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Borbolla-Jiménez FV, Del Prado-Audelo ML, Cisneros B, Caballero-Florán IH, Leyva-Gómez G, Magaña JJ. New Perspectives of Gene Therapy on Polyglutamine Spinocerebellar Ataxias: From Molecular Targets to Novel Nanovectors. Pharmaceutics 2021; 13:1018. [PMID: 34371710 PMCID: PMC8309146 DOI: 10.3390/pharmaceutics13071018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Seven of the most frequent spinocerebellar ataxias (SCAs) are caused by a pathological expansion of a cytosine, adenine and guanine (CAG) trinucleotide repeat located in exonic regions of unrelated genes, which in turn leads to the synthesis of polyglutamine (polyQ) proteins. PolyQ proteins are prone to aggregate and form intracellular inclusions, which alter diverse cellular pathways, including transcriptional regulation, protein clearance, calcium homeostasis and apoptosis, ultimately leading to neurodegeneration. At present, treatment for SCAs is limited to symptomatic intervention, and there is no therapeutic approach to prevent or reverse disease progression. This review provides a compilation of the experimental advances obtained in cell-based and animal models toward the development of gene therapy strategies against polyQ SCAs, providing a discussion of their potential application in clinical trials. In the second part, we describe the promising potential of nanotechnology developments to treat polyQ SCA diseases. We describe, in detail, how the design of nanoparticle (NP) systems with different physicochemical and functionalization characteristics has been approached, in order to determine their ability to evade the immune system response and to enhance brain delivery of molecular tools. In the final part of this review, the imminent application of NP-based strategies in clinical trials for the treatment of polyQ SCA diseases is discussed.
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Affiliation(s)
- Fabiola V. Borbolla-Jiménez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico;
- Programa de Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - María Luisa Del Prado-Audelo
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, 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 (CINVESTAV), Ciudad de México 07360, Mexico;
| | - Isaac H. Caballero-Florán
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
- Departamento de Farmacia, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Ciudad de México 07360, Mexico
| | - Gerardo Leyva-Gómez
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico;
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey Campus Ciudad de México, Ciudad de México 14380, Mexico;
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52
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Epimutations and mutations, nurturing phenotypic diversity. Genetica 2021; 150:171-181. [PMID: 34114171 DOI: 10.1007/s10709-021-00124-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/26/2021] [Indexed: 12/22/2022]
Abstract
Epimutations and mutations are two dissimilar mechanisms that have contributed to the phenotypic diversities in organisms. Though dissimilar, many previous studies have revealed that the consequences of epimutations and mutations are not mutually exclusive. DNA rich in epigenetic modifications can be prone to mutations and vice versa. In order to get a better insight into the molecular evolution in organisms, it is important to consider the information of both genetic and epigenetic changes in their genomes. Understanding the similarities and differences between the consequences of epimutations and mutations is required for a better interpretation of phenotypic diversities in organisms. Factors contributing to epigenetic changes such as paramutations and mutation hotspots and, the correlation of the interdependence of mutations and epigenetic changes in DNA are important aspects that need to be considered for molecular evolutionary studies. Thus, this review explains what epimutations are, their causes, how they are similar/different from mutations, and the influence of epigenetic changes and mutations on each other, further emphasizing how molecular evolution involving both mutations and epimutations can lead to speciation. Considering this approach will aid in reorganizing taxonomic classifications, importantly, solving disparities in species identification.
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Tran Q, Sudasinghe A, Jones B, Xiong K, Cohen RE, Sharlin DS, Hartert KT, Goellner GM. FAM171B is a novel polyglutamine protein widely expressed in the mammalian brain. Brain Res 2021; 1766:147540. [PMID: 34052262 DOI: 10.1016/j.brainres.2021.147540] [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: 10/12/2020] [Revised: 05/14/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
Mutation in proteins containing polyglutamine (polyQ) tracts has been shown to underlie a number of severe human neurodegenerative disorders such as Huntington's Disease and Spinocerebellar Ataxia. In this study, we identify and describe FAM171B as a novel polyQ protein containing fourteen consecutive glutamine residues in its National Center for Biotechnology Information (NCBI) referenced sequence. Utilizing western blotting, in situ hybridization, and immunohistochemistry, we demonstrate that FAM171B is widely expressed in mouse brain with pronounced localization in the hippocampus, cerebellum, and cerebral cortex. Furthermore, immunofluorescence experiments reveal that FAM171B predominantly localizes to vesicle-like structures in the cytoplasm of neurons. Finally, bioinformatic analysis suggests that FAM171B is robustly expressed in human brain, and (similar to other polyQ disease genes) its polyQ tract is polymorphic within the general human population. Thus, as a polyQ protein that is expressed in brain, FAM171B should be considered a candidate gene for an as yet molecularly uncharacterized neurodegenerative disease.
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Affiliation(s)
- Quan Tran
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Ashani Sudasinghe
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Brooke Jones
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Ka Xiong
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Rachel E Cohen
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - David S Sharlin
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Keenan T Hartert
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States
| | - Geoffrey M Goellner
- Department of Biological Sciences, Trafton South 242, Minnesota State University, Mankato, MN 56001, United States.
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54
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Wu Z, Gong H, Zhang M, Tong X, Ai H, Xiao S, Perez-Enciso M, Yang B, Huang L. A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations. Genet Sel Evol 2021; 53:39. [PMID: 33892623 PMCID: PMC8063339 DOI: 10.1186/s12711-021-00631-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00631-4.
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Affiliation(s)
- Zhongzi Wu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingpeng Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xinkai Tong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Miguel Perez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain.,ICREA, Passeig de Lluís Companys 23, Barcelona, Spain
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
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Ajjugal Y, Kolimi N, Rathinavelan T. Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS. Sci Rep 2021; 11:8163. [PMID: 33854084 PMCID: PMC8046799 DOI: 10.1038/s41598-021-87097-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
CGG tandem repeat expansion in the 5'-untranslated region of the fragile X mental retardation-1 (FMR1) gene leads to unusual nucleic acid conformations, hence causing genetic instabilities. We show that the number of G…G (in CGG repeat) or C…C (in CCG repeat) mismatches (other than A…T, T…A, C…G and G…C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The circular dichroism (CD) spectra and electrophoretic mobility shift assay (EMSA) reveal that CGG DNA (sense strand of the FMR1 gene) and its transcript favor a quadruplex structure. CD, EMSA and molecular dynamics (MD) simulations also show that more than four C…C mismatches cannot be accommodated in the RNA duplex consisting of the CCG repeat (antisense transcript); instead, it favors an i-motif conformational intermediate. Such a preference for unusual secondary structures provides a convincing justification for the RNA foci formation due to the sequestration of RNA-binding proteins to the bidirectional transcripts and the repeat-associated non-AUG translation that are observed in FXTAS. The results presented here also suggest that small molecule modulators that can destabilize FMR1 CGG DNA and RNA quadruplex structures could be promising candidates for treating FXTAS.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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57
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Lai Y, Beaver JM, Laverde E, Liu Y. Trinucleotide repeat instability via DNA base excision repair. DNA Repair (Amst) 2021; 93:102912. [PMID: 33087278 DOI: 10.1016/j.dnarep.2020.102912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Trinucleotide repeat (TNR) instability is the cause of over 40 human neurodegenerative diseases and certain types of cancer. TNR instability can result from DNA replication, repair, recombination, and gene transcription. Emerging evidence indicates that DNA base damage and base excision repair (BER) play an active role in regulating somatic TNR instability. These processes may potentially modulate the onset and progression of TNR-related diseases, given that TNRs are hotspots of DNA base damage that are present in mammalian cells with a high frequency. In this review, we discuss the recent advances in our understanding of the molecular mechanisms underlying BER-mediated TNR instability. We initially discuss the roles of the BER pathway and locations of DNA base lesions in TNRs and their interplay with non-B form DNA structures in governing repeat instability. We then discuss how the coordinated activities of BER enzymes can modulate a balance between the removal and addition of TNRs to regulate somatic TNR instability. We further discuss how this balance can be disrupted by the crosstalk between BER and DNA mismatch repair (MMR) machinery resulting in TNR expansion. Finally, we suggest future directions regarding BER-mediated somatic TNR instability and its association with TNR disease prevention and treatment.
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Affiliation(s)
- Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States; Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States
| | - Jill M Beaver
- Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States
| | - Eduardo Laverde
- Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States; Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States; Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, United States.
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58
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Khampang S, Parnpai R, Mahikul W, Easley CA, Cho IK, Chan AWS. CAG repeat instability in embryonic stem cells and derivative spermatogenic cells of transgenic Huntington's disease monkey. J Assist Reprod Genet 2021; 38:1215-1229. [PMID: 33611676 DOI: 10.1007/s10815-021-02106-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The expansion of CAG (glutamine; Q) trinucleotide repeats (TNRs) predominantly occurs through male lineage in Huntington's disease (HD). As a result, offspring will have larger CAG repeats compared to their fathers, which causes an earlier onset of the disease called genetic anticipation. This study aims to develop a novel in vitro model to replicate CAG repeat instability in early spermatogenesis and demonstrate the biological process of genetic anticipation by using the HD stem cell model for the first time. METHODS HD rhesus monkey embryonic stem cells (rESCs) were cultured in vitro for an extended period. Male rESCs were used to derive spermatogenic cells in vitro with a 10-day differentiation. The assessment of CAG repeat instability was performed by GeneScan and curve fit analysis. RESULTS Spermatogenic cells derived from rESCs exhibit progressive expansion of CAG repeats with high daily expansion rates compared to the extended culture of rESCs. The expansion of CAG repeats is cell type-specific and size-dependent. CONCLUSIONS Here, we report a novel stem cell model that replicates genome instability and CAG repeat expansion in in vitro derived HD monkey spermatogenic cells. The in vitro spermatogenic cell model opens a new opportunity for studying TNR instability and the underlying mechanism of genetic anticipation, not only in HD but also in other TNR diseases.
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Affiliation(s)
- Sujittra Khampang
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA.,Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Rangsun Parnpai
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wiriya Mahikul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Charles A Easley
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA.,Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - In Ki Cho
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
| | - Anthony W S Chan
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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Crosstalk between Different DNA Repair Pathways Contributes to Neurodegenerative Diseases. BIOLOGY 2021; 10:biology10020163. [PMID: 33669593 PMCID: PMC7922961 DOI: 10.3390/biology10020163] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary Constant exposure to endogenous and environmental factors induces oxidative stress and DNA damage. Rare brain disorders caused by defects in DNA repair and DNA damage response (DDR) signaling establish that failure to process DNA damage may lead to neurodegeneration. In this review, we present mechanisms that link DDR with neurodegeneration in these disorders and discuss their relevance for common age-related neurodegenerative diseases (NDDs). Moreover, we highlight recent insight into the crosstalk between the DDR and other cellular processes known to be disturbed during NDDs. Abstract Genomic integrity is maintained by DNA repair and the DNA damage response (DDR). Defects in certain DNA repair genes give rise to many rare progressive neurodegenerative diseases (NDDs), such as ocular motor ataxia, Huntington disease (HD), and spinocerebellar ataxias (SCA). Dysregulation or dysfunction of DDR is also proposed to contribute to more common NDDs, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Amyotrophic Lateral Sclerosis (ALS). Here, we present mechanisms that link DDR with neurodegeneration in rare NDDs caused by defects in the DDR and discuss the relevance for more common age-related neurodegenerative diseases. Moreover, we highlight recent insight into the crosstalk between the DDR and other cellular processes known to be disturbed during NDDs. We compare the strengths and limitations of established model systems to model human NDDs, ranging from C. elegans and mouse models towards advanced stem cell-based 3D models.
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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Mitsuhashi S, Frith MC, Matsumoto N. Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population. BMC Med Genomics 2021; 14:17. [PMID: 33413375 PMCID: PMC7791882 DOI: 10.1186/s12920-020-00853-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. It is difficult to predict which tandem repeats may cause a disease. One hypothesis is that changeable tandem repeats are the source of genetic diseases, because disease-causing repeats are polymorphic in healthy individuals. However, it is not clear whether disease-causing repeats are more polymorphic than other repeats. METHODS We performed a genome-wide survey of the millions of human tandem repeats using publicly available long read genome sequencing data from 21 humans. We measured tandem repeat copy number changes using tandem-genotypes. Length variation of known disease-associated repeats was compared to other repeat loci. RESULTS We found that known Mendelian disease-causing or disease-associated repeats, especially CAG and 5'UTR GGC repeats, are relatively long and polymorphic in the general population. We also show that repeat lengths of two disease-causing tandem repeats, in ATXN3 and GLS, are correlated with near-by GWAS SNP genotypes. CONCLUSIONS We provide a catalog of polymorphic tandem repeats across a variety of repeat unit lengths and sequences, from long read sequencing data. This method especially if used in genome wide association study, may indicate possible new candidates of pathogenic or biologically important tandem repeats in human genomes.
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Affiliation(s)
- Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, M&D Tower 24F, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
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Xu TT, Li YJ, Afshari NA, Aleff RA, Rinkoski TA, Patel SV, Maguire LJ, Edwards AO, Brown WL, Fautsch MP, Wieben ED, Baratz KH. Disease Expression and Familial Transmission of Fuchs Endothelial Corneal Dystrophy With and Without CTG18.1 Expansion. Invest Ophthalmol Vis Sci 2021; 62:17. [PMID: 33444430 PMCID: PMC7814354 DOI: 10.1167/iovs.62.1.17] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose To characterize inheritance, penetrance, and trinucleotide repeat expansion stability in Fuchs endothelial corneal dystrophy (FECD). Methods One thousand unrelated and related subjects with and without FECD were prospectively recruited. CTG18.1 repeat length (CTG18.1L) was determined via short tandem repeat assay and Southern blotting of leukocyte DNA. Multivariable logistic regression and generalized estimating equation models were employed. Results There were 546 unrelated FECD cases (67.6% female; 70 ± 10 years) and 235 controls (63.8% female; 73 ± 8 years; all ≥ 50 years). CTG18.1 expansion (CTG18.1exp+) was observed in 424 (77.7%) cases and 18 (7.7%) controls (P = 2.48 × 10-44). CTG18.1 expansion was associated with FECD severity (P = 5.62 × 10-7). The family arm of the study included 331 members from 112 FECD-affected families; 87 families were CTG18.1exp+. Autosomal dominant inheritance with variable expression of FECD was observed, regardless of expansion status. FECD penetrance of CTG18.1 expansion increased with age, ranging from 44.4% in the youngest (19-46 years) to 86.2% in the oldest (64-91 years) age quartiles. Among 62 parent-offspring transmissions of CTG18.1exp+, 48 (77.4%) had a change in CTG18.1L ≤ 10 repeats, and eight (12.9%) were ≥50 repeats, including five large expansions (∼1000-2000 repeats) that contracted. Among 44 offspring who did not inherit the CTG18.1exp+ allele, eight (18.2%) exhibited FECD. Conclusions CTG18.1 expansion was highly associated with FECD but demonstrated incomplete penetrance. CTG18.1L instability occurred in a minority of parent-offspring transmissions, with large expansions exhibiting contraction. The observation of FECD without CTG18.1 expansion among family members in CTG18.1exp+ families highlights the complexity of the relationship between the FECD phenotype and CTG18.1 expansion.
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Affiliation(s)
- Timothy T. Xu
- Alix School of Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States
| | - Natalie A. Afshari
- Shiley Eye Institute, University of California, San Diego, La Jolla, California, United States
| | - Ross A. Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Tommy A. Rinkoski
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Sanjay V. Patel
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Leo J. Maguire
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Albert O. Edwards
- Oregon Retina Division, Sterling Vision, Eugene, Oregon, United States
- Casey Eye Institute, Oregon Health Sciences University, Portland, Oregon, United States
| | - William L. Brown
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Michael P. Fautsch
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Eric D. Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Keith H. Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
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Pal A, Greenblatt HM, Levy Y. Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6. Biochemistry 2020; 59:4822-4832. [PMID: 33319999 PMCID: PMC7872316 DOI: 10.1021/acs.biochem.0c00669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA
mismatch repair (MMR) is an important postreplication process
that eliminates mispaired or unpaired nucleotides to ensure genomic
replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two
mismatch repair initiation factors that recognize DNA lesions. While
X-ray crystal structures exist for these proteins in complex with
DNA lesions, little is known about their structures during the initial
search along nonspecific double-stranded DNA, because they are short-lived
and difficult to determine experimentally. In this study, various
computational approaches were used to sidestep these difficulties.
All-atom and coarse-grained simulations based on the crystal structures
of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting
that the initial search conformation differs from the lesion-bound
crystal structure. We modeled probable search-mode structures of MSH
proteins and showed, using coarse-grained molecular dynamics simulations,
that they can perform rotation-coupled diffusion on DNA, which is
a suitable and efficient search mechanism for their function and one
predicted earlier by fluorescence resonance energy transfer and fluorescence
microscopy studies. This search mechanism is implemented by electrostatic
interactions among the mismatch-binding domain (MBD), the clamp domains,
and the DNA backbone. During simulations, their diffusion rate did
not change significantly with an increasing salt concentration, which
is consistent with observations from experimental studies. When the
gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused
mostly via the clamp domains while Msh2-Msh6 still diffused using
the MBD, reproducing the experimentally measured lower diffusion coefficient
of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating
from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex.
This is consistent with the experimental observation that Msh2-Msh3,
unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our
models provide a molecular picture of the different mismatch search
mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity
of their structures.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Nakayama Y, Adachi K, Shioda N, Maeta S, Nanba E, Kugoh H. Establishment of FXS-A9 panel with a single human X chromosome from fragile X syndrome-associated individual. Exp Cell Res 2020; 398:112419. [PMID: 33296661 DOI: 10.1016/j.yexcr.2020.112419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
Fragile X syndrome (FXS) is the most common inheritable form of intellectual disability. FMR1, the gene responsible for FXS, is located on human chromosome Xq27.3 and contains a stretch of CGG trinucleotide repeats in its 5' untranslated region. FXS is caused by CGG repeats that expand beyond 200, resulting in FMR1 silencing via promoter hypermethylation. The molecular mechanism underlying CGG repeat expansion, a fundamental cause of FXS, remains poorly understood, partly due to a lack of experimental systems. Accumulated evidence indicates that the large chromosomal region flanking a CGG repeat is critical for repeat dynamics. In the present study, we isolated and introduced whole human X chromosomes from healthy, FXS premutation carriers, or FXS patients who carried disease condition-associated CGG repeat lengths, into mouse A9 cells via microcell-mediated chromosome transfer. The CGG repeat length-associated methylation status and human FMR1 expression in these monochromosomal hybrid cells mimicked those in humans. Thus, this set of A9 cells containing CGG repeats from three different origins (FXS-A9 panel) may provide a valuable resource for investigating a series of genetic and epigenetic CGG repeat dynamics during FXS pathogenesis.
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Affiliation(s)
- Yuji Nakayama
- Division of Radioisotope Science, Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Kaori Adachi
- Division of Genomic Science, Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Nofirifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Shoya Maeta
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Eiji Nanba
- Office for Research Strategy, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Hiroyuki Kugoh
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan; Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
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65
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Schwartz JL, Jones KL, Yeo GW. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies. Crit Rev Biochem Mol Biol 2020; 56:31-53. [PMID: 33172304 PMCID: PMC8192115 DOI: 10.1080/10409238.2020.1841726] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG50–3,500 in DMPK; DM2, CCTG75–11,000 in ZNF9), fragile X tremor ataxia syndrome (FXTAS, CGG50–200 in FMR1), spinal bulbar muscular atrophy (SBMA, CAG40–55 in AR), Huntington’s disease (HD, CAG36–121 in HTT), C9ORF72-amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD and C9-ALS/FTD, GGGGCC in C9ORF72), and many others, like ataxias. Recent research has highlighted several mechanisms that may contribute to pathology in this heterogeneous class of neurological MRE disorders – bidirectional transcription, intranuclear RNA foci, and repeat associated non-AUG (RAN) translation – which are the subject of this review. Additionally, many MRE disorders share similar underlying molecular pathologies that have been recently targeted in experimental and preclinical contexts. We discuss the therapeutic potential of versatile therapeutic strategies that may selectively target disrupted RNA-based processes and may be readily adaptable for the treatment of multiple MRE disorders. Collectively, the strategies under consideration for treatment of multiple MRE disorders include reducing levels of toxic RNA, preventing RNA foci formation, and eliminating the downstream cellular toxicity associated with peptide repeats produced by RAN translation. While treatments are still lacking for the majority of MRE disorders, several promising therapeutic strategies have emerged and will be evaluated within this review.
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Affiliation(s)
- Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten Leigh Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
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66
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Zhang J, Fakharzadeh A, Pan F, Roland C, Sagui C. Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids. Nucleic Acids Res 2020; 48:9899-9917. [PMID: 32821947 PMCID: PMC7515735 DOI: 10.1093/nar/gkaa665] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 11/13/2022] Open
Abstract
Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich's ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA strand bonds with the hybrid duplex (collapsed R-loops, where the two DNA strands remain antiparallel). For both Y·R:Y and R·R:Y DNA triplexes, the parallel third strand orientation is more stable; both parallel and antiparallel protonated d(GA+A)·d(GAA):d(TTC) triplexes are stable. Apparent contradictions in the literature about the R·R:Y triplex stability is probably due to lack of molecular resolution, since shifting the third strand by a single nucleotide alters the stability ranking. In the collapsed R-loops, antiparallel d(TTC+)·d(GAA):r(UUC) is unstable, while parallel d(GAA)·r(GAA):d(TTC) and d(GA+A)·r(GAA):d(TTC) are stable. In addition to providing new structural perspectives for specific therapeutic aims, our results contribute to a systematic structural basis for the emerging field of quantitative R-loop biology.
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Affiliation(s)
- Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA.,Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2020; 117:27493-27501. [PMID: 33077593 DOI: 10.1073/pnas.2004111117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochromatic domains are complex structures composed of nucleosome arrays that are bound by silencing factors. This composition raises the possibility that certain configurations of nucleosome arrays facilitate heterochromatic silencing. We tested this possibility in Saccharomyces cerevisiae by systematically altering the distance between heterochromatic nucleosome-depleted regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, serial deletions that altered the distance between heterochromatic NDRs revealed a striking oscillatory relationship between inter-NDR distance and defects in nucleosome positioning. Furthermore, conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit epigenetic transcriptional states. These findings strongly suggest that nucleosome positioning can contribute to formation and maintenance of functional heterochromatin and point to previously unappreciated roles of NDR positioning within heterochromatic domains.
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68
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Hayward BE, Steinbach PJ, Usdin K. A point mutation in the nuclease domain of MLH3 eliminates repeat expansions in a mouse stem cell model of the Fragile X-related disorders. Nucleic Acids Res 2020; 48:7856-7863. [PMID: 32619224 DOI: 10.1093/nar/gkaa573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
The Fragile X-related disorders (FXDs) are Repeat Expansion Diseases, genetic disorders that result from the expansion of a disease-specific microsatellite. In those Repeat Expansion Disease models where it has been examined, expansion is dependent on functional mismatch repair (MMR) factors, including MutLγ, a heterodimer of MLH1/MLH3, one of the three MutL complexes found in mammals and a minor player in MMR. In contrast, MutLα, a much more abundant MutL complex that is the major contributor to MMR, is either not required for expansion or plays a limited role in expansion in many model systems. How MutLγ acts to generate expansions is unclear given its normal role in protecting against microsatellite instability and while MLH3 does have an associated endonuclease activity, whether that contributes to repeat expansion is uncertain. We show here, using a gene-editing approach, that a point mutation that eliminates the endonuclease activity of MLH3 eliminates expansions in an FXD mouse embryonic stem cell model. This restricts the number of possible models for repeat expansion and supports the idea that MutLγ may be a useful druggable target to reduce somatic expansion in those disorders where it contributes to disease pathology.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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69
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Guo P, Lam SL. Minidumbbell structures formed by ATTCT pentanucleotide repeats in spinocerebellar ataxia type 10. Nucleic Acids Res 2020; 48:7557-7568. [PMID: 32520333 PMCID: PMC7367182 DOI: 10.1093/nar/gkaa495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/02/2023] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is a progressive genetic disorder caused by ATTCT pentanucleotide repeat expansions in intron 9 of the ATXN10 gene. ATTCT repeats have been reported to form unwound secondary structures which are likely linked to large-scale repeat expansions. In this study, we performed high-resolution nuclear magnetic resonance spectroscopic investigations on DNA sequences containing two to five ATTCT repeats. Strikingly, we found the first two repeats of all these sequences well folded into highly compact minidumbbell (MDB) structures. The 3D solution structure of the sequence containing two ATTCT repeats was successfully determined, revealing the MDB comprises a regular TTCTA and a quasi TTCT/A pentaloops with extensive stabilizing loop-loop interactions. We further carried out in vitro primer extension assays to examine if the MDB formed in the primer could escape from the proofreading function of DNA polymerase. Results showed that when the MDB was formed at 5-bp or farther away from the priming site, it was able to escape from the proofreading by Klenow fragment of DNA polymerase I and thus retained in the primer. The intriguing structural findings bring about new insights into the origin of genetic instability in SCA10.
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Affiliation(s)
- Pei Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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70
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Truta B, Wohler E, Sobreira N, Datta LW, Brant SR. Role of telomere shortening in anticipation of inflammatory bowel disease. World J Gastrointest Pharmacol Ther 2020; 11:69-78. [PMID: 32953227 PMCID: PMC7475772 DOI: 10.4292/wjgpt.v11.i4.69] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/25/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The existence of genetic anticipation has been long disputed in inflammatory bowel disease (IBD) in the absence of the explanatory mechanism.
AIM To determine whether it was predictive of genetic anticipation, we evaluated telomere length in IBD. We hypothesized that multiplex IBD families exhibit a genetic defect impacting telomere maintenance mechanisms.
METHODS We studied three IBD families with multiple affected members in three successive generations. We determined telomere length (TL) in lymphocytes and granulocytes from peripheral blood of the affected members using flow cytometry and fluorescence in-situ hybridization (flow FISH). We also performed whole exome sequencing in the blood of all available family members and used PhenoDB to identify potential candidate gene variants with recessive or dominant modes of inheritance.
RESULTS Out of twenty-four patients of European descent selected to participate in the study, eleven patients, eight parent-child pairs affected by IBD, were included in the genetic anticipation analysis. Median difference in age at diagnosis between two successive generations was 16.5 years, with earlier age at onset in the younger generations. In most of the affected members, the disease harbored similar gastrointestinal and extraintestinal involvement but was more aggressive among the younger generations. TL was not associated with earlier age at onset or more severe disease in members of successive generations affected by IBD. NOD2 gene mutations were present in the Crohn’s disease patients of one family. However, no gene variants were identified as potential candidates for inheritance.
CONCLUSION Telomere shortening appears unlikely to be involved in mechanisms of possible genetic anticipation in IBD. Further studies using a larger sample size are required to confirm or refute our findings.
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Affiliation(s)
- Brindusa Truta
- Steven R Brant, Division of Gastroenterology & Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD 21210, United States
| | - Elizabeth Wohler
- McKusick-Nathan Institute of Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Nara Sobreira
- McKusick-Nathan Institute of Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Lisa W. Datta
- Steven R Brant, Division of Gastroenterology & Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD 21210, United States
| | - Steven R. Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers-Robert Wood Johnson Medical School, NJ, 08901, United States
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71
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Damasceno JD, Marques CA, Beraldi D, Crouch K, Lapsley C, Obonaga R, Tosi LR, McCulloch R. Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife 2020; 9:58030. [PMID: 32897188 PMCID: PMC7511235 DOI: 10.7554/elife.58030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
DNA replication is needed to duplicate a cell’s genome in S phase and segregate it during cell division. Previous work in Leishmania detected DNA replication initiation at just a single region in each chromosome, an organisation predicted to be insufficient for complete genome duplication within S phase. Here, we show that acetylated histone H3 (AcH3), base J and a kinetochore factor co-localise in each chromosome at only a single locus, which corresponds with previously mapped DNA replication initiation regions and is demarcated by localised G/T skew and G4 patterns. In addition, we describe previously undetected subtelomeric DNA replication in G2/M and G1-phase-enriched cells. Finally, we show that subtelomeric DNA replication, unlike chromosome-internal DNA replication, is sensitive to hydroxyurea and dependent on 9-1-1 activity. These findings indicate that Leishmania’s genome duplication programme employs subtelomeric DNA replication initiation, possibly extending beyond S phase, to support predominantly chromosome-internal DNA replication initiation within S phase.
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Affiliation(s)
- Jeziel Dener Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Dario Beraldi
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Ricardo Obonaga
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ro Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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Laverde EE, Lai Y, Leng F, Balakrishnan L, Freudenreich CH, Liu Y. R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities. J Biol Chem 2020; 295:13902-13913. [PMID: 32763971 DOI: 10.1074/jbc.ra120.014161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/04/2020] [Indexed: 12/27/2022] Open
Abstract
Trinucleotide repeat (TNR) expansion and deletion are responsible for over 40 neurodegenerative diseases and associated with cancer. TNRs can undergo somatic instability that is mediated by DNA damage and repair and gene transcription. Recent studies have pointed toward a role for R-loops in causing TNR expansion and deletion, and it has been shown that base excision repair (BER) can result in CAG repeat deletion from R-loops in yeast. However, it remains unknown how BER in R-loops can mediate TNR instability. In this study, using biochemical approaches, we examined BER enzymatic activities and their influence on TNR R-loops. We found that AP endonuclease 1 incised an abasic site on the nontemplate strand of a TNR R-loop, creating a double-flap intermediate containing an RNA:DNA hybrid that subsequently inhibited polymerase β (pol β) synthesis of TNRs. This stimulated flap endonuclease 1 (FEN1) cleavage of TNRs engaged in an R-loop. Moreover, we showed that FEN1 also efficiently cleaved the RNA strand, facilitating pol β loop/hairpin bypass synthesis and the resolution of TNR R-loops through BER. Consequently, this resulted in fewer TNRs synthesized by pol β than those removed by FEN1, thereby leading to repeat deletion. Our results indicate that TNR R-loops preferentially lead to repeat deletion during BER by disrupting the balance between the addition and removal of TNRs. Our discoveries open a new avenue for the treatment and prevention of repeat expansion diseases and cancer.
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Affiliation(s)
- Eduardo E Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Fenfei Leng
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana Purdue University Indianapolis, Indianapolis, Indiana, USA
| | | | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, Florida, USA; Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA.
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Fautsch MP, Wieben ED, Baratz KH, Bhattacharyya N, Sadan AN, Hafford-Tear NJ, Tuft SJ, Davidson AE. TCF4-mediated Fuchs endothelial corneal dystrophy: Insights into a common trinucleotide repeat-associated disease. Prog Retin Eye Res 2020; 81:100883. [PMID: 32735996 PMCID: PMC7988464 DOI: 10.1016/j.preteyeres.2020.100883] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 (TCF4) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field. FECD is a common, age-related corneal dystrophy. The majority of cases are associated with expansion of a CTG repeat (CTG18.1). FECD is the most common trinucleotide repeat expansion disease in humans. Evidence supports multiple molecular mechanisms underlying the pathophysiology. Novel CTG18.1-targeted therapeutics are in development.
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Affiliation(s)
- Michael P Fautsch
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, 200 1st St SW, Mayo Clinic, Rochester, MN, USA.
| | - Keith H Baratz
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Amanda N Sadan
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| | | | - Stephen J Tuft
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
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74
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Clever F, Cho IK, Yang J, Chan AWS. Progressive Polyglutamine Repeat Expansion in Peripheral Blood Cells and Sperm of Transgenic Huntington's Disease Monkeys. J Huntingtons Dis 2020; 8:443-448. [PMID: 31561381 PMCID: PMC6839466 DOI: 10.3233/jhd-190359] [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] [Indexed: 12/22/2022]
Abstract
The expanded CAG repeat results in somatic mosaicism and genetic anticipation in Huntington’s disease (HD). Here we report a longitudinal study examining CAG repeat instability in lymphocytes and sperm of three HD monkeys throughout their whole life-span that encompass the prodromal to symptomatic stages of HD. We demonstrate a progressive increase in CAG repeat length in lymphocytes and sperm as the animals aged. We also examined the impact of CAG repeat length on expansion rate, which showed a clear linear correlation up to 62Q, and high instability after. Our findings stress the importance of further investigation in CAG instability in peripheral blood cells longitudinally.
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Affiliation(s)
- Faye Clever
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - In Ki Cho
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jingjing Yang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anthony W S Chan
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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75
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Drake VE, Gelbard A, Sobriera N, Wohler E, Berry LL, Hussain LL, Hillel A. Familial Aggregation in Idiopathic Subglottic Stenosis. Otolaryngol Head Neck Surg 2020; 163:1011-1017. [PMID: 32600122 DOI: 10.1177/0194599820935402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To evaluate inheritance patterns and define the familial clustering rate of idiopathic subglottic stenosis (iSGS). STUDY DESIGN Retrospective observational study. SETTING International multicenter collaborative of >30 tertiary care centers. METHODS Patients with a clinically confirmed iSGS diagnosis within the North American Airway Collaborative's iSGS1000 cohort consented between 2014 and 2018 were eligible for enrollment. Patient demographics and disease severity were abstracted from the collaborative's iSGS longitudinal registry. Pedigrees of affected families were created. RESULTS A total of 810 patients with iSGS were identified. Positive family history for iSGS was reported in 44 patients in 20 families. The rate of familial clustering in iSGS is 2.5%. Mean age of disease onset is 42.6 years. Of the 44 patients with familial aggregation of iSGS, 42 were female and 2 were male; 13 were mother-daughter pairs and 2 were father-daughter pairs. There were 3 sister-sister pairs. There was 1 niece-aunt pair and 2 groups of 3 family members. One pedigree demonstrated 2 affected mother-daughter pairs, with the mothers being first-degree paternal cousins. Inheritance is non-Mendelian, and anticipation is present in 11 of 13 (84%) parent-offspring pairs. The mean age of onset between parents (48.4 years) and offspring (36.1 years) was significantly different (P = .016). CONCLUSION This study quantifies the rate of familial clustering of iSGS at 2.5%. Inheritance is non-Mendelian, and disease demonstrates anticipation. These data suggest that there may be a genetic contribution in iSGS.
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Affiliation(s)
- Virginia E Drake
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alexander Gelbard
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nara Sobriera
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elizabeth Wohler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lynne L Berry
- Vanderbilt Center for Quantitative Sciences, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Lena L Hussain
- Vanderbilt Center for Quantitative Sciences, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Alexander Hillel
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, USA
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76
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Jakubosky D, Smith EN, D'Antonio M, Jan Bonder M, Young Greenwald WW, D'Antonio-Chronowska A, Matsui H, Stegle O, Montgomery SB, DeBoever C, Frazer KA. Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats. Nat Commun 2020; 11:2928. [PMID: 32522985 PMCID: PMC7287045 DOI: 10.1038/s41467-020-16481-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assemble a set of 719 deep whole genome sequencing (WGS) samples (mean 42×) from 477 distinct individuals which we use to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We use 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and develop a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.
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Affiliation(s)
- David Jakubosky
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093-0419, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA
| | - Erin N Smith
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | | | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Christopher DeBoever
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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77
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Mier P, Andrade-Navarro MA. The features of polyglutamine regions depend on their evolutionary stability. BMC Evol Biol 2020; 20:59. [PMID: 32448113 PMCID: PMC7247214 DOI: 10.1186/s12862-020-01626-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Polyglutamine regions (polyQ) are one of the most studied and prevalent homorepeats in eukaryotes. They have a particular length-dependent codon usage, which relates to a characteristic CAG-slippage mechanism. Pathologically expanded tracts of polyQ are known to form aggregates and are involved in the development of several human neurodegenerative diseases. The non-pathogenic function of polyQ is to mediate protein-protein interactions via a coiled-coil pairing with an interactor. They are usually located in a helical context. Results Here we study the stability of polyQ regions in evolution, using a set of 60 proteomes from four distinct taxonomic groups (Insecta, Teleostei, Sauria and Mammalia). The polyQ regions can be distinctly grouped in three categories based on their evolutionary stability: stable, unstable by length variation (inserted), and unstable by mutations (mutated). PolyQ regions in these categories can be significantly distinguished by their glutamine codon usage, and we show that the CAG-slippage mechanism is predominant in inserted polyQ of Sauria and Mammalia. The polyQ amino acid context is also influenced by the polyQ stability, with a higher proportion of proline residues around inserted polyQ. By studying the secondary structure of the sequences surrounding polyQ regions, we found that regarding the structural conformation around a polyQ, its stability category is more relevant than its taxonomic information. The protein-protein interaction capacity of a polyQ is also affected by its stability, as stable polyQ have more interactors than unstable polyQ. Conclusions Our results show that apart from the sequence of a polyQ, information about its orthologous sequences is needed to assess its function. Codon usage, amino acid context, structural conformation and the protein-protein interaction capacity of polyQ from all studied taxa critically depend on the region stability. There are however some taxa-specific polyQ features that override this importance. We conclude that a taxa-driven evolutionary analysis is of the highest importance for the comprehensive study of any feature of polyglutamine regions.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
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78
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Xu P, Pan F, Roland C, Sagui C, Weninger K. Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts. Nucleic Acids Res 2020; 48:2232-2245. [PMID: 31974547 PMCID: PMC7049705 DOI: 10.1093/nar/gkaa036] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/11/2019] [Accepted: 01/15/2020] [Indexed: 01/08/2023] Open
Abstract
DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetraloops, compared with alternative 5′-CAG-3′ triloops. To accommodate the tetraloop, even(odd)-numbered repeats have an even(odd) number of hanging bases in the hairpin stem. In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n = even, but such situation cannot occur in (CAG)n = odd, where the hairpin is “frustrated’’ and slips back and forth between states with one TR hanging at the 5′ or 3′ end. Trinucleotide interrupts in the repeating CAG pattern associated with altered disease phenotypes select for specific conformers with favorable loop sequences. Molecular dynamics provide atomic-level insight into the loop configurations. Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins.
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Affiliation(s)
- Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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79
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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80
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Deficiency in classical nonhomologous end-joining-mediated repair of transcribed genes is linked to SCA3 pathogenesis. Proc Natl Acad Sci U S A 2020; 117:8154-8165. [PMID: 32205441 DOI: 10.1073/pnas.1917280117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a dominantly inherited neurodegenerative disease caused by CAG (encoding glutamine) repeat expansion in the Ataxin-3 (ATXN3) gene. We have shown previously that ATXN3-depleted or pathogenic ATXN3-expressing cells abrogate polynucleotide kinase 3'-phosphatase (PNKP) activity. Here, we report that ATXN3 associates with RNA polymerase II (RNAP II) and the classical nonhomologous end-joining (C-NHEJ) proteins, including PNKP, along with nascent RNAs under physiological conditions. Notably, ATXN3 depletion significantly decreased global transcription, repair of transcribed genes, and error-free double-strand break repair of a 3'-phosphate-containing terminally gapped, linearized reporter plasmid. The missing sequence at the terminal break site was restored in the recircularized plasmid in control cells by using the endogenous homologous transcript as a template, indicating ATXN3's role in PNKP-mediated error-free C-NHEJ. Furthermore, brain extracts from SCA3 patients and mice show significantly lower PNKP activity, elevated p53BP1 level, more abundant strand-breaks in the transcribed genes, and degradation of RNAP II relative to controls. A similar RNAP II degradation is also evident in mutant ATXN3-expressing Drosophila larval brains and eyes. Importantly, SCA3 phenotype in Drosophila was completely amenable to PNKP complementation. Hence, salvaging PNKP's activity can be a promising therapeutic strategy for SCA3.
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81
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Lai Y, Lei R, Ren Y, Liu Y. Methods to Study Trinucleotide Repeat Instability Induced by DNA Damage and Repair. Methods Mol Biol 2020; 1999:87-101. [PMID: 31127571 DOI: 10.1007/978-1-4939-9500-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Trinucleotide repeat (TNR) instability (expansion and deletion) is associated with more than 42 human neurodegenerative diseases and cancer and mediated by DNA replication, repair, recombination, and gene transcription. Somatic TNR instability is involved in the progression of TNR expansion diseases and can be modulated by DNA damage repair and gene transcription. Recent studies from our group and others have shown that DNA base damage and its repair play an active role in modulating TNR instability and are responsible for somatic age-dependent CAG repeat expansion in neurons of Huntington's disease mice induced by oxidative DNA damage. However, it remains to be elucidated how DNA damage, non-B form DNA structures, and DNA repair enzymes and cofactors can coordinate to regulate somatic TNR instability. Understanding the molecular mechanisms underlying DNA damage and repair-mediated somatic TNR instability is critically important for identification of new therapeutic targets for treatment and prevention of TNR-related diseases. Here we describe the methods to study the locations and distribution of DNA base lesions and their effects on TNR instability through DNA base excision repair in in vitro reconstituted human systems.
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Affiliation(s)
- Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Ruipeng Lei
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yaou Ren
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA. .,Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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82
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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83
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [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] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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84
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Polleys EJ, Freudenreich CH. Genetic Assays to Study Repeat Fragility in Saccharomyces cerevisiae. Methods Mol Biol 2020; 2056:83-101. [PMID: 31586342 DOI: 10.1007/978-1-4939-9784-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Trinucleotide repeats are common in the human genome and can undergo changes in repeat number and cause length-dependent chromosome fragility. Expanded CAG repeats have been linked to over 14 human diseases and are considered hotspots for breakage and genomic rearrangement. Here we describe two Saccharomyces cerevisiae based assays that evaluate the rate of chromosome breakage that occurs within a repeat tract (fragility), with variations that allow the role of transcription to be evaluated. The first fragility assay utilizes end-loss and subsequent telomere addition as the main mode of repair of a yeast artificial chromosome (YAC). The second fragility assay relies on the fact that a chromosomal break stimulates recombination-mediated repair. A PCR-based assay can be used to evaluate instability of the repeat in the same conditions used to measure repeat fragility. These assays have contributed to understanding the genetic mechanisms that cause chromosome breaks and tract-length changes at unstable trinucleotide repeats.
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85
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Lu Y, Dohno C, Nakatani K. A novel naphthyridine tetramer that recognizes tandem G–G mismatches by the formation of an interhelical complex. Chem Commun (Camb) 2020; 56:754-757. [DOI: 10.1039/c9cc08111a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel naphthyridine tetramer, p-NCTB, was reported to bind two distal CGGG/CGGG via noncovalent binding forming inter- and intrastrand complexes.
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Affiliation(s)
- Yihuan Lu
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - Chikara Dohno
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - Kazuhiko Nakatani
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
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86
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Abstract
Trinucleotide repeats are a peculiar class of microsatellites involved in many neurological as well as developmental disorders. Their propensity to generate very large expansions over time is supposedly due to their capacity to form specific secondary structures, such as imperfect hairpins, triple helices, or G-quadruplexes. These unusual structures were proposed to trigger expansions in vivo. Here, I review known technical issues linked to these structures, such as slippage during polymerase chain reaction and aberrant migration of long trinucleotide repeats during agarose gel electrophoresis. Our current understanding of interactions between trinucleotide repeat secondary structures and the mismatch-repair machinery is also quickly reviewed, and critical questions relevant to these interactions are addressed.
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Affiliation(s)
- Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS UMR3525, Paris, France.
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87
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88
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Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism. PLoS Genet 2019; 15:e1008494. [PMID: 31815930 PMCID: PMC6922473 DOI: 10.1371/journal.pgen.1008494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/19/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Faithful replication and repair of DNA lesions ensure genome maintenance. During replication in eukaryotic cells, DNA is unwound by the CMG helicase complex, which is composed of three major components: the Cdc45 protein, Mcm2-7, and the GINS complex. The CMG in complex with DNA polymerase epsilon (CMG-E) participates in the establishment and progression of the replisome. Impaired functioning of the CMG-E was shown to induce genomic instability and promote the development of various diseases. Therefore, CMG-E components play important roles as caretakers of the genome. In Saccharomyces cerevisiae, the GINS complex is composed of the Psf1, Psf2, Psf3, and Sld5 essential subunits. The Psf1-1 mutant form fails to interact with Psf3, resulting in impaired replisome assembly and chromosome replication. Here, we show increased instability of repeat tracts (mononucleotide, dinucleotide, trinucleotide and longer) in yeast psf1-1 mutants. To identify the mechanisms underlying this effect, we analyzed repeated sequence instability using derivatives of psf1-1 strains lacking genes involved in translesion synthesis, recombination, or mismatch repair. Among these derivatives, deletion of RAD52, RAD51, MMS2, POL32, or PIF1 significantly decreased DNA repeat instability. These results, together with the observed increased amounts of single-stranded DNA regions and Rfa1 foci suggest that recombinational mechanisms make important contributions to repeat tract instability in psf1-1 cells. We propose that defective functioning of the CMG-E complex in psf1-1 cells impairs the progression of DNA replication what increases the contribution of repair mechanisms such as template switch and break-induced replication. These processes require sequence homology search which in case of a repeated DNA tract may result in misalignment leading to its expansion or contraction. Processes that ensure genome stability are crucial for all organisms to avoid mutations and decrease the risk of diseases. The coordinated activity of mechanisms underlying the maintenance of high-fidelity DNA duplication and repair is critical to deal with the malfunction of replication forks or DNA damage. Repeated sequences in DNA are particularly prone to instability; these sequences undergo expansions or contractions, leading in humans to various neurological, neurodegenerative, and neuromuscular disorders. A mutant form of one of the noncatalytic subunits of active DNA helicase complex impairs DNA replication. Here, we show that this form also significantly increases the instability of mononucleotide, dinucleotide, trinucleotide and longer repeat tracts. Our results suggest that in cells that harbor a mutated variant of the helicase complex, continuation of DNA replication is facilitated by recombination processes, and this mechanism can be highly mutagenic during repair synthesis through repetitive regions, especially regions that form secondary structures. Our results indicate that proper functioning of the DNA helicase complex is crucial for maintenance of the stability of repeated DNA sequences, especially in the context of recently described disorders in which mutations or deregulation of the human homologs of genes encoding DNA helicase subunits were observed.
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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90
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Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair. Biomolecules 2019; 9:biom9110709. [PMID: 31698848 PMCID: PMC6920812 DOI: 10.3390/biom9110709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
DNA repeat domains implicated in DNA expansion diseases exhibit complex conformational and energy landscapes that impact biological outcomes. These landscapes include ensembles of entropically driven positional interchanges between isoenergetic, isomeric looped states referred to as rollamers. Here, we present evidence for the position-dependent impact on repeat DNA energy landscapes of an oxidative lesion (8oxodG) and of an abasic site analogue (tetrahydrofuran, F), the universal intermediate in base excision repair (BER). We demonstrate that these lesions modulate repeat bulge loop distributions within the wider dynamic rollamer triplet repeat landscapes. We showed that the presence of a lesion disrupts the energy degeneracy of the rollameric positional isomers. This lesion-induced disruption leads to the redistribution of loop isomers within the repeat loop rollamer ensemble, favoring those rollameric isomers where the lesion is positioned to be energetically least disruptive. These dynamic ensembles create a highly complex energy/conformational landscape of potential BER enzyme substrates to select for processing or to inhibit processing. We discuss the implications of such lesion-induced alterations in repeat DNA energy landscapes in the context of potential BER repair outcomes, thereby providing a biophysical basis for the intriguing in vivo observation of a linkage between pathogenic triplet repeat expansion and DNA repair.
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91
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Cammack AJ, Atassi N, Hyman T, van den Berg LH, Harms M, Baloh RH, Brown RH, van Es MA, Veldink JH, de Vries BS, Rothstein JD, Drain C, Jockel-Balsarotti J, Malcolm A, Boodram S, Salter A, Wightman N, Yu H, Sherman AV, Esparza TJ, McKenna-Yasek D, Owegi MA, Douthwright C, McCampbell A, Ferguson T, Cruchaga C, Cudkowicz M, Miller TM. Prospective natural history study of C9orf72 ALS clinical characteristics and biomarkers. Neurology 2019; 93:e1605-e1617. [PMID: 31578300 DOI: 10.1212/wnl.0000000000008359] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To define the natural history of the C9orf72 amyotrophic lateral sclerosis (C9ALS) patient population, develop disease biomarkers, and characterize patient pathologies. METHODS We prospectively collected clinical and demographic data from 116 symptomatic C9ALS and 12 non-amyotrophic lateral sclerosis (ALS) full expansion carriers across 7 institutions in the United States and the Netherlands. In addition, we collected blood samples for DNA repeat size assessment, CSF samples for biomarker identification, and autopsy samples for dipeptide repeat protein (DPR) size determination. Finally, we collected retrospective clinical data via chart review from 208 individuals with C9ALS and 450 individuals with singleton ALS. RESULTS The mean age at onset in the symptomatic prospective cohort was 57.9 ± 8.3 years, and median duration of survival after onset was 36.9 months. The monthly change was -1.8 ± 1.7 for ALS Functional Rating Scale-Revised and -1.4% ± 3.24% of predicted for slow vital capacity. In blood DNA, we found that G4C2 repeat size correlates positively with age. In CSF, we observed that concentrations of poly(GP) negatively correlate with DNA expansion size but do not correlate with measures of disease progression. Finally, we found that size of poly(GP) dipeptides in the brain can reach large sizes similar to that of their DNA repeat derivatives. CONCLUSIONS We present a thorough investigation of C9ALS natural history, providing the basis for C9ALS clinical trial design. We found that clinical features of this genetic subset are less variant than in singleton ALS. In addition, we identified important correlations of C9ALS patient pathologies with clinical and demographic data.
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Affiliation(s)
- Alexander J Cammack
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Nazem Atassi
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Theodore Hyman
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Leonard H van den Berg
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Matthew Harms
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Robert H Baloh
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Robert H Brown
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Michael A van Es
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Jan H Veldink
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Balint S de Vries
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Jeffrey D Rothstein
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Caroline Drain
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Jennifer Jockel-Balsarotti
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Amber Malcolm
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Sonia Boodram
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Amber Salter
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Nicholas Wightman
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Hong Yu
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Alexander V Sherman
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Thomas J Esparza
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Diane McKenna-Yasek
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Margaret A Owegi
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Catherine Douthwright
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | | | - Alexander McCampbell
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Toby Ferguson
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Carlos Cruchaga
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Merit Cudkowicz
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA
| | - Timothy M Miller
- From the Department of Neurology (A.J.C., T.H., C.D., J.J.-B., A.M., S.B., A.S., T.J.E., C.C., T.M.M.), Washington University School of Medicine, St. Louis, MO; Department of Neurology (N.A., H.Y., A.V.S., M.C.), Neurological Clinical Research Institute, Massachusetts General Hospital, Boston; Department of Neurology (L.H.v.d.B., M.A.v.E., J.H.V., B.S.d.V.), Brain Center Rudolf Magnus, University Medical Center Utrecht, University Utrecht, the Netherlands; Department of Neurology (M.H.), Columbia University, New York, NY; Department of Neurology (R.H. Baloh), Cedars-Sinai Medical Center, Los Angeles, CA; Department of Neurology (R.H. Brown, N.W., D.M.-Y., M.A.O., C.D.), University of Massachusetts, Worcester; Department of Neurology (J.D.R.), Johns Hopkins University, Baltimore, MD; and Biogen Inc. (A.M., T.F.), Boston, MA.
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92
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Naphade S, Tshilenge KT, Ellerby LM. Modeling Polyglutamine Expansion Diseases with Induced Pluripotent Stem Cells. Neurotherapeutics 2019; 16:979-998. [PMID: 31792895 PMCID: PMC6985408 DOI: 10.1007/s13311-019-00810-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polyglutamine expansion disorders, which include Huntington's disease, have expanded CAG repeats that result in polyglutamine expansions in affected proteins. How this specific feature leads to distinct neuropathies in 11 different diseases is a fascinating area of investigation. Most proteins affected by polyglutamine expansions are ubiquitously expressed, yet their mechanisms of selective neurotoxicity are unknown. Induced pluripotent stem cells have emerged as a valuable tool to model diseases, understand molecular mechanisms, and generate relevant human neural and glia subtypes, cocultures, and organoids. Ideally, this tool will generate specific neuronal populations that faithfully recapitulate specific polyglutamine expansion disorder phenotypes and mimic the selective vulnerability of a given disease. Here, we review how induced pluripotent technology is used to understand the effects of the disease-causing polyglutamine protein on cell function, identify new therapeutic targets, and determine how polyglutamine expansion affects human neurodevelopment and disease. We will discuss ongoing challenges and limitations in our use of induced pluripotent stem cells to model polyglutamine expansion diseases.
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Affiliation(s)
- Swati Naphade
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA
| | | | - Lisa M Ellerby
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA, 94945, USA.
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93
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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94
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Verma AK, Khan E, Mishra SK, Jain N, Kumar A. Piperine Modulates Protein Mediated Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome through Interacting Expanded CGG Repeat (r(CGG) exp) RNA. ACS Chem Neurosci 2019; 10:3778-3788. [PMID: 31264835 DOI: 10.1021/acschemneuro.9b00282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An expansion of CGG tandem repeats in the 5' untranslated region (5'-UTR) of fragile X mental retardation 1 (FMR1) gene causes fragile X-associated tremor/ataxia syndrome (FXTAS). The transcripts of these expanded repeats r(CGG)exp either form RNA foci or undergo the repeat-associated non-ATG (RAN) translation that produces toxic homopolymeric proteins in neuronal cells. The discovery of small molecule modulators that possess a strong binding affinity and high selectivity to these toxic expanded repeats RNA could be a promising therapeutic approach to cure the expanded repeat-associated neurological diseases. Therefore, here we sought to test the therapeutic potential of a natural alkaloid, piperine, by assessing its ability to bind and neutralize the toxicity of r(CGG)exp RNA motif. To accomplish this first, we have determined the affinity of piperine to r(CGG)exp RNA using fluorescence-based binding assay and isothermal titration calorimetry assay. These assays showed that piperine forms a thermodynamically favorable interaction with r(CGG)exp RNA with high selectivity to the G-rich RNA motif. Interaction of piperine with r(CGG)exp motif was further validated using several biophysical techniques such as CD, CD melting, NMR spectroscopy, and gel retardation assay. Moreover, piperine was also found to be effective for improving the r(CGG)exp associated splicing defects and RAN translation in a FXTAS cell model system. Our results effectively provided the evidence that piperine strongly interacts with r(CGG)exp RNA and could be used as a suitable candidate for therapeutic development against FXTAS.
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Affiliation(s)
- Arun Kumar Verma
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Eshan Khan
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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95
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Chakraborty U, Mackenroth B, Shalloway D, Alani E. Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences. Genetics 2019; 212:1147-1162. [PMID: 31221666 PMCID: PMC6707472 DOI: 10.1534/genetics.119.302395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker's yeast, such antirecombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH (MutShomolog) protein levels and by factors that excise nonhomologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair (MMR) factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106, and the histone deacetylase Sir2, acting to suppress heteroduplex rejection and the Rpd3, Hst3, and Hst4 deacetylases acting to promote heteroduplex rejection. These observations, and double-mutant analysis, have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with MMR factors that mediate heteroduplex rejection.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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96
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Sorek M, Cohen LRZ, Meshorer E. Open chromatin structure in PolyQ disease-related genes: a potential mechanism for CAG repeat expansion in the normal human population. NAR Genom Bioinform 2019; 1:e3. [PMID: 33575550 PMCID: PMC7671342 DOI: 10.1093/nargab/lqz003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/07/2019] [Accepted: 07/16/2019] [Indexed: 02/05/2023] Open
Abstract
The human genome contains dozens of genes that encode for proteins containing long poly-glutamine repeats (polyQ, usually encoded by CAG codons) of 10Qs or more. However, only nine of these genes have been reported to expand beyond the healthy variation and cause diseases. To address whether these nine disease-associated genes are unique in any way, we compared genetic and epigenetic features relative to other types of genes, especially repeat containing genes that do not cause diseases. Our analyses show that in pluripotent cells, the nine polyQ disease-related genes are characterized by an open chromatin profile, enriched for active chromatin marks and depleted for suppressive chromatin marks. By contrast, genes that encode for polyQ-containing proteins that are not associated with diseases, and other repeat containing genes, possess a suppressive chromatin environment. We propose that the active epigenetic landscape support decreased genomic stability and higher susceptibility for expansion mutations.
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Affiliation(s)
- Matan Sorek
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
| | - Lea R Z Cohen
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
| | - Eran Meshorer
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
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97
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Pan F, Zhang Y, Man VH, Roland C, Sagui C. E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats. Nucleic Acids Res 2019; 46:942-955. [PMID: 29190385 PMCID: PMC5778509 DOI: 10.1093/nar/gkx1186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/13/2017] [Indexed: 12/01/2022] Open
Abstract
Atypical DNA secondary structures play an important role in expandable trinucleotide repeat (TR) and hexanucleotide repeat (HR) diseases. The cytosine mismatches in C-rich homoduplexes and hairpin stems are weakly bonded; experiments show that for certain sequences these may flip out of the helix core, forming an unusual structure termed an ‘e-motif’. We have performed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. TRs have two non-equivalent reading frames, (GCC)n and (CCG)n; while HRs have three: (CCCGGC)n, (CGGCCC)n, (CCCCGG)n. We define three types of pseudo basepair steps related to the mismatches and show that the e-motif is only stable in (GCC)n and (CCCGGC)n homoduplexes due to the favorable stacking of pseudo GpC steps (whose nature depends on whether TRs or HRs are involved) and the formation of hydrogen bonds between the mismatched cytosine at position i and the cytosine (TRs) or guanine (HRs) at position i − 2 along the same strand. We also characterize the extended e-motif, where all mismatched cytosines are extruded, their extra-helical stacking additionally stabilizing the homoduplexes.
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Affiliation(s)
- Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Yuan Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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98
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Ni CW, Wei YJ, Shen YI, Lee IR. Long-Range Hairpin Slippage Reconfiguration Dynamics in Trinucleotide Repeat Sequences. J Phys Chem Lett 2019; 10:3985-3990. [PMID: 31241956 DOI: 10.1021/acs.jpclett.9b01524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Trinucleotide repeat (TNR) sequences, which are responsible for several neurodegenerative genetic diseases, fold into hairpins that interfere with the protein machinery in replication or repair, thus leading to dynamic mutation -abnormal expansions of the genome. Despite their high thermodynamic stability, these hairpins can undergo configurational rearrangements, which may be crucial for continuous dynamic mutation. Here, we used CTG repeats as a model system to study their structural dynamics at the single-molecule level. A unique dynamic two-state configuration interchange was discovered over a wide range of odd-numbered CTG repeat sequences. Employing repeat-number-dependent kinetic analysis, we proposed a bulge translocation model, which is driven by the local instability and can be extended reasonably to longer (pathologically relevant) hairpins, implying the potential role in error accumulation in repeat expansion.
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Affiliation(s)
- Cheng-Wei Ni
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - Yu-Jie Wei
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - Yang-I Shen
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - I-Ren Lee
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
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99
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Rafehi H, Szmulewicz DJ, Bennett MF, Sobreira NLM, Pope K, Smith KR, Gillies G, Diakumis P, Dolzhenko E, Eberle MA, Barcina MG, Breen DP, Chancellor AM, Cremer PD, Delatycki MB, Fogel BL, Hackett A, Halmagyi GM, Kapetanovic S, Lang A, Mossman S, Mu W, Patrikios P, Perlman SL, Rosemergy I, Storey E, Watson SRD, Wilson MA, Zee DS, Valle D, Amor DJ, Bahlo M, Lockhart PJ. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS. Am J Hum Genet 2019; 105:151-165. [PMID: 31230722 PMCID: PMC6612533 DOI: 10.1016/j.ajhg.2019.05.016] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/21/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - David J Szmulewicz
- Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC 3004, Australia; Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg, VIC 3084, Australia
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Katherine R Smith
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Egor Dolzhenko
- Illumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA
| | | | - María García Barcina
- Genetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain
| | - David P Breen
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, Scotland
| | - Andrew M Chancellor
- Department of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand
| | - Phillip D Cremer
- University of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Brent L Fogel
- Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia
| | - G Michael Halmagyi
- Neurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Solange Kapetanovic
- Servicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain
| | - Anthony Lang
- Edmond J. Safra Program in Parkinson disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada; Department of Medicine, Division of Neurology, University Health Network and the University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington 6021, New Zealand
| | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Susan L Perlman
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ian Rosemergy
- Department of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand
| | - Elsdon Storey
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shaun R D Watson
- Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Michael A Wilson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - David S Zee
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David J Amor
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia.
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Lai Y, Weizmann Y, Liu Y. The deoxyribose phosphate lyase of DNA polymerase β suppresses a processive DNA synthesis to prevent trinucleotide repeat instability. Nucleic Acids Res 2019; 46:8940-8952. [PMID: 30085293 PMCID: PMC6158618 DOI: 10.1093/nar/gky700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Trinucleotide repeat (TNR) instability is associated with over 42 neurodegenerative diseases and cancer, for which the molecular mechanisms remain to be elucidated. We have shown that the DNA base excision repair (BER) pathway and its central component, DNA polymerase β (pol β), in particular, its polymerase activity plays an active role in regulating somatic TNR instability. Herein, we revealed a unique role of the pol β dRP lyase in preventing somatic TNR instability. We found that deficiency of pol β deoxyribose phosphate (dRP) lyase activity locked the pol β dRP lyase domain to a dRP group, and this ‘tethered’ pol β to its template forcing the polymerase to perform a processive DNA synthesis. This subsequently promoted DNA strand slippage allowing pol β to skip over a template loop and causing TNR deletion. We showed that the effects were eliminated by complementation of the dRP lyase deficiency with wild-type pol β protein. The results indicate that pol β dRP lyase activity restrained the pol β-dRP interaction to suppress a pol β processive DNA synthesis, thereby preventing TNR deletion. This further implicates a potential of pol β dRP lyase inhibition as a novel treatment of TNR-expansion diseases.
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Affiliation(s)
- Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Yossi Weizmann
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA.,Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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