 Latina, Italy
| | - Caterina Mariotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Alessia Mongelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Mario Fichera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy
| | - Alessandra Rufini
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy.,Fratagene Therapeutics Srl, Rome, 00144 Rome, Italy.,Saint Camillus International University of Health and Medical Sciences, 00131 Rome, Italy
| | - Ivano Condò
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Giuseppe Novelli
- Section of Medical Genetics, Dept. of Biomedicine and Prevention, University of Rome "Tor Vergata", 00133 Rome, Italy.,Neuromed Institute, IRCCS, 86077 Pozzilli, Italy
| | - Roberto Testi
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy.,Fratagene Therapeutics Srl, Rome, 00144 Rome, Italy
| | - Francesca Amati
- Section of Medical Genetics, Dept. of Biomedicine and Prevention, University of Rome "Tor Vergata", 00133 Rome, Italy.,Department for the Promotion of Human Science and Quality of Life, University San Raffaele, 00166 Rome, Italy
| | - Florence Malisan
- Laboratory of Signal Transduction, Dept. of Biomedicine and Prevention; University of Rome "Tor Vergata", 00133 Rome, Italy
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3
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Venugopal C, Shobha K, Rai KS, Dhanushkodi A. Neurogenic and cognitive enhancing effects of human dental pulp stem cells and its secretome in animal model of hippocampal neurodegeneration. Brain Res Bull 2022; 180:46-58. [PMID: 34979238 DOI: 10.1016/j.brainresbull.2021.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/11/2021] [Accepted: 12/28/2021] [Indexed: 12/26/2022]
Abstract
Progressive hippocampal neuronal losses, neuroinflammation, declined neurogenesis and impaired hippocampal functions are pathological features of Alzheimer's disease and temporal lobe epilepsy (TLE). Halting neuroinflammation and progressive neurodegeneration in the hippocampus is a major challenge in treating such disease conditions which, if unsuccessful would lead to learning/memory dysfunction and co-morbidities like anxiety/depression. Mesenchymal stem cells (MSCs) therapy provides hope for treating neurodegenerative diseases by either replacing lost neurons by transplantation of MSCs which might differentiate into appropriate neuronal phenotypes or by stimulating the resident neural stem cells for proliferation/differentiation. In this current study, we demonstrate that the intrahippocampal transplantation of ectoderm originated dental pulp stem cells (DPSCs) or intrahippocampal injection of DPSCs condition medium (DPSCs-CM) in a mouse model of hippocampal neurodegeneration could efficiently prevent neurodegeneration, neuroinflammation, enhance hippocampal neurogenesis and spatial learning and memory functions much superior to commonly used bone marrow mesenchymal stem cells (BM-MSCs) or its secretome. Probing the possible mechanisms of neuroprotection revealed that DPSCs/DPSCs-CM treatment upregulated an array of hosts' endogenous neural survival factors expression, reduced pro-apoptotic caspase activity and upregulated the anti-apoptotic factors BCL-2 and phosphorylated PI3K prominently than BM-MSCs/BM-MSCs-CM, suggesting that among MSCs, neural crest originated DPSCs might be a better adult stem cell candidate for treating neurodegenerative diseases.
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Affiliation(s)
- Chaitra Venugopal
- Manipal Institute of Regenerative Medicine, Bangalore, Manipal Academy of Higher Education, Manipal, India
| | - K Shobha
- Manipal Institute of Regenerative Medicine, Bangalore, Manipal Academy of Higher Education, Manipal, India
| | - Kiranmai S Rai
- Dept. of Physiology, Melaka Manipal Medical College, Manipal Academy of Higher, Education, Manipal, Karnataka, India
| | - Anandh Dhanushkodi
- Manipal Institute of Regenerative Medicine, Bangalore, Manipal Academy of Higher Education, Manipal, India.
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4
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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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5
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Misiorek JO, Schreiber AM, Urbanek-Trzeciak MO, Jazurek-Ciesiołka M, Hauser LA, Lynch DR, Napierala JS, Napierala M. A Comprehensive Transcriptome Analysis Identifies FXN and BDNF as Novel Targets of miRNAs in Friedreich's Ataxia Patients. Mol Neurobiol 2020; 57:2639-2653. [PMID: 32291635 PMCID: PMC7253519 DOI: 10.1007/s12035-020-01899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Abstract
Friedreich's ataxia (FRDA) is a genetic neurodegenerative disease that is caused by guanine-adenine-adenine (GAA) nucleotide repeat expansions in the first intron of the frataxin (FXN) gene. Although present in the intron, this mutation leads to a substantial decrease in protein expression. Currently, no effective treatment is available for FRDA, and, in addition to FXN, other targets with therapeutic potential are continuously sought. As miRNAs can regulate the expression of a broad spectrum of genes, are used as biomarkers, and can serve as therapeutic tools, we decided to identify and characterize differentially expressed miRNAs and their targets in FRDA cells compared to unaffected control (CTRL) cells. In this study, we performed an integrated miRNAseq and RNAseq analysis using the same cohort of primary FRDA and CTRL cells. The results of the transcriptome studies were supported by bioinformatic analyses and validated by qRT-PCR. miRNA interactions with target genes were assessed by luciferase assays, qRT-PCR, and immunoblotting. In silico analysis identified the FXN transcript as a target of five miRNAs upregulated in FRDA cells. Further studies confirmed that miRNA-224-5p indeed targets FXN, resulting in decreases in mRNA and protein levels. We also validated the ability of miRNA-10a-5p to bind and regulate the levels of brain-derived neurotrophic factor (BDNF), an important modulator of neuronal growth. We observed a significant decrease in the levels of miRNA-10a-5p and increase in the levels of BDNF upon correction of FRDA cells via zinc-finger nuclease (ZFN)-mediated excision of expanded GAA repeats. Our comprehensive transcriptome analyses identified miRNA-224-5p and miRNA-10a-5p as negative regulators of the FXN and BDNF expression, respectively. These results emphasize not only the importance of miRNAs in the pathogenesis of FRDA but also their potential as therapeutic targets for this disease.
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Affiliation(s)
- Julia O. Misiorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna M. Schreiber
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - Lauren A. Hauser
- Department of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - David R. Lynch
- Department of Pediatrics and Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Jill S. Napierala
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL USA
| | - Marek Napierala
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham, Birmingham, AL USA
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6
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Nuzhny EP, Abramycheva NY, Nikolaeva NS, Ershova MV, Klyushnikov SA, Illarioshkin SN, Fedotova EY. [Epigenetic regulation of clinical manifestations of Friedreich's disease]. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:20-26. [PMID: 32105265 DOI: 10.17116/jnevro202012001120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM To study a methylation profile of FXN gene and its influence on the clinical phenotype of Friedreich's desease (FD). MATERIAL AND METHODS The methylation pattern was analyzed in 17 patients with FD. Forty-five CpG-sites in the promoter region and the region of intron 1 of FXN: before the GAA-expansion (UP-GAA) and after the GAA-expansion (DOWN-GAA), were studied. RESULTS Correlations between the methylation level of CpG-sites in UP-GAA and DOWN-GAA and the number of GAA repeats in both expanded FXN alleles in patients with FD were found. An analysis revealed an earlier onset and a more severe course of FD in cases with hypermethylation of several CpG-sites in the UP-GAA region. The correlation between the methylation pattern and the presence of extraneural manifestations of FD was also revealed. In FD patients with cardiomyopathy, a hypomethylated CpG-site in the promoter region was found. In FD patients with carbohydrate metabolism disorders, two hypomethylated CpG-sites in the DOWN-GAA region were observed. CONCLUSION The results indicate a significant contribution of epigenetic modifications of FXN to the clinical presentation of FA.
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Affiliation(s)
- E P Nuzhny
- Research Center of Neurology, Moscow, Russia
| | | | | | - M V Ershova
- Research Center of Neurology, Moscow, Russia
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7
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Kumfu S, Chattipakorn S, Chattipakorn N. Antioxidant and chelator cocktails to prevent oxidative stress under iron-overload conditions. Pathology 2020. [DOI: 10.1016/b978-0-12-815972-9.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Quesada MP, García-Bernal D, Pastor D, Estirado A, Blanquer M, García-Hernández AM, Moraleda JM, Martínez S. Safety and Biodistribution of Human Bone Marrow-Derived Mesenchymal Stromal Cells Injected Intrathecally in Non-Obese Diabetic Severe Combined Immunodeficiency Mice: Preclinical Study. Tissue Eng Regen Med 2019; 16:525-538. [PMID: 31624707 DOI: 10.1007/s13770-019-00202-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Background Mesenchymal stromal cells (MSCs) have potent immunomodulatory and neuroprotective properties, and have been tested in neurodegenerative diseases resulting in meaningful clinical improvements. Regulatory guidelines specify the need to perform preclinical studies prior any clinical trial, including biodistribution assays and tumourigenesis exclusion. We conducted a preclinical study of human bone marrow MSCs (hBM-MSCs) injected by intrathecal route in Non-Obese Diabetic Severe Combined Immunodeficiency mice, to explore cellular biodistribution and toxicity as a privileged administration method for cell therapy in Friedreich's Ataxia. Methods For this purpose, 3 × 105 cells were injected by intrathecal route in 12 animals (experimental group) and the same volume of culture media in 6 animals (control group). Blood samples were collected at 24 h (n = 9) or 4 months (n = 9) to assess toxicity, and nine organs were harvested for histology and safety studies. Genomic DNA was isolated from all tissues, and mouse GAPDH and human β2M and β-actin genes were amplified by qPCR to analyze hBM-MSCs biodistribution. Results There were no deaths nor acute or chronic toxicity. Hematology, biochemistry and body weight were in the range of normal values in all groups. At 24 h hBM-MSCs were detected in 4/6 spinal cords and 1/6 hearts, and at 4 months in 3/6 hearts and 1/6 brains of transplanted mice. No tumours were found. Conclusion This study demonstrated that intrathecal injection of hBM-MSCs is safe, non toxic and do not produce tumors. These results provide further evidence that hBM-MSCs might be used in a clinical trial in patients with FRDA.
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Affiliation(s)
- Mari Paz Quesada
- 1Cellular Therapy and Hematopoietic Transplant Unit, Hematology Department, Virgen de la Arrixaca Clinical University Hospital, Biomedical Research Institute of Murcia, IMIB-Arrixaca, Campus of International Excellence "Campus Mare Nostrum" University of Murcia, Carretera Acceso Urbanización Buenavista (1ªizda), 30120 El Palmar, Murcia, Spain
| | - David García-Bernal
- 1Cellular Therapy and Hematopoietic Transplant Unit, Hematology Department, Virgen de la Arrixaca Clinical University Hospital, Biomedical Research Institute of Murcia, IMIB-Arrixaca, Campus of International Excellence "Campus Mare Nostrum" University of Murcia, Carretera Acceso Urbanización Buenavista (1ªizda), 30120 El Palmar, Murcia, Spain.,2Internal Medicine Department, Medicine School, University of Murcia, Virgen de la Arrixaca Clinical University Hospital, Ctra. Madrid-Cartagena, s/n, 30120 El Palmar, Murcia, Spain
| | - Diego Pastor
- 3Sport Research Center, University Miguel Hernández of Elche, Av. de la Universidad s/n, 03202 Elche, Alicante, Spain
| | - Alicia Estirado
- 4Neuroscience Institute UMH-CSIC, University Miguel Hernández of Elche, Carretera de Valencia, Km 18, 03550 San Juan, Alicante, Spain
| | - Miguel Blanquer
- 1Cellular Therapy and Hematopoietic Transplant Unit, Hematology Department, Virgen de la Arrixaca Clinical University Hospital, Biomedical Research Institute of Murcia, IMIB-Arrixaca, Campus of International Excellence "Campus Mare Nostrum" University of Murcia, Carretera Acceso Urbanización Buenavista (1ªizda), 30120 El Palmar, Murcia, Spain.,2Internal Medicine Department, Medicine School, University of Murcia, Virgen de la Arrixaca Clinical University Hospital, Ctra. Madrid-Cartagena, s/n, 30120 El Palmar, Murcia, Spain
| | - Ana Mª García-Hernández
- 1Cellular Therapy and Hematopoietic Transplant Unit, Hematology Department, Virgen de la Arrixaca Clinical University Hospital, Biomedical Research Institute of Murcia, IMIB-Arrixaca, Campus of International Excellence "Campus Mare Nostrum" University of Murcia, Carretera Acceso Urbanización Buenavista (1ªizda), 30120 El Palmar, Murcia, Spain
| | - José M Moraleda
- 1Cellular Therapy and Hematopoietic Transplant Unit, Hematology Department, Virgen de la Arrixaca Clinical University Hospital, Biomedical Research Institute of Murcia, IMIB-Arrixaca, Campus of International Excellence "Campus Mare Nostrum" University of Murcia, Carretera Acceso Urbanización Buenavista (1ªizda), 30120 El Palmar, Murcia, Spain.,2Internal Medicine Department, Medicine School, University of Murcia, Virgen de la Arrixaca Clinical University Hospital, Ctra. Madrid-Cartagena, s/n, 30120 El Palmar, Murcia, Spain
| | - Salvador Martínez
- 4Neuroscience Institute UMH-CSIC, University Miguel Hernández of Elche, Carretera de Valencia, Km 18, 03550 San Juan, Alicante, Spain.,CIBERSAM-ISCIII, Avenida Blasco Ibáñez 15, 46010 Valencia, Spain.,6Human Anatomy Department, Medicine School, University Miguel Hernández of Elche, Carretera de Valencia, Km 18, 03550 San Juan, Alicante, Spain
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Lai JI, Nachun D, Petrosyan L, Throesch B, Campau E, Gao F, Baldwin KK, Coppola G, Gottesfeld JM, Soragni E. Transcriptional profiling of isogenic Friedreich ataxia neurons and effect of an HDAC inhibitor on disease signatures. J Biol Chem 2019; 294:1846-1859. [PMID: 30552117 PMCID: PMC6369281 DOI: 10.1074/jbc.ra118.006515] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Friedreich ataxia (FRDA) is a neurodegenerative disorder caused by transcriptional silencing of the frataxin (FXN) gene, resulting in loss of the essential mitochondrial protein frataxin. Based on the knowledge that a GAA·TTC repeat expansion in the first intron of FXN induces heterochromatin, we previously showed that 2-aminobenzamide-type histone deacetylase inhibitors (HDACi) increase FXN mRNA levels in induced pluripotent stem cell (iPSC)-derived FRDA neurons and in circulating lymphocytes from patients after HDACi oral administration. How the reduced expression of frataxin leads to neurological and other systemic symptoms in FRDA patients remains unclear. Similar to other triplet-repeat disorders, it is unknown why FRDA affects only specific cell types, primarily the large sensory neurons of the dorsal root ganglia and cardiomyocytes. The combination of iPSC technology and genome-editing techniques offers the unique possibility to address these questions in a relevant cell model of FRDA, obviating confounding effects of variable genetic backgrounds. Here, using "scarless" gene-editing methods, we created isogenic iPSC lines that differ only in the length of the GAA·TTC repeats. To uncover the gene expression signatures due to the GAA·TTC repeat expansion in FRDA neuronal cells and the effect of HDACi on these changes, we performed RNA-seq-based transcriptomic analysis of iPSC-derived central nervous system (CNS) and isogenic sensory neurons. We found that cellular pathways related to neuronal function, regulation of transcription, extracellular matrix organization, and apoptosis are affected by frataxin loss in neurons of the CNS and peripheral nervous system and that these changes are partially restored by HDACi treatment.
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Affiliation(s)
- Jiun-I Lai
- From the Departments of Molecular Medicine and
| | - Daniel Nachun
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | | | - Benjamin Throesch
- Neuroscience, The Scripps Research Institute, La Jolla, California 92037 and
| | | | - Fuying Gao
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Kristin K Baldwin
- Neuroscience, The Scripps Research Institute, La Jolla, California 92037 and
| | - Giovanni Coppola
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
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Circulating miR-323-3p is a biomarker for cardiomyopathy and an indicator of phenotypic variability in Friedreich's ataxia patients. Sci Rep 2017; 7:5237. [PMID: 28701783 PMCID: PMC5507909 DOI: 10.1038/s41598-017-04996-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/23/2017] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that contribute to gene expression modulation by regulating important cellular pathways. In this study, we used small RNA sequencing to identify a series of circulating miRNAs in blood samples taken from Friedreich’s ataxia patients. We were thus able to develop a miRNA biomarker signature to differentiate Friedreich’s ataxia (FRDA) patients from healthy people. Most research on FDRA has focused on understanding the role of frataxin in the mitochondria, and a whole molecular view of pathological pathways underlying FRDA therefore remains to be elucidated. We found seven differentially expressed miRNAs, and we propose that these miRNAs represent key mechanisms in the modulation of several signalling pathways that regulate the physiopathology of FRDA. If this is the case, miRNAs can be used to characterize phenotypic variation in FRDA and stratify patients’ risk of cardiomyopathy. In this study, we identify miR-323-3p as a candidate marker for phenotypic differentiation in FRDA patients suffering from cardiomyopathy. We propose the use of dynamic miRNAs as biomarkers for phenotypic characterization and prognosis of FRDA.
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11
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Katsu-Jiménez Y, Loría F, Corona JC, Díaz-Nido J. Gene Transfer of Brain-derived Neurotrophic Factor (BDNF) Prevents Neurodegeneration Triggered by FXN Deficiency. Mol Ther 2016; 24:877-89. [PMID: 26849417 PMCID: PMC4881769 DOI: 10.1038/mt.2016.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 02/07/2023] Open
Abstract
Friedreich's ataxia is a predominantly neurodegenerative disease caused by recessive mutations that produce a deficiency of frataxin (FXN). Here, we have used a herpesviral amplicon vector carrying a gene encoding for brain-derived neurotrophic factor (BDNF) to drive its overexpression in neuronal cells and test for its effect on FXN-deficient neurons both in culture and in the mouse cerebellum in vivo. Gene transfer of BDNF to primary cultures of mouse neurons prevents the apoptosis which is triggered by the knockdown of FXN gene expression. This neuroprotective effect of BDNF is also observed in vivo in a viral vector-based knockdown mouse cerebellar model. The injection of a lentiviral vector carrying a minigene encoding for a FXN-specific short hairpin ribonucleic acid (shRNA) into the mouse cerebellar cortex triggers a FXN deficit which is accompanied by significant apoptosis of granule neurons as well as loss of calbindin in Purkinje cells. These pathological changes are accompanied by a loss of motor coordination of mice as assayed by the rota-rod test. Coinjection of a herpesviral vector encoding for BDNF efficiently prevents both the development of cerebellar neuropathology and the ataxic phenotype. These data demonstrate the potential therapeutic usefulness of neurotrophins like BDNF to protect FXN-deficient neurons from degeneration.
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Affiliation(s)
- Yurika Katsu-Jiménez
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
| | - Frida Loría
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
| | - Juan Carlos Corona
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
- Current address: Hospital Infantil de México “Federico Gómez”, México, D.F., México
| | - Javier Díaz-Nido
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
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