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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024:10.1038/s41576-024-00696-z. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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2
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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3
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Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
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Giménez-Bejarano A, Alegre-Cortés E, Yakhine-Diop SMS, Gómez-Suaga P, Fuentes JM. Mitochondrial Dysfunction in Repeat Expansion Diseases. Antioxidants (Basel) 2023; 12:1593. [PMID: 37627588 PMCID: PMC10451345 DOI: 10.3390/antiox12081593] [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: 06/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Repeat expansion diseases are a group of neuromuscular and neurodegenerative disorders characterized by expansions of several successive repeated DNA sequences. Currently, more than 50 repeat expansion diseases have been described. These disorders involve diverse pathogenic mechanisms, including loss-of-function mechanisms, toxicity associated with repeat RNA, or repeat-associated non-ATG (RAN) products, resulting in impairments of cellular processes and damaged organelles. Mitochondria, double membrane organelles, play a crucial role in cell energy production, metabolic processes, calcium regulation, redox balance, and apoptosis regulation. Its dysfunction has been implicated in the pathogenesis of repeat expansion diseases. In this review, we provide an overview of the signaling pathways or proteins involved in mitochondrial functioning described in these disorders. The focus of this review will be on the analysis of published data related to three representative repeat expansion diseases: Huntington's disease, C9orf72-frontotemporal dementia/amyotrophic lateral sclerosis, and myotonic dystrophy type 1. We will discuss the common effects observed in all three repeat expansion disorders and their differences. Additionally, we will address the current gaps in knowledge and propose possible new lines of research. Importantly, this group of disorders exhibit alterations in mitochondrial dynamics and biogenesis, with specific proteins involved in these processes having been identified. Understanding the underlying mechanisms of mitochondrial alterations in these disorders can potentially lead to the development of neuroprotective strategies.
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Affiliation(s)
- Alberto Giménez-Bejarano
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Eva Alegre-Cortés
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Sokhna M. S. Yakhine-Diop
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Patricia Gómez-Suaga
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - José M. Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
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5
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De Rosa M, Opresko PL. Translating the telomeres. Trends Genet 2023; 39:593-595. [PMID: 37179160 PMCID: PMC11160114 DOI: 10.1016/j.tig.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Telomeres are transcribed into long noncoding telomeric repeat-containing RNA (TERRA). Or so we thought. Recently, Al-Turki and Griffith provided evidence that TERRA can code for valine-arginine (VR) or glycine-leucine (GL) dipeptide repeat proteins by undergoing repeat-associated non-ATG (RAN) translation. This finding uncovers a new mechanism by which telomeres can impact cellular function.
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Affiliation(s)
- Mariarosaria De Rosa
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Piwecka M, Fiszer A, Rolle K, Olejniczak M. RNA regulation in brain function and disease 2022 (NeuroRNA): A conference report. Front Mol Neurosci 2023; 16:1133209. [PMID: 36993784 PMCID: PMC10040806 DOI: 10.3389/fnmol.2023.1133209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023] Open
Abstract
Recent research integrates novel technologies and methods from the interface of RNA biology and neuroscience. This advancing integration of both fields creates new opportunities in neuroscience to deepen the understanding of gene expression programs and their regulation that underlies the cellular heterogeneity and physiology of the central nervous system. Currently, transcriptional heterogeneity can be studied in individual neural cell types in health and disease. Furthermore, there is an increasing interest in RNA technologies and their application in neurology. These aspects were discussed at an online conference that was shortly named NeuroRNA.
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7
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Johnson SL, Tsou WL, Prifti MV, Harris AL, Todi SV. A survey of protein interactions and posttranslational modifications that influence the polyglutamine diseases. Front Mol Neurosci 2022; 15:974167. [PMID: 36187346 PMCID: PMC9515312 DOI: 10.3389/fnmol.2022.974167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 01/20/2023] Open
Abstract
The presence and aggregation of misfolded proteins has deleterious effects in the nervous system. Among the various diseases caused by misfolded proteins is the family of the polyglutamine (polyQ) disorders. This family comprises nine members, all stemming from the same mutation—the abnormal elongation of a polyQ repeat in nine different proteins—which causes protein misfolding and aggregation, cellular dysfunction and disease. While it is the same type of mutation that causes them, each disease is distinct: it is influenced by regions and domains that surround the polyQ repeat; by proteins with which they interact; and by posttranslational modifications they receive. Here, we overview the role of non-polyQ regions that control the pathogenicity of the expanded polyQ repeat. We begin by introducing each polyQ disease, the genes affected, and the symptoms experienced by patients. Subsequently, we provide a survey of protein-protein interactions and posttranslational modifications that regulate polyQ toxicity. We conclude by discussing shared processes and pathways that bring some of the polyQ diseases together and may serve as common therapeutic entry points for this family of incurable disorders.
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Affiliation(s)
- Sean L. Johnson
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Matthew V. Prifti
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Autumn L. Harris
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
| | - Sokol V. Todi
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
- Maximizing Access to Research Careers (MARC) Program, Wayne State University, Detroit, MI, United States
- Department of Neurology, Wayne State University, Detroit, MI, United States
- *Correspondence: Sokol V. Todi,
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8
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Liu Y, Li H, Liu X, Wang B, Yang H, Wan B, Sun M, Xu X. Clinical and mechanism advances of neuronal intranuclear inclusion disease. Front Aging Neurosci 2022; 14:934725. [PMID: 36177481 PMCID: PMC9513122 DOI: 10.3389/fnagi.2022.934725] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Due to the high clinical heterogeneity of neuronal intranuclear inclusion disease (NIID), it is easy to misdiagnose this condition and is considered to be a rare progressive neurodegenerative disease. More evidence demonstrates that NIID involves not only the central nervous system but also multiple systems of the body and shows a variety of symptoms, which makes a clinical diagnosis of NIID more difficult. This review summarizes the clinical symptoms in different systems and demonstrates that NIID is a multiple-system intranuclear inclusion disease. In addition, the core triad symptoms in the central nervous system, such as dementia, parkinsonism, and psychiatric symptoms, are proposed as an important clue for the clinical diagnosis of NIID. Recent studies have demonstrated that expanded GGC repeats in the 5′-untranslated region of the NOTCH2NLC gene are the cause of NIID. The genetic advances and possible underlying mechanisms of NIID (expanded GGC repeat-induced DNA damage, RNA toxicity, and polyglycine-NOTCH2NLC protein toxicity) are briefly summarized in this review. Interestingly, inflammatory cell infiltration and inflammation were observed in the affected tissues of patients with NIID. As a downstream pathological process of NIID, inflammation could be a therapeutic target for NIID.
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Affiliation(s)
- Yueqi Liu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Hao Li
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Xuan Liu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bin Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Yang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, China
- Bo Wan,
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Miao Sun,
| | - Xingshun Xu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China
- *Correspondence: Xingshun Xu,
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