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Lian M, Tan VJ, Taguchi R, Zhao M, Phang GP, Tan AS, Liu S, Lee CG, Chong SS. Preimplantation Genetic Testing of Spinocerebellar Ataxia Type 3/Machado-Joseph Disease-Robust Tools for Direct and Indirect Detection of the ATXN3 (CAG) n Repeat Expansion. Int J Mol Sci 2024; 25:8073. [PMID: 39125643 PMCID: PMC11311680 DOI: 10.3390/ijms25158073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) is a neurodegenerative disorder caused by the ATXN3 CAG repeat expansion. Preimplantation genetic testing for monogenic disorders (PGT-M) of SCA3/MJD should include reliable repeat expansion detection coupled with high-risk allele determination using informative linked markers. One couple underwent SCA3/MJD PGT-M combining ATXN3 (CAG)n triplet-primed PCR (TP-PCR) with customized linkage-based risk allele genotyping on whole-genome-amplified trophectoderm cells. Microsatellites closely linked to ATXN3 were identified and 16 markers were genotyped on 187 anonymous DNAs to verify their polymorphic information content. In the SCA3/MJD PGT-M case, the ATXN3 (CAG)n TP-PCR and linked marker analysis results concurred completely. Among the three unaffected embryos, a single embryo was transferred and successfully resulted in an unaffected live birth. A total of 139 microsatellites within 1 Mb upstream and downstream of the ATXN3 CAG repeat were identified and 8 polymorphic markers from each side were successfully co-amplified in a single-tube reaction. A PGT-M assay involving ATXN3 (CAG)n TP-PCR and linkage-based risk allele identification has been developed for SCA3/MJD. A hexadecaplex panel of highly polymorphic microsatellites tightly linked to ATXN3 has been developed for the rapid identification of informative markers in at-risk couples for use in the PGT-M of SCA3/MJD.
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Affiliation(s)
- Mulias Lian
- Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore 119074, Singapore
| | - Vivienne J. Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Riho Taguchi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Mingjue Zhao
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Gui-Ping Phang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Arnold S. Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Shuling Liu
- KKIVF Centre, Reproductive Medicine, KK Women’s & Children’s Hospital, Singapore 229899, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Samuel S. Chong
- Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore 119074, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore 119074, Singapore
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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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Volozonoka L, Miskova A, Gailite L. Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing. Int J Mol Sci 2022; 23:4819. [PMID: 35563216 PMCID: PMC9102663 DOI: 10.3390/ijms23094819] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA.
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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia;
| | - Anna Miskova
- Department of Obstetrics and Gynaecology, Riga Stradins University, LV-1007 Riga, Latvia;
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia;
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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In Vitro Fertilization Using Preimplantation Genetic Testing in a Romanian Couple Carrier of Mutations in the TTN Gene: A Case Report and Literature Review. Diagnostics (Basel) 2021; 11:diagnostics11122328. [PMID: 34943567 PMCID: PMC8699826 DOI: 10.3390/diagnostics11122328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/04/2022] Open
Abstract
Severe congenital myopathy with fatal cardiomyopathy (EOMFC) is a rare genetic neuromuscular disorder inherited in an autosomal recessive manner. Here we presented a successful pregnancy obtained by in vitro fertilization (IVF) using preimplantation genetic testing (PGT) in one young Romanian carrier couple that already lost mutation(s) within the TNN gene and whose first baby passed away due to multiple complications. It was delivered via emergency C-section at 36 weeks and fully dependent on artificial ventilation for a couple of months, weighing 2200 g and an APGAR score of 3. The aCGH + SNP analysis revealed an abnormal profile of the first newborn; three areas associated with loss of heterozygosity on chromosome 1 (q25.1–q25.3) of 6115 kb, 5 (p15.2–p15.1) of 2589 kb and 8 (q11.21–q11.23) of 4830 kb, a duplication of 1104 kb on chromosome 10 in the position q11.22, and duplication of 1193 kb on chromosome 16 in the position p11.2p11.1. Subsequently, we proceeded to test the parents and showed that both parents are carriers; confirmed by Sanger and NGS sequencing—father—on Chr2(GRCh37):g.179396832_179396833del—TTN variant c.104509_104510del p.(Leu34837Glufs*12)—exon 358 and mother—on Chr2(GRCh37):g.179479653G>C—TTN variant c.48681C>G p.(Tyr16227*)—exon 260. Their first child died shortly after birth due to multiple organ failures, possessing both parent’s mutations; weighing 2200 g at birth and received an APGAR score of 3 following premature delivery via emergency C-section at 36 weeks. Two embryos were obtained following the IVF protocol; one possessed the mother’s mutation, and the other had no mutations and was normal (WT). In contrast with the first birth, the second one was uneventful. A healthy female baby weighing 2990 g was delivered by C-section at 38 weeks, receiving an APGAR score of 9.
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Zhang S, Lei C, Wu J, Xiao M, Zhou J, Zhu S, Fu J, Lu D, Sun X, Xu C. A comprehensive and universal approach for embryo testing in patients with different genetic disorders. Clin Transl Med 2021; 11:e490. [PMID: 34323405 PMCID: PMC8265165 DOI: 10.1002/ctm2.490] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/01/2021] [Accepted: 06/20/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In vitro fertilization (IVF) with preimplantation genetic testing (PGT) has markedly improved clinical pregnancy outcomes for carriers of gene mutations or chromosomal structural rearrangements by the selection of embryos free of disease-causing genes and chromosome abnormalities. However, for detecting whole or segmental chromosome aneuploidies, gene variants or balanced chromosome rearrangements in the same embryo require separate procedures, and none of the existing detection platforms is universal for all patients with different genetic disorders. METHODS Here, we report a cost-effective, family-based haplotype phasing approach that can simultaneously evaluate multiple genetic variants, including monogenic disorders, aneuploidy, and balanced chromosome rearrangements in the same embryo with a single test. A total of 12 monogenic diseases carrier couples and either of them carried chromosomal rearrangements were enrolled simultaneously in this present study. Genome-wide genotyping was performed with single-nucleotide polymorphism (SNP)-array, and aneuploidies were analyzed through SNP allele frequency and Log R ratio. Parental haplotypes were phased by an available genotype from a close relative, and the embryonic genome-wide haplotypes were determined through family haplotype linkage analysis (FHLA). Disease-causing genes and chromosomal rearrangements were detected by haplotypes located within the 2 Mb region covering the targeted genes or breakpoint regions. RESULTS Twelve blastocysts were thawed, and then transferred into the uterus of female patients. Nine pregnancies had reached the second trimester and five healthy babies have been born. Fetus validation results, performed with the amniotic fluid or umbilical cord blood samples, were consistent with those at the blastocyst stage diagnosed by PGT. CONCLUSIONS We demonstrate that SNP-based FHLA enables the accurate genetic detection of a wide spectrum of monogenic diseases and chromosome abnormalities in embryos, preventing the transfer of parental genetic abnormalities to the fetus. This method can be implemented as a universal platform for embryo testing in patients with different genetic disorders.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Jing Fu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life ScienceFudan UniversityShanghaiChina
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family PlanningScience and Technology Research InstituteChongqingChina
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology HospitalFudan UniversityShanghaiChina
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Ye Z, Hu W, Wu B, Zhang Y, Lei C, Williams I, Shouval DS, Kanegane H, Kim KM, de Ridder L, Shah N, Ling G, Yerushalmi B, Kotlarz D, Snapper S, Horn R, Klein C, Muise AM, Huang Y, Uhlig HH. Predictive Prenatal Diagnosis for Infantile-onset Inflammatory Bowel Disease Because of Interleukin-10 Signalling Defects. J Pediatr Gastroenterol Nutr 2021; 72:276-281. [PMID: 32925557 PMCID: PMC8191811 DOI: 10.1097/mpg.0000000000002937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Advances in genetic technologies provide opportunities for patient care and ethical challenges. Clinical care of patients with rare Mendelian disorders is often at the forefront of those developments. Whereas in classical polygenic inflammatory bowel disease (IBD), the predictive value of genetic variants is very low, predictive prenatal genetic diagnosis can inform families at high risk of severe genetic disorders. Patients with IL-10 signalling defects because of pathogenic variants in IL10RA, Il10RB, and IL10 develop severe infantile onset inflammatory bowel disease that is completely penetrant and has a high morbidity and substantial mortality despite treatment. METHODS We performed a survey among tertiary specialist paediatric centers of 10 countries on the utilization of predictive prenatal genetic diagnosis in IL-10 signalling defects. We retrospectively report prenatal genetics in a series of 8 families. RESULTS International variation in legislation, guidelines, expert opinion, as well as cultural and religious background of families and clinicians results in variable utilization of preimplantation and prenatal genetic testing for IL-10 signalling defects. Eleven referrals for prenatal diagnosis for IL-10 signalling defects were identified across 4 countries. We report on 8 families who underwent prenatal preimplantation monogenic testing after in vitro fertilization (n = 2) and/or by amniocentesis/chorion villus sampling (n = 6). A genetic diagnosis was established in 1 foetus and excluded in 7 foetuses (all IL10RA variants). CONCLUSIONS Prenatal genetic testing for IL10R-defects is feasible, yet the legal and ethical considerations are complex and controversial. In some countries, predictive genetics for IL-10-related signalling defects is entering clinical practice.
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Affiliation(s)
- Ziqing Ye
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai, China
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Wenhui Hu
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Key Lab of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Yueping Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Isabelle Williams
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Dror S. Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramag Gan, Israel and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kyung Mo Kim
- Department of Pediatrics, University of Ulsan College of Medicine, Asan Medical Center Children’s Hospital 88, Olympic-Ro 43 Gil, Songpa-Gu, Seoul, Korea
| | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus University Medical Center Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Neil Shah
- Department of Paediatric Gastroenterology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Galina Ling
- Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Scott Snapper
- Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Ruth Horn
- Wellcome Centre for Ethics and Humanities and the Ethox Centre, University of Oxford, UK
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aleixo M. Muise
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Ying Huang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai, China
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit
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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: 161] [Impact Index Per Article: 40.3] [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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