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Yu Y, Pang D, Huang J, Li C, Cui Y, Shang H. Downregulation of Lnc-ABCA12-3 modulates UBQLN1 expression and protein homeostasis pathways in amyotrophic lateral sclerosis. Sci Rep 2024; 14:21383. [PMID: 39271939 PMCID: PMC11399266 DOI: 10.1038/s41598-024-72666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neuron degeneration. Dysregulation of long non-coding RNAs (lncRNAs) has been implicated in ALS pathogenesis but their roles remain unclear. Previous studies found lnc-ABCA12-3 was downregulated in ALS patients. We aim to characterize the expression and function of lnc-ABCA12-3 in ALS and explore its mechanisms of action. Lnc-ABCA12-3 expression was analyzed in PBMCs from ALS patients and correlated with clinical outcomes. Effect of modulating lnc-ABCA12-3 expression was assessed in cell models using assays of apoptosis, protein homeostasis and pathway analysis. RNA pull-down and interaction studies were performed to identify lnc-ABCA12-3 binding partners. Lnc-ABCA12-3 was downregulated in ALS patients, correlating with faster progression and shorter survival. Overexpression of lnc-ABAC12-3 conferred protection against oxidative stress-induced apoptosis, while knockdown lnc-ABCA12-3 enhanced cell death. Lnc-ABCA12-3 maintained protein quality control pathways, including ubiquitination, autophagy and stress granule formation, by regulating the ubiquitin shuttle protein UBQLN1. This study identified lnc-ABCA12-3 as a novel regulatory lncRNA implicated in ALS pathogenesis by modulating cellular survival and stress responses through interactions with UBQLN1, influencing disease progression. Lnc-ABCA12-3 may influence ALS through regulating protein homeostasis pathways.
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Affiliation(s)
- Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Yiyuan Cui
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No.37, Guoxue Lane, Chengdu, 610041, China.
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2
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Ferreira RS, da Silva RA, Feltran GDS, da Silva EP, de Assis RIF, Rovai ES, Zambuzzi WF, Andia DC. JARID1B represses the osteogenic potential of human periodontal ligament mesenchymal cells. Oral Dis 2024; 30:3971-3981. [PMID: 37994179 DOI: 10.1111/odi.14814] [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: 06/23/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Here, we evaluated whether the histone lysine demethylase 5B (JARID1B), is involved in osteogenic phenotype commitment of periodontal ligament cells (PDLCs), by considering their heterogeneity for osteoblast differentiation. MATERIALS AND METHODS Epigenetic, transcriptional, and protein levels of a gene set, involved in the osteogenesis, were investigated by performing genome-wide DNA (hydroxy)methylation, mRNA expression, and western blotting analysis at basal (without osteogenic induction), and at the 3rd and 10th days of osteogenic stimulus, in vitro, using PDLCs with low (l) and high (h) osteogenic potential as biological models. RESULTS h-PDLCs showed reduced levels of JARID1B, compared to l-PDLCs, with significant inversely proportional correlations between RUNX2 and RUNX2/p57. Epigenetically, a significant reduction in the global H3K4me3 content was observed only in h-PDLCs. Immunoblotting data reveal a significant reduction in the global H3K4me3 content, at 3 days of induction only in h-PDLCs, while an increase in the global H3K4me3 content was observed at 10 days for both PDLCs. Additionally, positive correlations were found between global H3K4me3 levels and JARID1B gene expression. CONCLUSIONS Altogether, our results show the crucial role of JARID1B in repressing PDLCs osteogenic phenotype and this claims to pre-clinical protocols proposing JARID1B as a potential therapeutic target.
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Affiliation(s)
- Rogério S Ferreira
- School of Dentistry, Health Science Institute, Paulista University, São Paulo, Brazil
| | - Rodrigo A da Silva
- CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University - UNIP, São Paulo, Brazil
- Department of Chemistry and Biochemistry, Lab. of Bioassays and Cellular Dynamics, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, Brazil
| | - Geórgia Da S Feltran
- Department of Chemistry and Biochemistry, Lab. of Bioassays and Cellular Dynamics, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, Brazil
| | - Ericka Patricia da Silva
- CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University - UNIP, São Paulo, Brazil
| | - Rahyza I F de Assis
- Department of Clinical Dentistry, Federal University of Espírito Santo, Vitória, Brazil
| | - Emanuel Silva Rovai
- Division of Periodontics, Institute of Science and Technology, UNESP - São Paulo State University, São Paulo, Brazil
| | - Willian F Zambuzzi
- Department of Chemistry and Biochemistry, Lab. of Bioassays and Cellular Dynamics, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, Brazil
| | - Denise C Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo, Brazil
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3
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Sujkowski A, Ranxhi B, Bangash ZR, Chbihi ZM, Prifti MV, Qadri Z, Alam N, Todi SV, Tsou WL. Progressive degeneration in a new Drosophila model of spinocerebellar ataxia type 7. Sci Rep 2024; 14:14332. [PMID: 38906973 PMCID: PMC11192756 DOI: 10.1038/s41598-024-65172-4] [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: 11/10/2023] [Accepted: 06/18/2024] [Indexed: 06/23/2024] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a progressive neurodegenerative disorder resulting from abnormal expansion of an uninterrupted polyglutamine (polyQ) repeat in its disease protein, ataxin-7 (ATXN7). ATXN7 is part of Spt-Ada-Gcn5 acetyltransferase (SAGA), an evolutionarily conserved transcriptional coactivation complex with critical roles in chromatin remodeling, cell signaling, neurodifferentiation, mitochondrial health and autophagy. SCA7 is dominantly inherited and characterized by genetic anticipation and high repeat-length instability. Patients with SCA7 experience progressive ataxia, atrophy, spasticity, and blindness. There is currently no cure for SCA7, and therapies are aimed at alleviating symptoms to increase quality of life. Here, we report novel Drosophila lines of SCA7 with polyQ repeats in wild-type and human disease patient range. We find that ATXN7 expression has age- and polyQ repeat length-dependent reduction in fruit fly survival and retinal instability, concomitant with increased ATXN7 protein aggregation. These new lines will provide important insight on disease progression that can be used in the future to identify therapeutic targets for SCA7 patients.
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Affiliation(s)
- Alyson Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Zoya R Bangash
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Zachary M Chbihi
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Matthew V Prifti
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Zaina Qadri
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Nadir Alam
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, 540 E Canfield, Scott Hall Rm 3108, Detroit, MI, 48201, USA.
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4
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Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Ehmke N, Seelow D, Fradin M, Kornak U, Fischer-Zirnsak B. Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy. Hum Genet 2024; 143:683-694. [PMID: 38592547 PMCID: PMC11098864 DOI: 10.1007/s00439-024-02669-y] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Generalized lipodystrophy is a feature of various hereditary disorders, often leading to a progeroid appearance. In the present study we identified a missense and a frameshift variant in a compound heterozygous state in SUPT7L in a boy with intrauterine growth retardation, generalized lipodystrophy, and additional progeroid features. SUPT7L encodes a component of the transcriptional coactivator complex STAGA. By transcriptome sequencing, we showed the predicted missense variant to cause aberrant splicing, leading to exon truncation and thereby to a complete absence of SUPT7L in dermal fibroblasts. In addition, we found altered expression of genes encoding DNA repair pathway components. This pathway was further investigated and an increased rate of DNA damage was detected in proband-derived fibroblasts and genome-edited HeLa cells. Finally, we performed transient overexpression of wildtype SUPT7L in both cellular systems, which normalizes the number of DNA damage events. Our findings suggest SUPT7L as a novel disease gene and underline the link between genome instability and progeroid phenotypes.
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Affiliation(s)
- Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Leonard A Koch
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
| | - Hristiana Lyubenova
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Oliver Küchler
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, F-35033, France
- Univercity Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, F-35000, France
| | - Erika Launay
- Service de Cytogénétique et Biologie cellulaire, Hôpital Pontchaillou - CHU Rennes, 2 rue Henri Le Guilloux - Rennes cedex 9, France, Rennes, F-35033, France
| | - Sebastian Brachs
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre Référence Déficiences Intellectuelles CRDI, Hôpital Sud - CHU Rennes, 16 boulevard de Bulgarie - BP 90347, Rennes cedex 2, Rennes, F-35203, France
- Service de Génétique, CH Saint Brieuc, St Brieuc, 22000, France
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany.
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5
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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Sujkowski AL, Ranxhi B, Prifti MV, Alam N, Todi SV, Tsou WL. Progressive degeneration in a new Drosophila model of Spinocerebellar Ataxia type 7. RESEARCH SQUARE 2023:rs.3.rs-3592641. [PMID: 38045332 PMCID: PMC10690306 DOI: 10.21203/rs.3.rs-3592641/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a progressive neurodegenerative disorder resulting from abnormal expansion of polyglutamine (polyQ) in its disease protein, ataxin-7 (ATXN7). ATXN7 is part of Spt-Ada-Gcn5 acetyltransferase (SAGA), an evolutionarily conserved transcriptional coactivation complex with critical roles in chromatin remodeling, cell signaling, neurodifferentiation, mitochondrial health and autophagy. SCA7 is dominantly inherited and characterized by genetic anticipation and high repeat-length instability. Patients with SCA7 experience progressive ataxia, atrophy, spasticity, and blindness. There is currently no cure for SCA7, and therapies are aimed at alleviating symptoms to increase quality of life. Here, we report novel Drosophila lines of SCA7 with polyQ repeats in wild-type and human disease patient range. We find that ATXN7 expression has age- and polyQ repeat length-dependent reduction in survival and retinal instability, concomitant with increased ATXN7 protein aggregation. These new lines will provide important insight on disease progression that can be used in the future to identify therapeutic targets for SCA7 patients.
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Affiliation(s)
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University School of Medicine
| | - Matthew V Prifti
- Department of Pharmacology, Wayne State University School of Medicine
| | - Nadir Alam
- Department of Pharmacology, Wayne State University School of Medicine
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine
- Department of Neurology, Wayne State University School of Medicine
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine
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7
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Sujkowski AL, Ranxhi B, Prifti MV, Alam N, Todi SV, Tsou WL. Progressive degeneration in a new Drosophila model of Spinocerebellar Ataxia type 7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566106. [PMID: 37986914 PMCID: PMC10659390 DOI: 10.1101/2023.11.07.566106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a progressive neurodegenerative disorder resulting from abnormal expansion of polyglutamine (polyQ) in its disease protein, ataxin-7 (ATXN7). ATXN7 is part of Spt-Ada-Gcn5 acetyltransferase (SAGA), an evolutionarily conserved transcriptional coactivation complex with critical roles in chromatin remodeling, cell signaling, neurodifferentiation, mitochondrial health and autophagy. SCA7 is dominantly inherited and characterized by genetic anticipation and high repeat-length instability. Patients with SCA7 experience progressive ataxia, atrophy, spasticity, and blindness. There is currently no cure for SCA7, and therapies are aimed at alleviating symptoms to increase quality of life. Here, we report novel Drosophila lines of SCA7 with polyQ repeats in wild-type and human disease patient range. We find that ATXN7 expression has age- and polyQ repeat length-dependent reduction in survival and retinal instability, concomitant with increased ATXN7 protein aggregation. These new lines will provide important insight on disease progression that can be used in the future to identify therapeutic targets for SCA7 patients.
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8
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Yu D, Wu Y, Zhu L, Wang Y, Sheng D, Zhao X, Liang G, Gan L. The landscape of the long non-coding RNAs in developing mouse retinas. BMC Genomics 2023; 24:252. [PMID: 37165305 PMCID: PMC10173636 DOI: 10.1186/s12864-023-09354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available. RESULTS Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways. CONCLUSIONS In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.
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Affiliation(s)
- Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Leilei Zhu
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yuying Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Donglai Sheng
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Xiaofeng Zhao
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Guoqing Liang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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Yu J, Lu Z, Liu R, Wang P, Ma H, Zhao Y. Characterization of the lncRNA-miRNA-mRNA regulatory network to reveal potential functional competing endogenous RNAs in traumatic brain injury. Front Neurosci 2023; 16:1089857. [PMID: 36711143 PMCID: PMC9874919 DOI: 10.3389/fnins.2022.1089857] [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: 11/04/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Traumatic brain injury (TBI) is one of the most common acute central nervous system injury diseases. Given the medical and socio-economic burdens of TBI patients, the pathogenesis in TBI and the latent intervention targets needed to be further illuminated. Long non-coding RNAs (lncRNAs) had been revealed to play a vital role in the regulation of pathogenesis after TBI. However, the mutual communication and adjustment of lncRNA associated competing for endogenous RNA (ceRNA) networks in TBI have not been explored to date. In this study, we systematically sequenced the whole transcriptome of lncRNAs, miRNAs, and mRNAs between sham and TBI groups and a total of 939 differentially expressed (DE) lncRNAs, 46 DE miRNAs, and 1,951 DE mRNAs were obtained. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein interaction relationship analyses were conducted for DE mRNAs to identify hub DE genes in TBI. Based on the criteria of bioinformatics prediction, the lncRNA associated ceRNA network covering 201 lncRNAs, 22 miRNAs, and 79 mRNAs was constructed. This study provides a novel perspective on the molecular mechanism of lncRNA in TBI and identifies certain lncRNAs as potential therapeutic targets against TBI.
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Affiliation(s)
- Jiangtao Yu
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zijun Lu
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ruining Liu
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Pengcheng Wang
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoli Ma
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Zhao
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
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10
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Suárez-Sánchez R, Ávila-Avilés RD, Hernández-Hernández JM, Sánchez-Celis D, Azotla-Vilchis CN, Gómez-Macías ER, Leyva-García N, Ortega A, Magaña JJ, Cisneros B, Hernández-Hernández O. RNA Foci Formation in a Retinal Glial Model for Spinocerebellar Ataxia Type 7. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010023. [PMID: 36675972 PMCID: PMC9861853 DOI: 10.3390/life13010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder characterized by cerebellar ataxia and retinopathy. SCA7 is caused by a CAG expansion in the ATXN7 gene, which results in an extended polyglutamine (polyQ) tract in the encoded protein, the ataxin-7. PolyQ expanded ataxin-7 elicits neurodegeneration in cerebellar Purkinje cells, however, its impact on the SCA7-associated retinopathy remains to be addressed. Since Müller glial cells play an essential role in retinal homeostasis, we generate an inducible model for SCA7, based on the glial Müller MIO-M1 cell line. The SCA7 pathogenesis has been explained by a protein gain-of-function mechanism, however, the contribution of the mutant RNA to the disease cannot be excluded. In this direction, we found nuclear and cytoplasmic foci containing mutant RNA accompanied by subtle alternative splicing defects in MIO-M1 cells. RNA foci were also observed in cells from different lineages, including peripheral mononuclear leukocytes derived from SCA7 patient, suggesting that this molecular mark could be used as a blood biomarker for SCA7. Collectively, our data showed that our glial cell model exhibits the molecular features of SCA7, which makes it a suitable model to study the RNA toxicity mechanisms, as well as to explore therapeutic strategies aiming to alleviate glial dysfunction.
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Affiliation(s)
- Rocío Suárez-Sánchez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
| | - Rodolfo Daniel Ávila-Avilés
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - J. Manuel Hernández-Hernández
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Daniel Sánchez-Celis
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Cuauhtli N. Azotla-Vilchis
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Enue R. Gómez-Macías
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Norberto Leyva-García
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
| | - Arturo Ortega
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del, Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
- Escuela de Ingeniería y Ciencias, Departamento de Bioingeniería, Tecnológico de Monterrey-Campus Ciudad de México, Ciudad de México 14380, Mexico
| | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico
| | - Oscar Hernández-Hernández
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis, Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico
- Correspondence: or ; Tel.: +52-(55)-5999-1000 (ext. 14710)
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11
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Sujkowski A, Hong L, Wessells RJ, Todi SV. The protective role of exercise against age-related neurodegeneration. Ageing Res Rev 2022; 74:101543. [PMID: 34923167 PMCID: PMC8761166 DOI: 10.1016/j.arr.2021.101543] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/01/2021] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
Endurance exercise is a widely accessible, low-cost intervention with a variety of benefits to multiple organ systems. Exercise improves multiple indices of physical performance and stimulates pronounced health benefits reducing a range of pathologies including metabolic, cardiovascular, and neurodegenerative disorders. Endurance exercise delays brain aging, preserves memory and cognition, and improves symptoms of neurodegenerative pathologies like Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and various ataxias. Potential mechanisms underlying the beneficial effects of exercise include neuronal survival and plasticity, neurogenesis, epigenetic modifications, angiogenesis, autophagy, and the synthesis and release of neurotrophins and cytokines. In this review, we discuss shared benefits and molecular pathways driving the protective effects of endurance exercise on various neurodegenerative diseases in animal models and in humans.
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Affiliation(s)
- Alyson Sujkowski
- Department of Physiology, Wayne State University School of Medicine, USA; Department of Pharmacology, Wayne State University School of Medicine, USA
| | - Luke Hong
- Department of Pharmacology, Wayne State University School of Medicine, USA; Department of Neurology, Wayne State University School of Medicine, USA
| | - R J Wessells
- Department of Physiology, Wayne State University School of Medicine, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, USA; Department of Neurology, Wayne State University School of Medicine, USA.
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12
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Bhatti GK, Khullar N, Sidhu IS, Navik US, Reddy AP, Reddy PH, Bhatti JS. Emerging role of non-coding RNA in health and disease. Metab Brain Dis 2021; 36:1119-1134. [PMID: 33881724 PMCID: PMC8058498 DOI: 10.1007/s11011-021-00739-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Human diseases have always been a significant turf of concern since the origin of mankind. It is cardinal to know the cause, treatment, and cure for every disease condition. With the advent and advancement in technology, the molecular arena at the microscopic level to study the mechanism, progression, and therapy is more rational and authentic pave than a macroscopic approach. Non-coding RNAs (ncRNAs) have now emerged as indispensable players in the diagnosis, development, and therapeutics of every abnormality concerning physiology, pathology, genetics, epigenetics, oncology, and developmental diseases. This is a comprehensive attempt to collate all the existing and proven strategies, techniques, mechanisms of genetic disorders including Silver Russell Syndrome, Fascio- scapula humeral muscular dystrophy, cardiovascular diseases (atherosclerosis, cardiac fibrosis, hypertension, etc.), neurodegenerative diseases (Spino-cerebral ataxia type 7, Spino-cerebral ataxia type 8, Spinal muscular atrophy, Opitz-Kaveggia syndrome, etc.) cancers (cervix, breast, lung cancer, etc.), and infectious diseases (viral) studied so far. This article encompasses discovery, biogenesis, classification, and evolutionary prospects of the existence of this junk RNA along with the integrated networks involving chromatin remodelling, dosage compensation, genome imprinting, splicing regulation, post-translational regulation and proteomics. In conclusion, all the major human diseases are discussed with a facilitated technology transfer, advancements, loopholes, and tentative future research prospects have also been proposed.
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Affiliation(s)
- Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab India
| | | | - Uma Shanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | | | - P. Hemachandra Reddy
- Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Cell Biology & Biochemistry, Neuroscience & Pharmacology, Neurology, Public Health, School of Health Professions, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430 USA
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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13
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Dong X, Cong S. The emerging roles of long non-coding RNAs in polyglutamine diseases. J Cell Mol Med 2021; 25:8095-8102. [PMID: 34318578 PMCID: PMC8419158 DOI: 10.1111/jcmm.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022] Open
Abstract
Polyglutamine (polyQ) diseases are characterized by trinucleotide repeat amplifications within genes, thus resulting in the formation of polyQ peptides, selective neuronal degeneration and possibly death due to neurodegenerative diseases (NDDs). Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides in length, have been shown to play important roles in several pathological processes of NDDs, including polyQ diseases. Some lncRNAs have been consistently identified to be specific to polyQ diseases, and circulating lncRNAs are among the most promising novel candidates in the search for non-invasive biomarkers for the diagnosis and prognosis of polyQ diseases. In this review, we describe the emerging roles of lncRNAs in polyQ diseases and provide an overview of the general biology of lncRNAs, their implications in pathophysiology and their potential roles as future biomarkers and applications for therapy.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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14
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Koscianska E, Kozlowska E, Fiszer A. Regulatory Potential of Competing Endogenous RNAs in Myotonic Dystrophies. Int J Mol Sci 2021; 22:6089. [PMID: 34200099 PMCID: PMC8201210 DOI: 10.3390/ijms22116089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have been reported to be implicated in cell fate determination and various human diseases. All ncRNA molecules are emerging as key regulators of diverse cellular processes; however, little is known about the regulatory interaction among these various classes of RNAs. It has been proposed that the large-scale regulatory network across the whole transcriptome is mediated by competing endogenous RNA (ceRNA) activity attributed to both protein-coding and ncRNAs. ceRNAs are considered to be natural sponges of miRNAs that can influence the expression and availability of multiple miRNAs and, consequently, the global mRNA and protein levels. In this review, we summarize the current understanding of the role of ncRNAs in two neuromuscular diseases, myotonic dystrophy type 1 and 2 (DM1 and DM2), and the involvement of expanded CUG and CCUG repeat-containing transcripts in miRNA-mediated RNA crosstalk. More specifically, we discuss the possibility that long repeat tracts present in mutant transcripts can be potent miRNA sponges and may affect ceRNA crosstalk in these diseases. Moreover, we highlight practical information related to innovative disease modelling and studying RNA regulatory networks in cells. Extending knowledge of gene regulation by ncRNAs, and of complex regulatory ceRNA networks in DM1 and DM2, will help to address many questions pertinent to pathogenesis and treatment of these disorders; it may also help to better understand general rules of gene expression and to discover new rules of gene control.
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Affiliation(s)
- Edyta Koscianska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (E.K.); (A.F.)
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15
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Su H, Xie J, Wen L, Wang S, Chen S, Li J, Qi C, Zhang Q, He X, Zheng L, Wang L. LncRNA Gas5 regulates Fn1 deposition via Creb5 in renal fibrosis. Epigenomics 2021; 13:699-713. [PMID: 33876672 DOI: 10.2217/epi-2020-0449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Although studies on lncRNAs in renal fibrosis have focused on target genes and functions of lncRNAs, a comprehensive interaction analysis of lncRNAs is lacking. Materials & methods: Differentially expressed genes in renal fibrosis were screened, and the interaction between lncRNAs and miRNAs was searched. Results: We constructed a ceRNA network associated with renal fibrosis, by which we found the transcription factor Creb5, a target gene of lncRNA Gas5 that might regulate extracellular Fn1 deposition. Conclusion: Our study not only provides a theoretical basis for the ceRNA regulation mechanism of Gas5 but also provides experimental evidence supporting the use of Gas5 targeting in the treatment of renal fibrosis.
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Affiliation(s)
- Huanhou Su
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Jingzhou Xie
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Lijing Wen
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Shunyi Wang
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Sishuo Chen
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Jiangchao Li
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Cuiling Qi
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Qianqian Zhang
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Xiaodong He
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Lingyun Zheng
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
| | - Lijing Wang
- School of Life Sciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, Guangdong, P.R. China
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16
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Current Status of Gene Therapy Research in Polyglutamine Spinocerebellar Ataxias. Int J Mol Sci 2021; 22:ijms22084249. [PMID: 33921915 PMCID: PMC8074016 DOI: 10.3390/ijms22084249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Polyglutamine spinocerebellar ataxias (PolyQ SCAs) are a group of 6 rare autosomal dominant diseases, which arise from an abnormal CAG repeat expansion in the coding region of their causative gene. These neurodegenerative ataxic disorders are characterized by progressive cerebellar degeneration, which translates into progressive ataxia, the main clinical feature, often accompanied by oculomotor deficits and dysarthria. Currently, PolyQ SCAs treatment is limited only to symptomatic mitigation, and no therapy is available to stop or delay the disease progression, which culminates with death. Over the last years, many promising gene therapy approaches were investigated in preclinical studies and could lead to a future treatment to stop or delay the disease development. Here, we summed up the most promising of these therapies, categorizing them in gene augmentation therapy, gene silencing strategies, and gene edition approaches. While several of the reviewed strategies are promising, there is still a gap from the preclinical results obtained and their translation to clinical studies. However, there is an increase in the number of approved gene therapies, as well as a constant development in their safety and efficacy profiles. Thus, it is expected that in a near future some of the promising strategies reviewed here could be tested in a clinical setting and if successful provide hope for SCAs patients.
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17
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Yang S, Lim KH, Kim SH, Joo JY. Molecular landscape of long noncoding RNAs in brain disorders. Mol Psychiatry 2021; 26:1060-1074. [PMID: 33173194 DOI: 10.1038/s41380-020-00947-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/28/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023]
Abstract
According to current paradigms, various risk factors, such as genetic mutations, oxidative stress, neural network dysfunction, and abnormal protein degradation, contribute to the progression of brain disorders. Through the cooperation of gene transcripts in biological processes, the study of noncoding RNAs can lead to insights into the cause and treatment of brain disorders. Recently, long noncoding RNAs (lncRNAs) which are longer than 200 nucleotides in length have been suggested as key factors in various brain disorders. Accumulating evidence suggests the potential of lncRNAs as diagnostic or prognostic biomarkers and therapeutic targets. High-throughput screening-based sequencing has been instrumental in identification of lncRNAs that demand new approaches to understanding the progression of brain disorders. In this review, we discuss the recent progress in the study of lncRNAs, and addresses the pathogenesis of brain disorders that involve lncRNAs and describes the associations of lncRNAs with neurodegenerative disorders such as Alzheimer disease (AD), Parkinson disease (PD), and neurodevelopmental disorders. We also discuss potential targets of lncRNAs and their promise as novel therapeutics and biomarkers in brain disorders.
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Affiliation(s)
- Sumin Yang
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Key-Hwan Lim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Sung-Hyun Kim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Jae-Yeol Joo
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea.
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18
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Burman RJ, Watson LM, Smith DC, Raimondo JV, Ballo R, Scholefield J, Cowley SA, Wood MJA, Kidson SH, Greenberg LJ. Molecular and electrophysiological features of spinocerebellar ataxia type seven in induced pluripotent stem cells. PLoS One 2021; 16:e0247434. [PMID: 33626063 PMCID: PMC7904216 DOI: 10.1371/journal.pone.0247434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/07/2021] [Indexed: 11/19/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by a polyglutamine repeat expansion in the ATXN7 gene. Patients with this disease suffer from a degeneration of their cerebellar Purkinje neurons and retinal photoreceptors that result in a progressive ataxia and loss of vision. As with many neurodegenerative diseases, studies of pathogenesis have been hindered by a lack of disease-relevant models. To this end, we have generated induced pluripotent stem cells (iPSCs) from a cohort of SCA7 patients in South Africa. First, we differentiated the SCA7 affected iPSCs into neurons which showed evidence of a transcriptional phenotype affecting components of STAGA (ATXN7 and KAT2A) and the heat shock protein pathway (DNAJA1 and HSP70). We then performed electrophysiology on the SCA7 iPSC-derived neurons and found that these cells show features of functional aberrations. Lastly, we were able to differentiate the SCA7 iPSCs into retinal photoreceptors that also showed similar transcriptional aberrations to the SCA7 neurons. Our findings give technical insights on how iPSC-derived neurons and photoreceptors can be derived from SCA7 patients and demonstrate that these cells express molecular and electrophysiological differences that may be indicative of impaired neuronal health. We hope that these findings will contribute towards the ongoing efforts to establish the cell-derived models of neurodegenerative diseases that are needed to develop patient-specific treatments.
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Affiliation(s)
- Richard J. Burman
- Department of Human Biology, University of Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, South Africa
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Lauren M. Watson
- Department of Pathology, University of Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Danielle C. Smith
- Department of Pathology, University of Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Joseph V. Raimondo
- Department of Human Biology, University of Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Robea Ballo
- Department of Human Biology, University of Cape Town, South Africa
| | - Janine Scholefield
- Gene Expression & Biophysics Group, Synthetic Biology ERA, CSIR Biosciences, Pretoria, Gauteng, South Africa
| | - Sally A. Cowley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Matthew J. A. Wood
- Department of Paediatrics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Susan H. Kidson
- Department of Human Biology, University of Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Leslie J. Greenberg
- Department of Pathology, University of Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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19
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Biasini A, Abdulkarim B, de Pretis S, Tan JY, Arora R, Wischnewski H, Dreos R, Pelizzola M, Ciaudo C, Marques AC. Translation is required for miRNA-dependent decay of endogenous transcripts. EMBO J 2021; 40:e104569. [PMID: 33300180 PMCID: PMC7849302 DOI: 10.15252/embj.2020104569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 10/30/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022] Open
Abstract
Post-transcriptional repression of gene expression by miRNAs occurs through transcript destabilization or translation inhibition. mRNA decay is known to account for most miRNA-dependent repression. However, because transcript decay occurs co-translationally, whether target translation is a requirement for miRNA-dependent transcript destabilization remains unknown. To decouple these two molecular processes, we used cytosolic long noncoding RNAs (lncRNAs) as models for endogenous transcripts that are not translated. We show that, despite interacting with the miRNA-loaded RNA-induced silencing complex, the steady-state abundance and decay rates of these transcripts are minimally affected by miRNA loss. To further validate the apparent requirement of translation for miRNA-dependent decay, we fused two lncRNA candidates to the 3'-end of a protein-coding gene reporter and found this results in their miRNA-dependent destabilization. Further analysis revealed that the few natural lncRNAs whose levels are regulated by miRNAs in mESCs tend to associate with translating ribosomes, and possibly represent misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. In summary, our analyses suggest that translation is required for miRNA-dependent transcript destabilization, and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs.
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Affiliation(s)
- Adriano Biasini
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Baroj Abdulkarim
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Stefano de Pretis
- Center for Genomic SciencesIstituto Italiano di Tecnologia (IIT)MilanoItaly
| | - Jennifer Y Tan
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
| | - Rajika Arora
- Institute of Molecular Health SciencesETHZZurichSwitzerland
| | | | - Rene Dreos
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Mattia Pelizzola
- Center for Genomic SciencesIstituto Italiano di Tecnologia (IIT)MilanoItaly
| | | | - Ana Claudia Marques
- Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
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20
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Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21249582. [PMID: 33339180 PMCID: PMC7765627 DOI: 10.3390/ijms21249582] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is classically considered the main cause of neuronal death in neurodegenerative diseases (NDDs). However, increasing evidence suggests that alteration of RNA metabolism is a key factor in the etiopathogenesis of these complex disorders. Non-coding RNAs are the major contributor to the human transcriptome and are particularly abundant in the central nervous system, where they have been proposed to be involved in the onset and development of NDDs. Interestingly, some ncRNAs (such as lncRNAs, circRNAs and pseudogenes) share a common functionality in their ability to regulate gene expression by modulating miRNAs in a phenomenon known as the competing endogenous RNA mechanism. Moreover, ncRNAs are found in body fluids where their presence and concentration could serve as potential non-invasive biomarkers of NDDs. In this review, we summarize the ceRNA networks described in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and spinocerebellar ataxia type 7, and discuss their potential as biomarkers of these NDDs. Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
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21
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Neves-Carvalho A, Duarte-Silva S, Teixeira-Castro A, Maciel P. Polyglutamine spinocerebellar ataxias: emerging therapeutic targets. Expert Opin Ther Targets 2020; 24:1099-1119. [PMID: 32962458 DOI: 10.1080/14728222.2020.1827394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Six of the most frequent dominantly inherited spinocerebellar ataxias (SCAs) worldwide - SCA1, SCA2, SCA3, SCA6, SCA7, and SCA17 - are caused by an expansion of a polyglutamine (polyQ) tract in the corresponding proteins. While the identification of the causative mutation has advanced knowledge on the pathogenesis of polyQ SCAs, effective therapeutics able to mitigate the severe clinical manifestation of these highly incapacitating disorders are not yet available. AREAS COVERED This review provides a comprehensive and critical perspective on well-established and emerging therapeutic targets for polyQ SCAs; it aims to inspire prospective drug discovery efforts. EXPERT OPINION The landscape of polyQ SCAs therapeutic targets and strategies includes (1) the mutant genes and proteins themselves, (2) enhancement of endogenous protein quality control responses, (3) abnormal protein-protein interactions of the mutant proteins, (4) disturbed neuronal function, (5) mitochondrial function, energy availability and oxidative stress, and (6) glial dysfunction, growth factor or hormone imbalances. Challenges include gaining a clearer definition of therapeutic targets for the drugs in clinical development, the discovery of novel drug-like molecules for challenging key targets, and the attainment of a stronger translation of preclinical findings to the clinic.
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Affiliation(s)
- Andreia Neves-Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory , Braga, Guimarães, Portugal
| | - Sara Duarte-Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory , Braga, Guimarães, Portugal
| | - Andreia Teixeira-Castro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory , Braga, Guimarães, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho , Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory , Braga, Guimarães, Portugal
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22
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Sun L, Chen X, Jin Z. Emerging roles of non‐coding RNAs in retinal diseases: A review. Clin Exp Ophthalmol 2020; 48:1085-1101. [PMID: 32519377 DOI: 10.1111/ceo.13806] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Lan‐Fang Sun
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Xue‐Jiao Chen
- Laboratory of Stem Cell and Retinal Regeneration, Division of Ophthalmic Genetics, The Eye Hospital Wenzhou Medical University Wenzhou China
| | - Zi‐Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory Beijing China
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23
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Huang T, Li H, Zhang S, Liu F, Wang D, Xu J. Nrn1 Overexpression Attenuates Retinal Ganglion Cell Apoptosis, Promotes Axonal Regeneration, and Improves Visual Function Following Optic Nerve Crush in Rats. J Mol Neurosci 2020; 71:66-79. [DOI: 10.1007/s12031-020-01627-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
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24
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Ala U. Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. Cells 2020; 9:E1574. [PMID: 32605220 PMCID: PMC7407898 DOI: 10.3390/cells9071574] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
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25
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Biasini A, Smith AAT, Abdulkarim B, Ferreira da Silva M, Tan JY, Marques AC. The Contribution of lincRNAs at the Interface between Cell Cycle Regulation and Cell State Maintenance. iScience 2020; 23:101291. [PMID: 32619701 PMCID: PMC7334372 DOI: 10.1016/j.isci.2020.101291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Cell cycle progression is controlled by the interplay of established cell cycle regulators. Changes in these regulators' activity underpin differences in cell cycle kinetics between cell types. We investigated whether long intergenic noncoding RNAs (lincRNAs) contribute to embryonic stem cell cycle adaptations. Using single-cell RNA sequencing data for mouse embryonic stem cells (mESCs) staged as G1, S, or G2/M we found differentially expressed lincRNAs are enriched among cell cycle-regulated genes. These lincRNAs (CC-lincRNAs) are co-expressed with genes involved in cell cycle regulation. We tested the impact of two CC-lincRNA candidates and show using CRISPR activation that increasing their expression is associated with deregulated cell cycle progression. Interestingly, CC-lincRNAs are often differentially expressed between G1 and S, their promoters are enriched in pluripotency transcription factor (TF) binding sites, and their transcripts are frequently co-regulated with genes involved in the maintenance of pluripotency, suggesting a contribution of CC-lincRNAs to mESC cell cycle adaptations. Genes differentially expressed between mESC cell cycle stages are enriched in lincRNAs CC-lincRNAs are co-expressed with cell cycle and pluripotency genes CC-lincRNAs are often mESC specific and their promoters enriched in pluripotency TFs Upregulation of two CC-lincRNAs results in deregulated mESC cell cycle progression
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Affiliation(s)
- Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Baroj Abdulkarim
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
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26
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Niewiadomska-Cimicka A, Hache A, Trottier Y. Gene Deregulation and Underlying Mechanisms in Spinocerebellar Ataxias With Polyglutamine Expansion. Front Neurosci 2020; 14:571. [PMID: 32581696 PMCID: PMC7296114 DOI: 10.3389/fnins.2020.00571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
Polyglutamine spinocerebellar ataxias (polyQ SCAs) include SCA1, SCA2, SCA3, SCA6, SCA7, and SCA17 and constitute a group of adult onset neurodegenerative disorders caused by the expansion of a CAG repeat sequence located within the coding region of specific genes, which translates into polyglutamine tract in the corresponding proteins. PolyQ SCAs are characterized by degeneration of the cerebellum and its associated structures and lead to progressive ataxia and other diverse symptoms. In recent years, gene and epigenetic deregulations have been shown to play a critical role in the pathogenesis of polyQ SCAs. Here, we provide an overview of the functions of wild type and pathogenic polyQ SCA proteins in gene regulation, describe the extent and nature of gene expression changes and their pathological consequences in diseases, and discuss potential avenues to further investigate converging and distinct disease pathways and to develop therapeutic strategies.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Antoine Hache
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Yvon Trottier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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27
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Corso-Díaz X, Gentry J, Rebernick R, Jaeger C, Brooks MJ, van Asten F, Kooragayala K, Gieser L, Nellissery J, Covian R, Cogliati T, Mondal AK, Jiang K, Swaroop A. Genome-wide Profiling Identifies DNA Methylation Signatures of Aging in Rod Photoreceptors Associated with Alterations in Energy Metabolism. Cell Rep 2020; 31:107525. [PMID: 32320661 PMCID: PMC7228806 DOI: 10.1016/j.celrep.2020.107525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/11/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
Aging-associated functional decline is accompanied by alterations in the epigenome. To explore DNA modifications that could influence visual function with age, we perform whole-genome bisulfite sequencing of purified mouse rod photoreceptors at four ages and identify 2,054 differentially methylated regions (DMRs). We detect many DMRs during early stages of aging and in rod regulatory regions, and some of these cluster at chromosomal hotspots, especially on chromosome 10, which includes a longevity interactome. Integration of methylome to age-related transcriptome changes, chromatin signatures, and first-order protein-protein interactions uncover an enrichment of DMRs in altered pathways that are associated with rod function, aging, and energy metabolism. In concordance, we detect reduced basal mitochondrial respiration and increased fatty acid dependency with retinal age in ex vivo assays. Our study reveals age-dependent genomic and chromatin features susceptible to DNA methylation changes in rod photoreceptors and identifies a link between DNA methylation and energy metabolism in aging.
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Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Gentry
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Rebernick
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine Jaeger
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew J Brooks
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keshav Kooragayala
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linn Gieser
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacob Nellissery
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raul Covian
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiziana Cogliati
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupam K Mondal
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ke Jiang
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, 6 Center Drive, MSC0610, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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28
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An insight into structural plasticity and conformational transitions of transcriptional co-activator Sus1. PLoS One 2020; 15:e0229216. [PMID: 32134955 PMCID: PMC7058303 DOI: 10.1371/journal.pone.0229216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/31/2020] [Indexed: 11/30/2022] Open
Abstract
RNA biogenesis and mRNA transport are an intricate process for every eukaryotic cell. SAGA, a transcriptional coactivator and TREX-2 are the two major complexes participate in this process. Sus1 is a transcription export factor and part of both the SAGA and the TREX-2 complex. The competitive exchange of Sus1 molecule between SAGA and TREX-2 complex modulates their function which is credited to structural plasticity of Sus1. Here, we portray the biophysical characterization of Sus1 from S. cerevisiae. The recombinant Sus1 is a α-helical structure which is stable at various pH conditions. We reported the α-helix to β-sheet transition at the low pH as well as at high pH. Sus1 showed 50% reduction in the fluorescence intensity at pH-2 as compared to native protein. The fluorescence studies demonstrated the unfolding of tertiary structure of the protein with variation in pH as compared to neutral pH. The same results were obtained in the ANS binding and acrylamide quenching studies. Similarly, the secondary structure of the Sus1 was found to be stable till 55% alcohol concentration while tertiary structure was stable up to 20% alcohol concentration. Further increase in the alcohol concentration destabilizes the secondary as well as tertiary structure. The 300 mM concentration of ammonium sulfate also stabilizes the secondary structure of the protein. The structural characterization of this protein is expected to unfold the process of the transportation of the mRNA with cooperation of different proteins.
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29
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Hou TY, Zhou Y, Zhu LS, Wang X, Pang P, Wang DQ, Liuyang ZY, Man H, Lu Y, Zhu LQ, Liu D. Correcting abnormalities in miR-124/PTPN1 signaling rescues tau pathology in Alzheimer's disease. J Neurochem 2020; 154:441-457. [PMID: 31951013 DOI: 10.1111/jnc.14961] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs have been implicated in diverse physiological and pathological processes. We previously reported that aberrant microRNA-124 (miR-124)/non-receptor-type protein phosphatase 1 (PTPN1) signaling plays an important role in the synaptic disorders associated with Alzheimer's disease (AD). In this study, we further investigated the potential role of miR-124/PTPN1 in the tau pathology of AD. We first treated the mice with intra-hippocampal stereotactic injections. Then, we used quantitative real-time reverse transcription PCR (qRT-PCR) to detect the expression of microRNAs. Western blotting was used to measure the level of PTPN1, the level of tau protein, the phosphorylation of tau at AD-related sites, and alterations in the activity of glycogen synthase kinase 3β (GSK-3β) and protein phosphatase 2 (PP2A). Immunohistochemistry was also used to detect changes in tau phosphorylation levels at AD-related sites and somadendritic aggregation. Soluble and insoluble tau protein was separated by 70% formic acid (FA) extraction to examine tau solubility. Finally, behavioral experiments (including the Morris water maze, fear conditioning, and elevated plus maze) were performed to examine learning and memory ability and emotion-related behavior. We found that artificially replicating the abnormalities in miR-124/PTPN1 signaling induced AD-like tau pathology in the hippocampus of wild-type mice, including hyperphosphorylation at multiple sites, insolubility and somadendritic aggregation, as well as learning/memory deficits. We also found that disruption of miR-124/PTPN1 signaling was caused by the loss of RE1-silencing transcription factor protein, which can be initiated by Aβ insults or oxidative stress, as observed in the brains of P301S mice. Correcting the deregulation of miR-124/PTPN1 signaling rescued the tau pathology and learning/memory impairments in the P301S mice. We also found that miR-124/PTPN1 abnormalities induced activation of glycogen synthase kinase 3 (GSK-3) and inactivation of protein phosphatase 2A (PP2A) by promoting tyrosine phosphorylation, implicating an imbalance in tau kinase/phosphatase. Thus, targeting the miR-124/PTPN1 signaling pathway is a promising therapeutic strategy for AD.
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Affiliation(s)
- Tong-Yao Hou
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Yang Zhou
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Ling-Shuang Zhu
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiong Wang
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Pei Pang
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Ding-Qi Wang
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhen-Yu Liuyang
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Hengye Man
- Department of Biology, Boston University, Boston, MA, USA
| | - Youming Lu
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Dan Liu
- Department of Pathophysiology, Key Laboratory of Neurological Disorders of the Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P.R. China.,Department of Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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30
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Li J, Lv H, Che YQ. Long non-coding RNA Gas5 potentiates the effects of microRNA-21 downregulation in response to ischaemic brain injury. Neuroscience 2020; 437:87-97. [PMID: 31982471 DOI: 10.1016/j.neuroscience.2020.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/28/2022]
Abstract
Brain ischaemia, which can cause severe nerve injury, is a global health challenge. Long non-coding RNA (lncRNA) growth-arrest specific 5 (Gas5) has been documented to exert tumour suppressive effects in several cancers. However, its role in cerebrovascular disease still requires further investigation. Therefore, in this study, we focused on the role of lncRNA regulatory signalling related to lncRNA Gas5 in ischaemic brain injury. Middle cerebral artery occlusion (MCAO) was employed as a model of ischaemic brain injury in rats. The expression of lncRNA Gas5 and microRNA-21 (miR-21) was altered in neurons to elucidate their effects in ischaemic brain injury and to identify the interactions among lncRNA Gas5, miR-21 and Pten. The neuronal survival rate, apoptosis and the expression of phosphatidyl inositol 3-kinase (PI3K)/Akt signalling pathway-related genes were also evaluated in vitro to determine the effects of lncRNA Gas5. In the brains of rats subjected to MCAO, the expression of lncRNA Gas5 and Pten was upregulated, while miR-21 was downregulated. LncRNA Gas5 inhibited miR-21 expression, leading to elevated levels of Pten. In vitro experiments revealed that lncRNA Gas5 depletion and miR-21 elevation resulted in the suppression of neuronal apoptosis, thus promoting neuronal survival via the PI3K/Akt signalling pathway. These findings demonstrate that lncRNA Gas5 increases miR-21 and activates Pten, contributing to the development of ischaemic brain injury, supporting the silencing of lncRNA Gas5 as a possible therapeutic target for the treatment of ischaemic brain injury.
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Affiliation(s)
- Jie Li
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China
| | - Hui Lv
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China
| | - Yu-Qin Che
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, PR China.
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31
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Niewiadomska-Cimicka A, Trottier Y. Molecular Targets and Therapeutic Strategies in Spinocerebellar Ataxia Type 7. Neurotherapeutics 2019; 16:1074-1096. [PMID: 31432449 PMCID: PMC6985300 DOI: 10.1007/s13311-019-00778-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a rare autosomal dominant neurodegenerative disorder characterized by progressive neuronal loss in the cerebellum, brainstem, and retina, leading to cerebellar ataxia and blindness as major symptoms. SCA7 is due to the expansion of a CAG triplet repeat that is translated into a polyglutamine tract in ATXN7. Larger SCA7 expansions are associated with earlier onset of symptoms and more severe and rapid disease progression. Here, we summarize the pathological and genetic aspects of SCA7, compile the current knowledge about ATXN7 functions, and then focus on recent advances in understanding the pathogenesis and in developing biomarkers and therapeutic strategies. ATXN7 is a bona fide subunit of the multiprotein SAGA complex, a transcriptional coactivator harboring chromatin remodeling activities, and plays a role in the differentiation of photoreceptors and Purkinje neurons, two highly vulnerable neuronal cell types in SCA7. Polyglutamine expansion in ATXN7 causes its misfolding and intranuclear accumulation, leading to changes in interactions with native partners and/or partners sequestration in insoluble nuclear inclusions. Studies of cellular and animal models of SCA7 have been crucial to unveil pathomechanistic aspects of the disease, including gene deregulation, mitochondrial and metabolic dysfunctions, cell and non-cell autonomous protein toxicity, loss of neuronal identity, and cell death mechanisms. However, a better understanding of the principal molecular mechanisms by which mutant ATXN7 elicits neurotoxicity, and how interconnected pathogenic cascades lead to neurodegeneration is needed for the development of effective therapies. At present, therapeutic strategies using nucleic acid-based molecules to silence mutant ATXN7 gene expression are under development for SCA7.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France
| | - Yvon Trottier
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France.
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32
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Xu S, Yang W, Yuan P, Yan J, Tang Y, Zheng Y, Li Z, Sun Y, Han S, Yin J, Peng B, He X, Pan Q, Liu W. The Long-Noncoding RNA lnc-NONH Enhances the Early Transcription of Prototype Foamy Virus Via Upregulating Expression of miR-34c-5p and Tas Protein. Intervirology 2019; 62:156-163. [PMID: 31430761 DOI: 10.1159/000502038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Prototype foamy virus (PFV) is a complex and unique retrovirus with the longest genome among the retroviruses and is used as a vector for gene therapies. The viral Tas protein transactivates the viral long terminal repeat promoter and is required for viral replication. We have utilized RNA sequencing to identify and characterize the long-noncoding RNA NONHSAG000101 (lnc-NONH), which markedly increases in PFV-infected cells. However, little is known about the function of lnc-NONH. OBJECTIVES We aim to explore the role of lnc-NONH during PFV infection. METHODS To assess the lnc-NONH role during PFV infection, the siRNAs were used to silence the lnc-NONH expression. The microRNA (miRNA) mimic and inhibitor were employed to explore the function of lnc-NONH-related miRNA miR-34c-5p. Quantitative real-time polymerase chain reaction assay and Western blotting were applied to measure the mRNA and protein levels of PFV transactivator Tas. Luciferase assay was used to determine the transcriptional activity of the PFV unique internal promoter (IP). RESULTS lnc-NONH promotes the expression of PFV Tas and miR-34c-5p. The interaction between lnc-NONH and miR-34c-5p enhances the transcriptional activity of the PFV IP. CONCLUSIONS In the current study, we report a novel mechanism for the lnc-NONH-mediated upregulation of Tas expression. Our findings contribute to the understanding of regulatory network of Tas expression and PFV replication.
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Affiliation(s)
- Shanshan Xu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Department of Allergy, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wenqiong Yang
- Department of Neurology, Dongfeng Hospital, Hubei University of Medicine, Shiyan, China
| | - Peipei Yuan
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Yan
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yinglian Tang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhi Li
- College of Life Sciences, Shanxi Normal University, Xi'an, China
| | - Yan Sun
- College of Life Sciences, Shanxi Normal University, Xi'an, China
| | - Song Han
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Yin
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Biwen Peng
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaohua He
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qin Pan
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China,
| | - Wanhong Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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33
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Li T, Hou X, Chen Z, Peng Y, Wang P, Xie Y, He L, Yuan H, Peng H, Qiu R, Xia K, Tang B, Jiang H. RNA Expression Profile and Potential Biomarkers in Patients With Spinocerebellar Ataxia Type 3 From Mainland China. Front Genet 2019; 10:566. [PMID: 31249598 PMCID: PMC6584761 DOI: 10.3389/fgene.2019.00566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 05/29/2019] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in growth, development, and reproduction and undoubtedly contribute to the pathogenesis and progression of diseases. Emerging evidence suggests the involvement of lncRNAs as regulatory factors in pathological conditions, including some neurodegenerative diseases. Spinocerebellar Ataxia Type 3/Machado–Joseph Disease (SCA3/MJD) has a prominent prevalence in China. Because the role of lncRNAs in SCA3/MJD pathogenesis has not yet been investigated, we conducted a pilot study to investigate the expression profile of lncRNAs by high-throughput sequencing in 12 patients and 12 healthy individuals. The sequencing analysis detected 5,540 known and 2,759 novel lncRNAs. Six lncRNAs were confirmed to be differentially expressed in peripheral blood mononuclear cells between SCA3/MJD patients and healthy individuals and were further validated in cerebellar tissue. Based on these results, NONHSAT022144.2 and NONHSAT165686.1 may be involved in the pathogenesis of SCA3/MJD and may be potential biomarkers for SCA3/MJD. Together with NONHSAT022144.2 and NONHSAT165686.1, the other four novel lncRNAs increase our understanding of lncRNA expression profile.
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Affiliation(s)
- Tianjiao Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaocan Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Puzhi Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yue Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lang He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Huirong Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rong Qiu
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Kun Xia
- Medical Genetics Research Center, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Medical Genetics Research Center, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Medical Genetics Research Center, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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34
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Sirey TM, Roberts K, Haerty W, Bedoya-Reina O, Rogatti-Granados S, Tan JY, Li N, Heather LC, Carter RN, Cooper S, Finch AJ, Wills J, Morton NM, Marques AC, Ponting CP. The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity. eLife 2019; 8:e45051. [PMID: 31045494 PMCID: PMC6542586 DOI: 10.7554/elife.45051] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation and, with miR-488-3p, represent novel targets for the modulation of complex I activity.
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Affiliation(s)
- Tamara M Sirey
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Kenny Roberts
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Wilfried Haerty
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Oscar Bedoya-Reina
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Sebastian Rogatti-Granados
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Jennifer Y Tan
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Nick Li
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Lisa C Heather
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Roderick N Carter
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Sarah Cooper
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Andrew J Finch
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Jimi Wills
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Nicholas M Morton
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
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35
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Upregulation of long noncoding RNA Gadd45a is associated with sevoflurane-induced neurotoxicity in rat neural stem cells. Neuroreport 2019. [PMID: 29521679 DOI: 10.1097/wnr.0000000000000980] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Emerging evidence has shown that long noncoding RNA (lncRNA) plays a crucial role in controlling neural stem cells' (NSCs) survival. However, the fundamental role of lncRNA underlying sevoflurane-induced neurotoxicity remains poorly elucidated. In the present study, we investigate the effect of sevoflurane-induced neurotoxicity in a concentration-dependent and duration-dependent manner. Furthermore, we assayed the differential profile of lncRNA in rat hippocampal NSCs following sevoflurane exposure, and identified lncRNA Gadd45a and the correlation between lncRNA Gadd45a and Gadd45a. We found that lncRNA Gadd45a and its nearby gene, Gadd45a, were significantly upregulated in NSCs exposed to sevoflurane. Notably, Gadd45a was enriched in the cell cycle-relative pathway including mitogen-activated protein kinases and P53 signaling, whereas lncRNA Gadd45a was positively correlated with Gadd45a. These results suggest lncRNA Gadd45a is associated with sevoflurane-induced toxicity, and thus shed light on a new key target for revealing the molecular mechanism of sevoflurane-induced toxicity.
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36
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Buijsen RAM, Toonen LJA, Gardiner SL, van Roon-Mom WMC. Genetics, Mechanisms, and Therapeutic Progress in Polyglutamine Spinocerebellar Ataxias. Neurotherapeutics 2019; 16:263-286. [PMID: 30607747 PMCID: PMC6554265 DOI: 10.1007/s13311-018-00696-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Autosomal dominant cerebellar ataxias (ADCAs) are a group of neurodegenerative disorders characterized by degeneration of the cerebellum and its connections. All ADCAs have progressive ataxia as their main clinical feature, frequently accompanied by dysarthria and oculomotor deficits. The most common spinocerebellar ataxias (SCAs) are 6 polyglutamine (polyQ) SCAs. These diseases are all caused by a CAG repeat expansion in the coding region of a gene. Currently, no curative treatment is available for any of the polyQ SCAs, but increasing knowledge on the genetics and the pathological mechanisms of these polyQ SCAs has provided promising therapeutic targets to potentially slow disease progression. Potential treatments can be divided into pharmacological and gene therapies that target the toxic downstream effects, gene therapies that target the polyQ SCA genes, and stem cell replacement therapies. Here, we will provide a review on the genetics, mechanisms, and therapeutic progress in polyglutamine spinocerebellar ataxias.
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Affiliation(s)
- Ronald A M Buijsen
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.
| | - Lodewijk J A Toonen
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Sarah L Gardiner
- Department of Human Genetics, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Neurology, LUMC, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
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Eszlari N, Millinghoffer A, Petschner P, Gonda X, Baksa D, Pulay AJ, Réthelyi JM, Breen G, Deakin JFW, Antal P, Bagdy G, Juhasz G. Genome-wide association analysis reveals KCTD12 and miR-383-binding genes in the background of rumination. Transl Psychiatry 2019; 9:119. [PMID: 30886212 PMCID: PMC6423133 DOI: 10.1038/s41398-019-0454-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/31/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Ruminative response style is a passive and repetitive way of responding to stress, associated with several disorders. Although twin and candidate gene studies have proven the genetic underpinnings of rumination, no genome-wide association study (GWAS) has been conducted yet. We performed a GWAS on ruminative response style and its two subtypes, brooding and reflection, among 1758 European adults recruited in the general population of Budapest, Hungary, and Manchester, United Kingdom. We evaluated single-nucleotide polymorphism (SNP)-based, gene-based and gene set-based tests, together with inferences on genes regulated by our most significant SNPs. While no genome-wide significant hit emerged at the SNP level, the association of rumination survived correction for multiple testing with KCTD12 at the gene level, and with the set of genes binding miR-383 at the gene set level. SNP-level results were concordant between the Budapest and Manchester subsamples for all three rumination phenotypes. SNP-level results and their links to brain expression levels based on external databases supported the role of KCTD12, SRGAP3, and SETD5 in rumination, CDH12 in brooding, and DPYSL5, MAPRE3, KCNK3, ATXN7L3B, and TPH2 in reflection, among others. The relatively low sample size is a limitation of our study. Results of the first GWAS on rumination identified genes previously implicated in psychiatric disorders underscoring the transdiagnostic nature of rumination, and pointed to the possible role of the dorsolateral prefrontal cortex, hippocampus, and cerebellum in this cognitive process.
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Affiliation(s)
- Nora Eszlari
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary. .,NAP-2-SE New Antidepressant Target Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary.
| | - Andras Millinghoffer
- 0000 0001 0942 9821grid.11804.3cNAP-2-SE New Antidepressant Target Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary ,0000 0001 2180 0451grid.6759.dDepartment of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Peter Petschner
- 0000 0001 0942 9821grid.11804.3cDepartment of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cMTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Xenia Gonda
- 0000 0001 0942 9821grid.11804.3cNAP-2-SE New Antidepressant Target Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cMTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cDepartment of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Daniel Baksa
- 0000 0001 0942 9821grid.11804.3cDepartment of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cSE-NAP 2 Genetic Brain Imaging Migraine Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary
| | - Attila J. Pulay
- 0000 0001 0942 9821grid.11804.3cDepartment of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - János M. Réthelyi
- 0000 0001 0942 9821grid.11804.3cDepartment of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cNAP2 Molecular Psychiatry Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary
| | - Gerome Breen
- 0000 0001 2322 6764grid.13097.3cSocial, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK
| | - John Francis William Deakin
- 0000000121662407grid.5379.8Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK ,0000 0004 0417 0074grid.462482.eManchester Academic Health Sciences Centre, Manchester, UK ,0000 0004 0430 6955grid.450837.dGreater Manchester Mental Health NHS Foundation Trust, Prestwich, Manchester, M25 3BL UK
| | - Peter Antal
- 0000 0001 2180 0451grid.6759.dDepartment of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gyorgy Bagdy
- 0000 0001 0942 9821grid.11804.3cDepartment of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cNAP-2-SE New Antidepressant Target Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cMTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Gabriella Juhasz
- 0000 0001 0942 9821grid.11804.3cDepartment of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cNAP-2-SE New Antidepressant Target Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cMTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary ,0000 0001 0942 9821grid.11804.3cSE-NAP 2 Genetic Brain Imaging Migraine Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary ,0000000121662407grid.5379.8Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK ,0000 0004 0417 0074grid.462482.eManchester Academic Health Sciences Centre, Manchester, UK
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38
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Sparber P, Filatova A, Khantemirova M, Skoblov M. The role of long non-coding RNAs in the pathogenesis of hereditary diseases. BMC Med Genomics 2019; 12:42. [PMID: 30871545 PMCID: PMC6416829 DOI: 10.1186/s12920-019-0487-6] [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] [Indexed: 12/22/2022] Open
Abstract
Background Thousands of long non-coding RNA (lncRNA) genes are annotated in the human genome. Recent studies showed the key role of lncRNAs in a variety of fundamental cellular processes. Dysregulation of lncRNAs can drive tumorigenesis and they are now considered to be a promising therapeutic target in cancer. However, how lncRNAs contribute to the development of hereditary diseases in human is still mostly unknown. Results This review is focused on hereditary diseases in the pathogenesis of which long non-coding RNAs play an important role. Conclusions Fundamental research in the field of molecular genetics of lncRNA is necessary for a more complete understanding of their significance. Future research will help translate this knowledge into clinical practice which will not only lead to an increase in the diagnostic rate but also in the future can help with the development of etiotropic treatments for hereditary diseases.
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Affiliation(s)
- Peter Sparber
- Research Center for Medical Genetics, Moscow, Russia.
| | | | - Mira Khantemirova
- Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Mikhail Skoblov
- Research Center for Medical Genetics, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
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39
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Riefolo M, Porcellini E, Dika E, Broseghini E, Ferracin M. Interplay between small and long non-coding RNAs in cutaneous melanoma: a complex jigsaw puzzle with missing pieces. Mol Oncol 2019; 13:74-98. [PMID: 30499222 PMCID: PMC6322194 DOI: 10.1002/1878-0261.12412] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
The incidence of cutaneous melanoma (CM) has increased in the past few decades. The biology of melanoma is characterized by a complex interaction between genetic, environmental and phenotypic factors. A greater understanding of the molecular mechanisms that promote melanoma cell growth and dissemination is crucial to improve diagnosis, prognostication, and treatment of CM. Both small and long non-coding RNAs (lncRNAs) have been identified to play a role in melanoma biology; microRNA and lncRNA expression is altered in transformed melanocytes and this in turn has functional effects on cell proliferation, apoptosis, invasion, metastasis, and immune response. Moreover, specific dysregulated ncRNAs were shown to have a diagnostic or prognostic role in melanoma and to drive the establishment of drug resistance. Here, we review the current literature on small and lncRNAs with a role in melanoma, with the aim of putting into some order this complex jigsaw puzzle.
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Affiliation(s)
- Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Emi Dika
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Elisabetta Broseghini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
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40
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Hwang DW, Choi Y, Kim D, Park HY, Kim KW, Kim MY, Park CK, Lee DS. Graphene oxide-quenching-based fluorescence in situ hybridization (G-FISH) to detect RNA in tissue: Simple and fast tissue RNA diagnostics. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 16:162-172. [PMID: 30594658 DOI: 10.1016/j.nano.2018.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 01/24/2023]
Abstract
FISH-based RNA detection in paraffin-embedded tissue can be challenging, with complicated procedures producing uncertain results and poor image quality. Here, we developed a robust RNA detection method based on graphene oxide (GO) quenching and recovery of fluorescence in situ hybridization (G-FISH) in formalin-fixed paraffin-embedded (FFPE) tissues. Using a fluorophore-labeled peptide nucleic acid (PNA) attached to GO, the endogenous long noncoding RNA BC1, the constitutive protein β-actin mRNA, and miR-124a and miR-21 could be detected in the cytoplasm of a normal mouse brain, primary cultured hippocampal neurons, an Alzheimer's disease model mouse brain, and glioblastoma multiforme tumor tissues, respectively. Coding and non-coding RNAs, either long or short, could be detected in deparaffinized FFPE or frozen tissues, as well as in clear lipid-exchanged anatomically rigid imaging/immunostaining-compatible tissue hydrogel (CLARITY)-transparent brain tissues. The fluorescence recovered by G-FISH correlated highly with the amount of miR-21, as measured by quantitative real time RT-PCR. We propose G-FISH as a simple, fast, inexpensive, and sensitive method for RNA detection, with a very low background, which could be applied to a variety of research or diagnostic purposes.
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Affiliation(s)
- Do Won Hwang
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine; Medical Research Center, Institute of Radiation Medicine, Seoul National University College of Medicine; Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University
| | - Yoori Choi
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine
| | - Dohyun Kim
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University
| | - Kyu Wan Kim
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine
| | - Mee Young Kim
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine; Cancer Research Institute, College of Medicine, The Catholic University of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University.
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Cai Y, Wan J. Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. Front Mol Neurosci 2018; 11:370. [PMID: 30344479 PMCID: PMC6182084 DOI: 10.3389/fnmol.2018.00370] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.
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Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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42
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Liu W, Liu X, Wu C, Jiang L. Transcriptome analysis demonstrates that long noncoding RNA is involved in the hypoxic response in Larimichthys crocea. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:1333-1347. [PMID: 29948448 DOI: 10.1007/s10695-018-0525-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
The large yellow croaker (Larimichthys crocea) has low hypoxia tolerance compared with other fish species, and the mRNA levels of hypoxia-inducible factor (HIF)-1α in its brain do not change markedly under hypoxic conditions. In this study, we investigated noncoding transcription in the hypoxic response mechanism of L. crocea. We generated a catalog of long noncoding RNAs (lncRNAs) from the brain of L. crocea individuals under hypoxic stress, investigated lncRNA expression patterns, and analyzed the HIF signaling pathway by RNA sequencing. Prolyl hydroxylase domain 2 (PHD2) expression significantly increased after 6 and 12 h of hypoxia, and a lncRNA (Linc_06633.1) was found in the upstream, antisense region of PHD2. Linc_06633.1 may be an important regulator that promotes PDH2 expression under hypoxia in L. crocea, and we constructed a regulatory profile of L. crocea under hypoxic conditions. To the best of our knowledge, it is the first study that has been conducted on hypoxia signaling pathway regulation by lncRNAs in L. crocea and elucidates the role played by lncRNAs in the regulation of the hypoxia stress response in teleost fish.
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Affiliation(s)
- Wei Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Xiaoxu Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China.
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43
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Genome-Wide Sequencing Reveals Small Nucleolar RNAs Downregulated in Cerebral Cavernous Malformations. Cell Mol Neurobiol 2018; 38:1369-1382. [DOI: 10.1007/s10571-018-0602-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/09/2018] [Indexed: 02/04/2023]
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Abstract
Polyglutamine diseases are hereditary degenerative disorders of the nervous system that have remained, to this date, untreatable. Promisingly, investigation into their molecular etiology and the development of increasingly perfected tools have contributed to the design of novel strategies with therapeutic potential. Encouraging studies have explored gene therapy as a means to counteract cell demise and loss in this context. The current chapter addresses the two main focuses of research in the area: the characteristics of the systems used to deliver nucleic acids to cells and the molecular and cellular actions of the therapeutic agents. Vectors used in gene therapy have to satisfyingly reach the tissues and cell types of interest, while eliciting the lowest toxicity possible. Both viral and non-viral systems have been developed for the delivery of nucleic acids to the central nervous system, each with its respective advantages and shortcomings. Since each polyglutamine disease is caused by mutation of a single gene, many gene therapy strategies have tried to halt degeneration by silencing the corresponding protein products, usually recurring to RNA interference. The potential of small interfering RNAs, short hairpin RNAs and microRNAs has been investigated. Overexpression of protective genes has also been evaluated as a means of decreasing mutant protein toxicity and operate beneficial alterations. Recent gene editing tools promise yet other ways of interfering with the disease-causing genes, at the most upstream points possible. Results obtained in both cell and animal models encourage further delving into this type of therapeutic strategies and support the future use of gene therapy in the treatment of polyglutamine diseases.
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45
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Groot M, Zhang D, Jin Y. Long Non-Coding RNA Review and Implications in Lung Diseases. JSM BIOINFORMATICS, GENOMICS AND PRETEOMICS 2018; 3:1033. [PMID: 30854513 PMCID: PMC6404970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Non-coding genes occupy the majority of the human genome and have recently garnered increased attention for their implications in a range of diseases. This review illustrates the current scientific landscape concerning long non-coding RNA biogenesis, regulation, and degradation, as well as their functional roles in lung pathogenesis. LncRNAs share many similar biogenesis and regulatory processes with mRNA, such as capping, polyadenylation, post-transcriptional modifications, and exonuclease degradation. Evidence suggests that these lncRNAs become dysregulated in lung diseases such as Acute Lung Injury, Idiopathic Pulmonary Fibrosis, COPD, Lung Cancer, and Pulmonary Arterial Fiypertension. Some lncRNAs have known functions, but the overwhelming majority requires further research to completely understand.
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Affiliation(s)
- Michael Groot
- Department of Medicine, Boston University Medical Campus, USA
| | - Duo Zhang
- Department of Medicine, Boston University Medical Campus, USA
| | - Yang Jin
- Department of Medicine, Boston University Medical Campus, USA
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Abstract
Aging-related neurodegenerative diseases are progressive and fatal neurological diseases that are characterized by irreversible neuron loss and gliosis. With a growing population of aging individuals, there is a pressing need to better understand the basic biology underlying these diseases. Although diverse disease mechanisms have been implicated in neurodegeneration, a common theme of altered RNA processing has emerged as a unifying contributing factor to neurodegenerative disease. RNA processing includes a series of distinct processes, including RNA splicing, transport and stability, as well as the biogenesis of non-coding RNAs. Here, we highlight how some of these mechanisms are altered in neurodegenerative disease, including the mislocalization of RNA-binding proteins and their sequestration induced by microsatellite repeats, microRNA biogenesis alterations and defective tRNA biogenesis, as well as changes to long-intergenic non-coding RNAs. We also highlight potential therapeutic interventions for each of these mechanisms. Summary: In this At a Glance review, Edward Lee and co-authors provide an overview of RNA metabolism defects, including mislocalization of RNA-binding proteins and microRNA biogenesis alterations, that contribute to neurodegenerative disease pathology.
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Affiliation(s)
- Elaine Y Liu
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
| | - Christopher P Cali
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratories, Perelman School of Med. Univ. of Pennsylvania, 613A Stellar Chance Laboratories, Philadelphia, PA 19104, USA
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Vieira AS, Dogini DB, Lopes-Cendes I. Role of non-coding RNAs in non-aging-related neurological disorders. ACTA ACUST UNITED AC 2018; 51:e7566. [PMID: 29898036 PMCID: PMC6002137 DOI: 10.1590/1414-431x20187566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022]
Abstract
Protein coding sequences represent only 2% of the human genome. Recent advances
have demonstrated that a significant portion of the genome is actively
transcribed as non-coding RNA molecules. These non-coding RNAs are emerging as
key players in the regulation of biological processes, and act as "fine-tuners"
of gene expression. Neurological disorders are caused by a wide range of genetic
mutations, epigenetic and environmental factors, and the exact pathophysiology
of many of these conditions is still unknown. It is currently recognized that
dysregulations in the expression of non-coding RNAs are present in many
neurological disorders and may be relevant in the mechanisms leading to disease.
In addition, circulating non-coding RNAs are emerging as potential biomarkers
with great potential impact in clinical practice. In this review, we discuss
mainly the role of microRNAs and long non-coding RNAs in several neurological
disorders, such as epilepsy, Huntington disease, fragile X-associated ataxia,
spinocerebellar ataxias, amyotrophic lateral sclerosis (ALS), and pain. In
addition, we give information about the conditions where microRNAs have
demonstrated to be potential biomarkers such as in epilepsy, pain, and ALS.
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Affiliation(s)
- A S Vieira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Instituto Brasileiro de Neurociência e Neurotecnologia, Campinas, SP, Brasil
| | - D B Dogini
- Departamento de Genética Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Instituto Brasileiro de Neurociência e Neurotecnologia, Campinas, SP, Brasil
| | - I Lopes-Cendes
- Departamento de Genética Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Instituto Brasileiro de Neurociência e Neurotecnologia, Campinas, SP, Brasil
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48
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Smillie CL, Sirey T, Ponting CP. Complexities of post-transcriptional regulation and the modeling of ceRNA crosstalk. Crit Rev Biochem Mol Biol 2018; 53:231-245. [PMID: 29569941 PMCID: PMC5935048 DOI: 10.1080/10409238.2018.1447542] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 01/09/2023]
Abstract
Control of gene and protein expression is required for cellular homeostasis and is disrupted in disease. Following transcription, mRNA turnover and translation is modulated, most notably by microRNAs (miRNAs). This modulation is controlled by transcriptional and post-transcriptional events that alter the availability of miRNAs for target binding. Recent studies have proposed that some transcripts - termed competitive endogenous RNAs (ceRNAs) - sequester a miRNA and diminish its repressive effects on other transcripts. Such ceRNAs thus mutually alter each other's abundance by competing for binding to a common set of miRNAs. Some question the relevance of ceRNA crosstalk, arguing that an individual transcript, when its abundance lies within a physiological range of gene expression, will fail to compete for miRNA binding due to the high abundance of other miRNA binding sites across the transcriptome. Despite this, some experimental evidence is consistent with the ceRNA hypothesis. In this review, we draw upon existing data to highlight mechanistic and theoretical aspects of ceRNA crosstalk. Our intent is to propose how understanding of ceRNA crosstalk mechanisms can be improved and what evidence is required to demonstrate a ceRNA mechanism. A greater understanding of factors affecting ceRNA crosstalk should shed light on its relevance in physiological states.
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Affiliation(s)
- Claire L. Smillie
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tamara Sirey
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris P. Ponting
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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Li Z, Liu Y, Guo X, Sun G, Ma Q, Dai Y, Zhu G, Sun Y. Long noncoding RNA myocardial infarction‑associated transcript is associated with the microRNA‑150‑5p/P300 pathway in cardiac hypertrophy. Int J Mol Med 2018; 42:1265-1272. [PMID: 29786749 PMCID: PMC6089782 DOI: 10.3892/ijmm.2018.3700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 05/17/2018] [Indexed: 01/09/2023] Open
Abstract
In numerous diseases, abnormal expression of myocardial infarction-associated transcript (MIAT) has been reported to be involved in cell proliferation, apoptosis and migration. However, whether this long non-coding RNA MIAT has a regulatory effect on heart hypertrophy requires further investigation. To this end, the present study evaluated MIAT in hypertrophic cardiomyocytes in vitro and in vivo. Neonatal rat ventricular myocytes (NRVMs) were induced by isoproterenol (ISO) to create a cell hypertrophy model, and mice were intraperitoneally injected with ISO to establish an animal model. Echocardiography, immunofluorescence staining, western blot analysis, RNA isolation and reverse transcription-polymerase chain reaction were applied to test the involvement of MIAT in cardiac hypertrophy. The results revealed that MIAT was upregulated under ISO stimulation at the mRNA level both in vivo and in vitro. Silencing of MIAT resulted in decreased expression levels of atrial natriuretic peptide and brain natriuretic peptide in ISO-treated NRVM cardiomyocytes, confirming the connection between MIAT and hypertrophy. Furthermore, MIAT small interfering RNA significantly increased microRNA (miR)-150 and decreased P300 expression in NRVMs. In conclusion, the MIAT/miR-150-5p axis targets P300 as a positive regulator of cardiomyocyte hypertrophy.
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Affiliation(s)
- Zhao Li
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Yamin Liu
- Department of Pharmacy, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xiaofan Guo
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Guozhe Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Qun Ma
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ying Dai
- Department of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Guangshuo Zhu
- Department of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Xiang C, Zhang S, Dong X, Ma S, Cong S. Transcriptional Dysregulation and Post-translational Modifications in Polyglutamine Diseases: From Pathogenesis to Potential Therapeutic Strategies. Front Mol Neurosci 2018; 11:153. [PMID: 29867345 PMCID: PMC5962650 DOI: 10.3389/fnmol.2018.00153] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023] Open
Abstract
Polyglutamine (polyQ) diseases are hereditary neurodegenerative disorders caused by an abnormal expansion of a trinucleotide CAG repeat in the coding region of their respective associated genes. PolyQ diseases mainly display progressive degeneration of the brain and spinal cord. Nine polyQ diseases are known, including Huntington's disease (HD), spinal and bulbar muscular atrophy (SBMA), dentatorubral-pallidoluysian atrophy (DRPLA), and six forms of spinocerebellar ataxia (SCA). HD is the best characterized polyQ disease. Many studies have reported that transcriptional dysregulation and post-translational disruptions, which may interact with each other, are central features of polyQ diseases. Post-translational modifications, such as the acetylation of histones, are closely associated with the regulation of the transcriptional activity. A number of groups have studied the interactions between the polyQ proteins and transcription factors. Pharmacological drugs or genetic manipulations aimed at correcting the dysregulation have been confirmed to be effective in the treatment of polyQ diseases in many animal and cellular models. For example, histone deaceylase inhibitors have been demonstrated to have beneficial effects in cases of HD, SBMA, DRPLA, and SCA3. In this review, we describe the transcriptional and post-translational dysregulation in polyQ diseases with special focus on HD, and we summarize and comment on potential treatment approaches targeting disruption of transcription and post-translation processes in these diseases.
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Affiliation(s)
| | | | | | | | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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