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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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2
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Gillani M, Pollastri G. Protein subcellular localization prediction tools. Comput Struct Biotechnol J 2024; 23:1796-1807. [PMID: 38707539 PMCID: PMC11066471 DOI: 10.1016/j.csbj.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Protein subcellular localization prediction is of great significance in bioinformatics and biological research. Most of the proteins do not have experimentally determined localization information, computational prediction methods and tools have been acting as an active research area for more than two decades now. Knowledge of the subcellular location of a protein provides valuable information about its functionalities, the functioning of the cell, and other possible interactions with proteins. Fast, reliable, and accurate predictors provides platforms to harness the abundance of sequence data to predict subcellular locations accordingly. During the last decade, there has been a considerable amount of research effort aimed at developing subcellular localization predictors. This paper reviews recent subcellular localization prediction tools in the Eukaryotic, Prokaryotic, and Virus-based categories followed by a detailed analysis. Each predictor is discussed based on its main features, strengths, weaknesses, algorithms used, prediction techniques, and analysis. This review is supported by prediction tools taxonomies that highlight their rele- vant area and examples for uncomplicated categorization and ease of understandability. These taxonomies help users find suitable tools according to their needs. Furthermore, recent research gaps and challenges are discussed to cover areas that need the utmost attention. This survey provides an in-depth analysis of the most recent prediction tools to facilitate readers and can be considered a quick guide for researchers to identify and explore the recent literature advancements.
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Affiliation(s)
- Maryam Gillani
- School of Computer Science, University College Dublin (UCD), Dublin, D04 V1W8, Ireland
| | - Gianluca Pollastri
- School of Computer Science, University College Dublin (UCD), Dublin, D04 V1W8, Ireland
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3
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Zhong S, Lian Y, Zhou B, Ren R, Duan L, Pan Y, Gong Y, Wu X, Cheng D, Zhang P, Lu B, Wang X, Ding J. Microglia contribute to polyG-dependent neurodegeneration in neuronal intranuclear inclusion disease. Acta Neuropathol 2024; 148:21. [PMID: 39150562 DOI: 10.1007/s00401-024-02776-0] [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: 02/15/2024] [Revised: 07/04/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024]
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disorder caused by the expansion of GGC trinucleotide repeats in NOTCH2NLC gene. Despite identifying uN2CpolyG, a toxic polyglycine (polyG) protein translated by expanded GGC repeats, the exact pathogenic mechanisms of NIID remain unclear. In this study, we investigated the role of polyG by expressing various forms of NOTCH2NLC in mice: the wild-type, the expanded form with 100 GGC repeats (either translating or not translating into uN2CpolyG), and the mutated form that encodes a pure polyG without GGC-repeat RNA and the C-terminal stretch (uN2CpolyG-dCT). Both uN2CpolyG and uN2CpolyG-dCT induced the formation of inclusions composed by filamentous materials and resulted in neurodegenerative phenotypes in mice, including impaired motor and cognitive performance, shortened lifespan, and pathologic lesions such as white-matter lesions, microgliosis, and astrogliosis. In contrast, expressing GGC-repeat RNA alone was non-pathogenic. Through bulk and single-nuclei RNA sequencing, we identified common molecular signatures linked to the expression of uN2CpolyG and uN2CpolyG-dCT, particularly the upregulation of inflammation and microglia markers, and the downregulation of immediate early genes and splicing factors. Importantly, microglia-mediated inflammation was visualized in NIID patients using positron emission tomography, correlating with levels of white-matter atrophy. Furthermore, microglia ablation ameliorated neurodegenerative phenotypes and transcriptional alterations in uN2CpolyG-expressing mice but did not affect polyG inclusions. Together, these results demonstrate that polyG is crucial for the pathogenesis of NIID and highlight the significant role of microglia in polyG-induced neurodegeneration.
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Affiliation(s)
- Shaoping Zhong
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yangye Lian
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Binbin Zhou
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Ruiqing Ren
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Lewei Duan
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuyin Pan
- Department of Neurology at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuchen Gong
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Wu
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Dengfeng Cheng
- Department of Nuclear Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Puming Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Boxun Lu
- Department of Neurology at Huashan Hospital, State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China.
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4
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Lewis SA, Ruttenberg A, Iyiyol T, Kong N, Jin SC, Kruer MC. Potential clinical applications of advanced genomic analysis in cerebral palsy. EBioMedicine 2024; 106:105229. [PMID: 38970919 PMCID: PMC11282942 DOI: 10.1016/j.ebiom.2024.105229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/08/2024] Open
Abstract
Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.
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Affiliation(s)
- Sara A Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States
| | - Andrew Ruttenberg
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tuğçe Iyiyol
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Nahyun Kong
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, United States; Departments of Child Health, Neurology, and Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, AZ, United States; Programs in Neuroscience and Molecular & Cellular Biology, School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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5
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Hoffman-Zacharska D, Sulek A. The New Face of Dynamic Mutation-The CAA [CAG]n CAA CAG Motif as a Mutable Unit in the TBP Gene Causative for Spino-Cerebellar Ataxia Type 17. Int J Mol Sci 2024; 25:8190. [PMID: 39125760 PMCID: PMC11312008 DOI: 10.3390/ijms25158190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/16/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Since 1991, several genetic disorders caused by unstable trinucleotide repeats (TNRs) have been identified, collectively referred to as triplet repeat diseases (TREDs). They share a common mutation mechanism: the expansion of repeats (dynamic mutations) due to the propensity of repeated sequences to form unusual DNA structures during replication. TREDs are characterized as neurodegenerative diseases or complex syndromes with significant neurological components. Spinocerebellar ataxia type 17 (SCA17) falls into the former category and is caused by the expansion of mixed CAA/CAG repeats in the TBP gene. To date, a five-unit organization of this region [(CAG)3 (CAA)3] [(CAG)n] [CAA CAG CAA] [(CAG)n] [CAA CAG], with expansion in the second [(CAG)n] unit being the most common, has been proposed. In this study, we propose an alternative organization scheme for the repeats. A search of the PubMed database was conducted to identify articles reporting both the number and composition of GAC/CAA repeats in TBP alleles. Nineteen reports were selected. The sequences of all identified CAG/CAA repeats in the TBP locus, including 67 cases (probands and b relatives), were analyzed in terms of their repetition structure and stability in inheritance, if possible. Based on the analysis of three units [(CAG)3 (CAA)2] [CAA (CAG)n CAA CAG] [CAA (CAG)n CAA CAG], the organization of repeats is proposed. Detailed analysis of the CAG/CAA repeat structure, not just the number of repeats, in TBP-expanded alleles should be performed, as it may have a prognostic value in the prediction of stability/instability during transmission and the possible anticipation of the disease.
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Affiliation(s)
- Dorota Hoffman-Zacharska
- Department of Medical Genetics, Institute of Mother and Child, 02-106 Warsaw, Poland
- Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland;
| | - Anna Sulek
- Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland;
- Faculty of Medicine, Lazarski University, 02-662 Warsaw, Poland
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Mokveld T, Dolzhenko E, Dashnow H, Nicholas TJ, Sasani T, van der Sanden B, Jadhav B, Pedersen B, Kronenberg Z, Tucci A, Sharp AJ, Quinlan AR, Gilissen C, Hoischen A, Eberle MA. TRGT-denovo: accurate detection of de novo tandem repeat mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.600745. [PMID: 39071386 PMCID: PMC11275785 DOI: 10.1101/2024.07.16.600745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Motivation Identifying de novo tandem repeat (TR) mutations on a genome-wide scale is essential for understanding genetic variability and its implications in rare diseases. While PacBio HiFi sequencing data enhances the accessibility of the genome's TR regions for genotyping, simple de novo calling strategies often generate an excess of likely false positives, which can obscure true positive findings, particularly as the number of surveyed genomic regions increases. Results We developed TRGT-denovo, a computational method designed to accurately identify all types of de novo TR mutations-including expansions, contractions, and compositional changes-within family trios. TRGT-denovo directly interrogates read evidence, allowing for the detection of subtle variations often overlooked in variant call format (VCF) files. TRGT-denovo improves the precision and specificity of de novo mutation (DNM) identification, reducing the number of de novo candidates by an order of magnitude compared to genotype-based approaches. In our experiments involving eight rare disease trios previously studiedTRGT-denovo correctly reclassified all false positive DNM candidates as true negatives. Using an expanded repeat catalog, it identified new candidates, of which 95% (19/20) were experimentally validated, demonstrating its effectiveness in minimizing likely false positives while maintaining high sensitivity for true discoveries. Availability and implementation Built in Rust, TRGT-denovo is available as source code and a pre-compiled Linux binary along with a user guide at: https://github.com/PacificBiosciences/trgt-denovo.
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Affiliation(s)
| | | | | | | | - T Sasani
- Univ. of Utah, Salt Lake City, UT
| | - B van der Sanden
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands
| | - B Jadhav
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - A Tucci
- Genomics England, London, UK
| | - A J Sharp
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - C Gilissen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands
| | - A Hoischen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud university medical center, Nijmegen, the Netherlands
- Department of Internal Medicine, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud university medical center, Nijmegen, the Netherlands
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7
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Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer. SCIENCE ADVANCES 2024; 10:eado1218. [PMID: 39018396 PMCID: PMC466953 DOI: 10.1126/sciadv.ado1218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic MAPK/AP1 signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such as ATG12 and XRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.
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Affiliation(s)
- Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Olivia M. Joyner
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Stacey M. Bagby
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lily L. Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ben G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Todd M. Pitts
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
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8
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De T, Sharma P, Upilli B, Vivekanand A, Bari S, Sonakar AK, Srivastava AK, Faruq M. Spinocerebellar ataxia type 27B (SCA27B) in India: insights from a large cohort study suggest ancient origin. Neurogenetics 2024:10.1007/s10048-024-00770-y. [PMID: 38976084 DOI: 10.1007/s10048-024-00770-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND The ethnic diversity of India provides a unique opportunity to study the history of the origin of mutations of genetic disorders. Spinocerebellar ataxia type 27B (SCA27B), a recently identified dominantly inherited cerebellar disorder is caused by GAA-repeat expansions in intron 1 of Fibroblast Growth Factor 14 (FGF14). Predominantly reported in the European population, we aimed to screen this mutation and study the founder haplotype of SCA27B in Indian ataxia patients. METHODS We have undertaken screening of GAA repeats in a large Indian cohort of ~ 1400 uncharacterised ataxia patients and kindreds and long-read sequencing-based GAA repeat length assessment. High throughput genotyping-based haplotype analysis was also performed. We utilized ~ 1000 Indian genomes to study the GAA at-risk expansion alleles. FINDINGS We report a high frequency of 1.83% (n = 23) of SCA27B in the uncharacterized Indian ataxia cohort. We observed several biallelic GAA expansion mutations (n = 5) with younger disease onset. We observed a risk haplotype (AATCCGTGG) flanking the FGF14-GAA locus over a 74 kb region in linkage disequilibrium. We further studied the frequency of this risk haplotype across diverse geographical population groups. The highest prevalence of the risk haplotype was observed in the European population (29.9%) followed by Indians (21.5%). The observed risk haplotype has existed through ~ 1100 generations (~ 22,000 years), assuming a correlated genealogy. INTERPRETATION This study provides valuable insights into SCA27B and its Upper Paleolithic origin in the Indian subcontinent. The high occurrence of biallelic expansion is probably relevant to the endogamous nature of the Indian population.
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Affiliation(s)
- Tiyasha De
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
| | - Pooja Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Bharathram Upilli
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - A Vivekanand
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Shreya Bari
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India
| | - Akhilesh Kumar Sonakar
- Neurology Department, Neuroscience Centre, All India Institute of Medical Sciences, Ansari Nagar, 110029, India
| | - Achal Kumar Srivastava
- Neurology Department, Neuroscience Centre, All India Institute of Medical Sciences, Ansari Nagar, 110029, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mall road, New Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Sector-19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India.
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Pellerin D, Méreaux JL, Boluda S, Danzi MC, Dicaire MJ, Davoine CS, Genis D, Spurdens G, Ashton C, Hammond JM, Gerhart BJ, Chelban V, Le PU, Safisamghabadi M, Yanick C, Lee H, Nageshwaran SK, Matos-Rodrigues G, Jaunmuktane Z, Petrecca K, Akbarian S, Nussenzweig A, Usdin K, Renaud M, Bonnet C, Ravenscroft G, Saporta MA, Napierala JS, Houlden H, Deveson IW, Napierala M, Brice A, Molina Porcel L, Seilhean D, Zuchner S, Durr A, Brais B. Somatic instability of the FGF14 -SCA27B GAA•TTC repeat reveals a marked expansion bias in the cerebellum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.01.24309777. [PMID: 39006414 PMCID: PMC11245061 DOI: 10.1101/2024.07.01.24309777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Spinocerebellar ataxia 27B (SCA27B) is a common autosomal dominant ataxia caused by an intronic GAA•TTC repeat expansion in FGF14 . Neuropathological studies have shown that neuronal loss is largely restricted to the cerebellum. Although the repeat locus is highly unstable during intergenerational transmission, it remains unknown whether it exhibits cerebral mosaicism and progressive instability throughout life. We conducted an analysis of the FGF14 GAA•TTC repeat somatic instability across 156 serial blood samples from 69 individuals, fibroblasts, induced pluripotent stem cells, and post-mortem brain tissues from six controls and six patients with SCA27B, alongside methylation profiling using targeted long-read sequencing. Peripheral tissues exhibited minimal somatic instability, which did not significantly change over periods of more than 20 years. In post-mortem brains, the GAA•TTC repeat was remarkably stable across all regions, except in the cerebellar hemispheres and vermis. The levels of somatic expansion in the cerebellar hemispheres and vermis were, on average, 3.15 and 2.72 times greater relative to other examined brain regions, respectively. Additionally, levels of somatic expansion in the brain increased with repeat length and tissue expression of FGF14 . We found no significant difference in methylation of wild-type and expanded FGF14 alleles in post-mortem cerebellar hemispheres between patients and controls. In conclusion, our study revealed that the FGF14 GAA•TTC repeat exhibits a cerebellar-specific expansion bias, which may explain the pure and late-onset cerebellar involvement in SCA27B.
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10
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Vegezzi E, Ishiura H, Bragg DC, Pellerin D, Magrinelli F, Currò R, Facchini S, Tucci A, Hardy J, Sharma N, Danzi MC, Zuchner S, Brais B, Reilly MM, Tsuji S, Houlden H, Cortese A. Neurological disorders caused by novel non-coding repeat expansions: clinical features and differential diagnosis. Lancet Neurol 2024; 23:725-739. [PMID: 38876750 DOI: 10.1016/s1474-4422(24)00167-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 06/16/2024]
Abstract
Nucleotide repeat expansions in the human genome are a well-known cause of neurological disease. In the past decade, advances in DNA sequencing technologies have led to a better understanding of the role of non-coding DNA, that is, the DNA that is not transcribed into proteins. These techniques have also enabled the identification of pathogenic non-coding repeat expansions that cause neurological disorders. Mounting evidence shows that adult patients with familial or sporadic presentations of epilepsy, cognitive dysfunction, myopathy, neuropathy, ataxia, or movement disorders can be carriers of non-coding repeat expansions. The description of the clinical, epidemiological, and molecular features of these recently identified non-coding repeat expansion disorders should guide clinicians in the diagnosis and management of these patients, and help in the genetic counselling for patients and their families.
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Affiliation(s)
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Pellerin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Stefano Facchini
- IRCCS Mondino Foundation, Pavia, Italy; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Arianna Tucci
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - John Hardy
- Department of Neurogedengerative Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Matt C Danzi
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
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Arpa Gutiérrez FJ, Abenza Abildúa MJ, Rouco Axpe I, Adarmes Gómez AD, Serrano Munuera C. Practical recommendations for the clinical evaluation of patients with hereditary ataxia and hereditary spastic paraplegia. Neurologia 2024; 39:515-522. [PMID: 36396094 DOI: 10.1016/j.nrleng.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hereditary ataxia (HA) and hereditary spastic paraplegia (HSP) are rare diseases; as such, they are rarely managed in general neurology consultations. We present a set of brief, practical recommendations for the diagnosis and management of these patients, as well as a standardised procedure for comprehensive evaluation of disability. We provide definitions for HA and "HA plus," and "pure" and "complicated" HSP; describe the clinical assessment of these patients, indicating the main complementary tests and clinical scales for physical and psychological assessment of the patients; and summarise the available treatments. These recommendations are intended to facilitate daily neurological practice and to unify clinical criteria and disability assessment protocols for patients with HA and HSP.
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Affiliation(s)
- F J Arpa Gutiérrez
- Facultad de Medicina de la Universidad Autónoma de Madrid, Fundación IdiPAZ, Madrid, Spain; Comisión de Ataxias y Paraparesias Espásticas de la Sociedad Española de Neurología (CEAPED)
| | - M J Abenza Abildúa
- Comisión de Ataxias y Paraparesias Espásticas de la Sociedad Española de Neurología (CEAPED); Sección de Neurología, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain.
| | - I Rouco Axpe
- Comisión de Ataxias y Paraparesias Espásticas de la Sociedad Española de Neurología (CEAPED); Unidad de Ataxias y Paraparesias Espásticas Hereditarias, Servicio de Neurología, Hospital Universitario de Cruces, Bilbao, Bizkaia, Spain
| | - A D Adarmes Gómez
- Comisión de Ataxias y Paraparesias Espásticas de la Sociedad Española de Neurología (CEAPED); Servicio de Neurología, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | - C Serrano Munuera
- Comisión de Ataxias y Paraparesias Espásticas de la Sociedad Española de Neurología (CEAPED); Servicio de Neurología, Hospital Sant Joan de Déu, Martorell, Spain
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12
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van der Sanden B, Neveling K, Pang AWC, Shukor S, Gallagher MD, Burke SL, Kamsteeg EJ, Hastie A, Hoischen A. Optical Genome Mapping for Applications in Repeat Expansion Disorders. Curr Protoc 2024; 4:e1094. [PMID: 38966883 DOI: 10.1002/cpz1.1094] [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: 07/06/2024]
Abstract
Short tandem repeat (STR) expansions are associated with more than 60 genetic disorders. The size and stability of these expansions correlate with the severity and age of onset of the disease. Therefore, being able to accurately detect the absolute length of STRs is important. Current diagnostic assays include laborious lab experiments, including repeat-primed PCR and Southern blotting, that still cannot precisely determine the exact length of very long repeat expansions. Optical genome mapping (OGM) is a cost-effective and easy-to-use alternative to traditional cytogenetic techniques and allows the comprehensive detection of chromosomal aberrations and structural variants >500 bp in length, including insertions, deletions, duplications, inversions, translocations, and copy number variants. Here, we provide methodological guidance for preparing samples and performing OGM as well as running the analysis pipelines and using the specific repeat expansion workflows to determine the exact repeat length of repeat expansions expanded beyond 500 bp. Together these protocols provide all details needed to analyze the length and stability of any repeat expansion with an expected repeat size difference from the expected wild-type allele of >500 bp. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Genomic ultra-high-molecular-weight DNA isolation, labeling, and staining Basic Protocol 2: Data generation and genome mapping using the Bionano Saphyr® System Basic Protocol 3: Manual De Novo Assembly workflow Basic Protocol 4: Local guided assembly workflow Basic Protocol 5: EnFocus Fragile X workflow Basic Protocol 6: Molecule distance script workflow.
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Affiliation(s)
- Bart van der Sanden
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Syukri Shukor
- Bionano Genomics Clinical and Scientific Affairs, San Diego, California
| | | | - Stephanie L Burke
- Bionano Genomics Clinical and Scientific Affairs, San Diego, California
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alex Hastie
- Bionano Genomics Clinical and Scientific Affairs, San Diego, California
| | - Alexander Hoischen
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
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13
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [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: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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14
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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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15
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Zhou X, He R, Zeng S, Li M, Pan H, Zhao Y, Liu Z, Xu Q, Guo J, Yan X, Li J, Tang B, Sun Q. Tremor-associated short tandem repeat intermediate and pathogenic expansions in familial essential tremor. Brain Commun 2024; 6:fcae217. [PMID: 38961870 PMCID: PMC11220504 DOI: 10.1093/braincomms/fcae217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/07/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024] Open
Abstract
There is an obvious clinical-pathological overlap between essential tremor and some known tremor-associated short tandem repeat expansion disorders. The aim is to analyse whether these short tandem repeat genes, including ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATXN8OS, ATXN10, PPP2R2B, TBP, BEAN1, NOP56, DAB1, ATN1, SADM12 and FMR1, are associated with familial essential tremor patients. Genetic analysis of repeat sizes in tremor-associated short tandem repeat expansions was performed in a large cohort of 515 familial essential tremor probands and 300 controls. The demographic and clinical features among carriers of pathogenic expansions, intermediate repeats and non-carriers were compared. A total of 18 out of 515 (18/515, 3.7%) patients were found to have repeats expansions, including 12 cases (12/515, 2.5%) with intermediate repeat expansions (one ATXN1, eight TBP, two FMR1, one ATN1), and six cases (6/515, 1.2%) with pathogenic expansions (one ATXN1, one ATXN2, one ATXN8OS, one PPP2R2B, one FMR1, one SAMD12). There were no statistically significant differences in intermediate repeats compared to healthy controls. Furthermore, there were no significant differences in demographics and clinical features among individuals with pathogenic expansions, intermediate repeat expansions carriers and non-carriers. Our study indicates that the intermediate repeat expansion in tremor-associated short tandem repeat expansions does not pose an increased risk for essential tremor, and rare pathogenic expansion carriers have been found in the familial essential tremor cohort. The diagnosis of essential tremor based solely on clinical symptoms remains a challenge in distinguishing it from known short tandem repeat expansions diseases with overlapping clinical-pathological features.
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Affiliation(s)
- Xun Zhou
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Runcheng He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Sheng Zeng
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Mingqiang Li
- Department of Neurology, Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421000, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jinchen Li
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Department of Neurology, Multi-Omics Research Center for Brain Disorders, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421000, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Qiying Sun
- Department of Geriatric Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan 410008, China
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16
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Ma R, Liu Z, Zhu B. The romance of replication: Hand in hand, from dawn to dusk. Sci Bull (Beijing) 2024:S2095-9273(24)00453-5. [PMID: 38969536 DOI: 10.1016/j.scib.2024.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Affiliation(s)
- Runze Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China
| | - Zijing Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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17
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Chiu R, Rajan-Babu IS, Friedman JM, Birol I. A comprehensive tandem repeat catalog of the human genome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24309173. [PMID: 38947075 PMCID: PMC11213036 DOI: 10.1101/2024.06.19.24309173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
With the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping of tandem repeat loci on a population scale becomes more feasible. Such efforts not only expand our knowledge of the tandem repeat landscape in the human genome but also enhance our ability to differentiate pathogenic tandem repeat mutations from benign polymorphisms. To this end, we analyzed 272 genomes assembled using datasets from three public initiatives that employed different long-read sequencing technologies. Here, we report a catalog of over 18 million tandem repeat loci, many of which were previously unannotated. Some of these loci are highly polymorphic, and many of them reside within coding sequences.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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18
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Shukla S, Gupta K, Singh K, Mishra A, Kumar A. An Updated Canvas of the RFC1-mediated CANVAS (Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome). Mol Neurobiol 2024:10.1007/s12035-024-04307-0. [PMID: 38898197 DOI: 10.1007/s12035-024-04307-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Proliferation of specific nucleotide sequences within the coding and non-coding regions of numerous genes has been implicated in approximately 40 neurodegenerative disorders. Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), a neurodegenerative disorder, is distinguished by a pathological triad of sensory neuropathy, bilateral vestibular areflexia and cerebellar impairments. It manifests in adults gradually and is autosomal recessive and multi-system ataxia. Predominantly, CANVAS is associated with biallelic AAGGG repeat expansions in intron 2 of the RFC1 gene. Although various motifs have been identified, only a subset induces pathological consequences, by forming stable secondary structures that disrupt gene functions both in vitro and in vivo. The pathogenesis of CANVAS remains a subject of intensive research, yet its precise mechanisms remain elusive. Herein, we aim to comprehensively review the epidemiology, clinical ramifications, molecular mechanisms, genetics, and potential therapeutics in light of the current findings, extending an overview of the most significant research on CANVAS.
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Affiliation(s)
- Sakshi Shukla
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Kanav Gupta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Krishna Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
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19
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Lee JM, McLean ZL, Correia K, Shin JW, Lee S, Jang JH, Lee Y, Kim KH, Choi DE, Long JD, Lucente D, Seong IS, Pinto RM, Giordano JV, Mysore JS, Siciliano J, Elezi E, Ruliera J, Gillis T, Wheeler VC, MacDonald ME, Gusella JF, Gatseva A, Ciosi M, Lomeikaite V, Loay H, Monckton DG, Wills C, Massey TH, Jones L, Holmans P, Kwak S, Sampaio C, Orth M, Bernhard Landwehrmeyer G, Paulsen JS, Ray Dorsey E, Myers RH. Genetic modifiers of somatic expansion and clinical phenotypes in Huntington's disease reveal shared and tissue-specific effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597797. [PMID: 38948755 PMCID: PMC11212857 DOI: 10.1101/2024.06.10.597797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Huntington's disease (HD), due to expansion of a CAG repeat in HTT , is representative of a growing number of disorders involving somatically unstable short tandem repeats. We find that overlapping and distinct genetic modifiers of clinical landmarks and somatic expansion in blood DNA reveal an underlying complexity and cell-type specificity to the mismatch repair-related processes that influence disease timing. Differential capture of non-DNA-repair gene modifiers by multiple measures of cognitive and motor dysfunction argues additionally for cell-type specificity of pathogenic processes. Beyond trans modifiers, differential effects are also illustrated at HTT by a 5'-UTR variant that promotes somatic expansion in blood without influencing clinical HD, while, even after correcting for uninterrupted CAG length, a synonymous sequence change at the end of the CAG repeat dramatically hastens onset of motor signs without increasing somatic expansion. Our findings are directly relevant to therapeutic suppression of somatic expansion in HD and related disorders and provide a route to define the individual neuronal cell types that contribute to different HD clinical phenotypes.
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Choi DE, Shin JW, Zeng S, Hong EP, Jang JH, Loupe JM, Wheeler VC, Stutzman HE, Kleinstiver B, Lee JM. Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease. eLife 2024; 12:RP89782. [PMID: 38869243 PMCID: PMC11175616 DOI: 10.7554/elife.89782] [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] [Indexed: 06/14/2024] Open
Abstract
An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and guide RNAs (gRNAs) efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.
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Affiliation(s)
- Doo Eun Choi
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jun Wan Shin
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Sophia Zeng
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Eun Pyo Hong
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jae-Hyun Jang
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jacob M Loupe
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
| | - Ben Kleinstiver
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
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21
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Zheng ZH, Cao CY, Cheng B, Yuan RY, Zeng YH, Guo ZB, Qiu YS, Lv WQ, Liang H, Li JL, Zhang WX, Fang MK, Sun YH, Lin W, Hong JM, Gan SR, Wang N, Chen WJ, Du GQ, Fang L. Characteristics of tandem repeat inheritance and sympathetic nerve involvement in GAA-FGF14 ataxia. J Hum Genet 2024:10.1038/s10038-024-01262-5. [PMID: 38866925 DOI: 10.1038/s10038-024-01262-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/12/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Intronic GAA repeat expansion ([GAA] ≥250) in FGF14 is associated with the late-onset neurodegenerative disorder, spinocerebellar ataxia 27B (SCA27B, GAA-FGF14 ataxia). We aim to determine the prevalence of the GAA repeat expansion in FGF14 in Chinese populations presenting late-onset cerebellar ataxia (LOCA) and evaluate the characteristics of tandem repeat inheritance, radiological features and sympathetic nerve involvement. METHODS GAA-FGF14 repeat expansion was screened in an undiagnosed LOCA cohort (n = 664) and variations in repeat-length were analyzed in families of confirmed GAA-FGF14 ataxia patients. Brain magnetic resonance imaging (MRI) was used to evaluate the radiological feature in GAA-FGF14 ataxia patients. Clinical examinations and sympathetic skin response (SSR) recordings in GAA-FGF14 patients (n = 16) were used to quantify sympathetic nerve involvement. RESULTS Two unrelated probands (2/664) were identified. Genetic screening for GAA-FGF14 repeat expansion was performed in 39 family members, 16 of whom were genetically diagnosed with GAA-FGF14 ataxia. Familial screening revealed expansion of GAA repeats in maternal transmissions, but contraction upon paternal transmission. Brain MRI showed slight to moderate cerebellar atrophy. SSR amplitude was lower in GAA-FGF14 patients in pre-symptomatic stage compared to healthy controls, and further decreased in the symptomatic stage. CONCLUSIONS GAA-FGF14 ataxia was rare among Chinese LOCA cases. Parental gender appears to affect variability in GAA repeat number between generations. Reduced SSR amplitude is a prominent feature in GAA-FGF14 patients, even in the pre-symptomatic stage.
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Affiliation(s)
- Ze-Hong Zheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Chun-Yan Cao
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Bi Cheng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Ru-Ying Yuan
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Yi-Heng Zeng
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Zhang-Bao Guo
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Yu-Sen Qiu
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wen-Qi Lv
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Hui Liang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Jin-Lan Li
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wei-Xiong Zhang
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Min-Kun Fang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Yu-Hao Sun
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wei Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Jing-Mei Hong
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shi-Rui Gan
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Gan-Qin Du
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China.
| | - Ling Fang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
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22
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Parasrampuria MA, White AA, Chilamkurthy R, Pater AA, El-Azzouzi F, Ovington KN, Jensik PJ, Gagnon KT. Sequencing-guided design of genetically encoded small RNAs targeting CAG repeats for selective inhibition of mutant huntingtin. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102206. [PMID: 38803421 PMCID: PMC11129097 DOI: 10.1016/j.omtn.2024.102206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Huntington's disease (HD) is an incurable neurodegenerative disorder caused by genetic expansion of a CAG repeat sequence in one allele of the huntingtin (HTT) gene. Reducing expression of the mutant HTT (mutHTT) protein has remained a clear therapeutic goal, but reduction of wild-type HTT (wtHTT) is undesirable, as it compromises gene function and potential therapeutic efficacy. One promising allele-selective approach involves targeting the CAG repeat expansion with steric binding small RNAs bearing central mismatches. However, successful genetic encoding requires consistent placement of mismatches to the target within the small RNA guide sequence, which involves 5' processing precision by cellular enzymes. Here, we used small RNA sequencing (RNA-seq) to monitor the processing precision of a limited set of CAG repeat-targeted small RNAs expressed from multiple scaffold contexts. Small RNA-seq identified expression constructs with high-guide strand 5' processing precision and promising allele-selective inhibition of mutHTT. Transcriptome-wide mRNA-seq also identified an allele-selective small RNA with a favorable off-target profile. These results support continued investigation and optimization of genetically encoded repeat-targeted small RNAs for allele-selective HD gene therapy and underscore the value of sequencing methods to balance specificity with allele selectivity during the design and selection process.
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Affiliation(s)
- Mansi A. Parasrampuria
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Adam A. White
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Ramadevi Chilamkurthy
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Adrian A. Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA
| | - Fatima El-Azzouzi
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Katy N. Ovington
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Philip J. Jensik
- Division of Physiology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Keith T. Gagnon
- Division of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA
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23
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Kojak N, Kuno J, Fittipaldi KE, Khan A, Wenger D, Glasser M, Donnianni RA, Tang Y, Zhang J, Huling K, Ally R, Mujica AO, Turner T, Magardino G, Huang PY, Kerk SY, Droguett G, Prissette M, Rojas J, Gomez T, Gagliardi A, Hunt C, Rabinowitz JS, Gong G, Poueymirou W, Chiao E, Zambrowicz B, Siao CJ, Kajimura D. Somatic and intergenerational G4C2 hexanucleotide repeat instability in a human C9orf72 knock-in mouse model. Nucleic Acids Res 2024; 52:5732-5755. [PMID: 38597682 PMCID: PMC11162798 DOI: 10.1093/nar/gkae250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Expansion of a G4C2 repeat in the C9orf72 gene is associated with familial Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). To investigate the underlying mechanisms of repeat instability, which occurs both somatically and intergenerationally, we created a novel mouse model of familial ALS/FTD that harbors 96 copies of G4C2 repeats at a humanized C9orf72 locus. In mouse embryonic stem cells, we observed two modes of repeat expansion. First, we noted minor increases in repeat length per expansion event, which was dependent on a mismatch repair pathway protein Msh2. Second, we found major increases in repeat length per event when a DNA double- or single-strand break (DSB/SSB) was artificially introduced proximal to the repeats, and which was dependent on the homology-directed repair (HDR) pathway. In mice, the first mode primarily drove somatic repeat expansion. Major changes in repeat length, including expansion, were observed when SSB was introduced in one-cell embryos, or intergenerationally without DSB/SSB introduction if G4C2 repeats exceeded 400 copies, although spontaneous HDR-mediated expansion has yet to be identified. These findings provide a novel strategy to model repeat expansion in a non-human genome and offer insights into the mechanism behind C9orf72 G4C2 repeat instability.
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Affiliation(s)
- Nada Kojak
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Junko Kuno
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - David Wenger
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Yajun Tang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jade Zhang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Katie Huling
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Roxanne Ally
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | - Pei Yi Huang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Sze Yen Kerk
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Jose Rojas
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Guochun Gong
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Eric Chiao
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
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24
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Hwang HY, Gim D, Yi H, Jung H, Lee J, Kim D. Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor. Nucleic Acids Res 2024; 52:5792-5803. [PMID: 38661210 PMCID: PMC11162781 DOI: 10.1093/nar/gkae310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Nucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor-mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications.
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Affiliation(s)
- Hye-Yeon Hwang
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Dongmin Gim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hwalin Yi
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyewon Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biohealth Regulatory Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Daesik Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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25
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Mouro Pinto R, Murtha R, Azevedo A, Douglas C, Kovalenko M, Ulloa J, Crescenti S, Burch Z, Oliver E, Vitalo A, Mota-Silva E, Riggs MJ, Correia K, Elezi E, Demelo B, Carroll JB, Gillis T, Gusella JF, MacDonald ME, Wheeler VC. Identification of genetic modifiers of Huntington's disease somatic CAG repeat instability by in vivo CRISPR-Cas9 genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.597823. [PMID: 38895438 PMCID: PMC11185783 DOI: 10.1101/2024.06.08.597823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Huntington's disease (HD), one of >50 inherited repeat expansion disorders (Depienne and Mandel, 2021), is a dominantly-inherited neurodegenerative disease caused by a CAG expansion in HTT (The Huntington's Disease Collaborative Research Group, 1993). Inherited CAG repeat length is the primary determinant of age of onset, with human genetic studies underscoring that the property driving disease is the CAG length-dependent propensity of the repeat to further expand in brain (Swami et al ., 2009; GeM-HD, 2015; Hensman Moss et al ., 2017; Ciosi et al ., 2019; GeM-HD, 2019; Hong et al ., 2021). Routes to slowing somatic CAG expansion therefore hold great promise for disease-modifying therapies. Several DNA repair genes, notably in the mismatch repair (MMR) pathway, modify somatic expansion in HD mouse models (Wheeler and Dion, 2021). To identify novel modifiers of somatic expansion, we have used CRISPR-Cas9 editing in HD knock-in mice to enable in vivo screening of expansion-modifier candidates at scale. This has included testing of HD onset modifier genes emerging from human genome-wide association studies (GWAS), as well as interactions between modifier genes, thereby providing new insight into pathways underlying CAG expansion and potential therapeutic targets.
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26
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Zhang M. STRAS:a snakemake pipeline for genome-wide short tandem repeats annotation and score. Hum Genet 2024; 143:735-738. [PMID: 38507015 DOI: 10.1007/s00439-024-02662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
High-throughput whole genome sequencing (WGS) is clinically used in finding single nucleotide variants and small indels. Several bioinformatics tools are developed to call short tandem repeats (STRs) copy numbers from WGS data, such as ExpansionHunter denovo, GangSTR and HipSTR. However, expansion disorders are rare and it is hard to find candidate expansions in single patient sequencing data with ~ 800,000 STRs calls. In this paper I describe a snakemake pipeline for genome-wide STRs Annotation and Score (STRAS) using a Random Forest (RF) model to predict pathogenicity. The predictor was validated by benchmark data from Clinvar and PUBMED. True positive rate was 93.8%. True negative rate was 98.0%.Precision was 98.6% and recall rate was 93.8%. F1-score was 0.961. Sensitivity was 93.8% and specificity was 99.6%. These results showed STRAS could be a useful tool for clinical researchers to find STR loci of interest and filter out neutral STRs. STRAS is freely available at https://github.com/fancheyu5/STRAS .
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Affiliation(s)
- Mengna Zhang
- Molecular Diagnosis Center, The Affiliated Hospital of Chengde Medical University, Chengde, 067000, China.
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27
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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28
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Milovanović A, Dragaševic‐Mišković N, Thomsen M, Borsche M, Hinrichs F, Westenberger A, Klein C, Brüggemann N, Branković M, Marjanović A, Svetel M, Kostić VS, Lohmann K. RFC1 and FGF14 Repeat Expansions in Serbian Patients with Cerebellar Ataxia. Mov Disord Clin Pract 2024; 11:626-633. [PMID: 38487929 PMCID: PMC11145142 DOI: 10.1002/mdc3.14020] [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: 10/06/2023] [Revised: 01/26/2024] [Accepted: 02/21/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND The newly discovered intronic repeat expansions in the genes encoding replication factor C subunit 1 (RFC1) and fibroblast growth factor 14 (FGF14) frequently cause late-onset cerebellar ataxia. OBJECTIVES To investigate the presence of RFC1 and FGF14 pathogenic repeat expansions in Serbian patients with adult-onset cerebellar ataxia. METHODS The study included 167 unrelated patients with sporadic or familial cerebellar ataxia. The RFC1 repeat expansion analysis was performed by duplex PCR and Sanger sequencing, while the FGF14 repeat expansion was tested for by long-range PCR, repeat-primed PCR, and Sanger sequencing. RESULTS We identified pathogenic repeat expansions in RFC1 in seven patients (7/167; 4.2%) with late-onset sporadic ataxia with neuropathy and chronic cough. Two patients also had bilateral vestibulopathy. Repeat expansions in FGF14 were found in nine unrelated patients (9/167; 5.4%) with ataxia, less than half of whom presented with neuropathy and two-thirds with global brain atrophy. Tremor and episodic features were the most frequent additional characteristics in carriers of uninterrupted FGF14 repeat expansions. Among the 122 sporadic cases, 12 (9.8%) carried an expansion in either RFC1 or FGF14, comparable to 4/45 (8.9%) among the patients with a positive family history. CONCLUSIONS Pathogenic repeat expansions in RFC1 and FGF14 are relatively frequent causes of adult-onset cerebellar ataxia, especially among sporadic patients, indicating that family history should not be considered when prioritizing ataxia patients for testing of RFC1 or FGF14 repeat expansions.
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Affiliation(s)
| | - Nataša Dragaševic‐Mišković
- Neurology ClinicUniversity Clinical Center of SerbiaBelgradeSerbia
- Medical FacultyUniversity BelgradeBelgradeSerbia
| | - Mirja Thomsen
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Max Borsche
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
- Department of NeurologyUniversity of Lübeck and University Hospital Schleswig‐Holstein, Campus LübeckLübeckGermany
| | | | | | | | - Norbert Brüggemann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
- Department of NeurologyUniversity of Lübeck and University Hospital Schleswig‐Holstein, Campus LübeckLübeckGermany
| | - Marija Branković
- Neurology ClinicUniversity Clinical Center of SerbiaBelgradeSerbia
| | - Ana Marjanović
- Neurology ClinicUniversity Clinical Center of SerbiaBelgradeSerbia
| | - Marina Svetel
- Neurology ClinicUniversity Clinical Center of SerbiaBelgradeSerbia
- Medical FacultyUniversity BelgradeBelgradeSerbia
| | - Vladimir S. Kostić
- Neurology ClinicUniversity Clinical Center of SerbiaBelgradeSerbia
- Medical FacultyUniversity BelgradeBelgradeSerbia
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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29
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Charlet-Berguerand N. An unexpected polyglycine route to spinocerebellar ataxia. Nat Genet 2024; 56:1039-1041. [PMID: 38811843 DOI: 10.1038/s41588-024-01770-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Affiliation(s)
- Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U-1258, CNRS UMR-7104, University of Strasbourg, Illkirch, France.
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30
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Zhang Y, Liu X, Li Z, Li H, Miao Z, Wan B, Xu X. Advances on the Mechanisms and Therapeutic Strategies in Non-coding CGG Repeat Expansion Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04239-9. [PMID: 38780719 DOI: 10.1007/s12035-024-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Non-coding CGG repeat expansions within the 5' untranslated region are implicated in a range of neurological disorders, including fragile X-associated tremor/ataxia syndrome, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. This review outlined the general characteristics of diseases associated with non-coding CGG repeat expansions, detailing their clinical manifestations and neuroimaging patterns, which often overlap and indicate shared pathophysiological traits. We summarized the underlying molecular mechanisms of these disorders, providing new insights into the roles that DNA, RNA, and toxic proteins play. Understanding these mechanisms is crucial for the development of targeted therapeutic strategies. These strategies include a range of approaches, such as antisense oligonucleotides, RNA interference, genomic DNA editing, small molecule interventions, and other treatments aimed at correcting the dysregulated processes inherent in these disorders. A deeper understanding of the shared mechanisms among non-coding CGG repeat expansion disorders may hold the potential to catalyze the development of innovative therapies, ultimately offering relief to individuals grappling with these debilitating neurological conditions.
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Affiliation(s)
- Yutong Zhang
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Xuan Liu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Zeheng Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Hao Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
- Department of Neurology, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215124, China
| | - Zhigang Miao
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Bo Wan
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Xingshun Xu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China.
- The Institute of Neuroscience, Soochow University, Suzhou City, China.
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
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31
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Hiatt L, Weisburd B, Dolzhenko E, VanNoy GE, Kurtas EN, Rehm HL, Quinlan A, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307682. [PMID: 38826469 PMCID: PMC11142282 DOI: 10.1101/2024.05.21.24307682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Approximately 3% of the human genome consists of repetitive elements called tandem repeats (TRs), which include short tandem repeats (STRs) of 1-6bp motifs and variable number tandem repeats (VNTRs) of 7+bp motifs. TR variants contribute to several dozen mono- and polygenic diseases but remain understudied and "enigmatic," particularly relative to single nucleotide variants. It remains comparatively challenging to interpret the clinical significance of TR variants. Although existing resources provide portions of necessary data for interpretation at disease-associated loci, it is currently difficult or impossible to efficiently invoke the additional details critical to proper interpretation, such as motif pathogenicity, disease penetrance, and age of onset distributions. It is also often unclear how to apply population information to analyses. We present STRchive (S-T-archive, http://strchive.org/ ), a dynamic resource consolidating information on TR disease loci in humans from research literature, up-to-date clinical resources, and large-scale genomic databases, with the goal of streamlining TR variant interpretation at disease-associated loci. We apply STRchive -including pathogenic thresholds, motif classification, and clinical phenotypes-to a gnomAD cohort of ∼18.5k individuals genotyped at 60 disease-associated loci. Through detailed literature curation, we demonstrate that the majority of TR diseases affect children despite being thought of as adult diseases. Additionally, we show that pathogenic genotypes can be found within gnomAD which do not necessarily overlap with known disease prevalence, and leverage STRchive to interpret locus-specific findings therein. We apply a diagnostic blueprint empowered by STRchive to relevant clinical vignettes, highlighting possible pitfalls in TR variant interpretation. As a living resource, STRchive is maintained by experts, takes community contributions, and will evolve as understanding of TR diseases progresses.
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32
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Nguyen L. Updates on Disease Mechanisms and Therapeutics for Amyotrophic Lateral Sclerosis. Cells 2024; 13:888. [PMID: 38891021 PMCID: PMC11172142 DOI: 10.3390/cells13110888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is a motor neuron disease. In ALS, upper and lower motor neurons in the brain and spinal cord progressively degenerate during the course of the disease, leading to the loss of the voluntary movement of the arms and legs. Since its first description in 1869 by a French neurologist Jean-Martin Charcot, the scientific discoveries on ALS have increased our understanding of ALS genetics, pathology and mechanisms and provided novel therapeutic strategies. The goal of this review article is to provide a comprehensive summary of the recent findings on ALS mechanisms and related therapeutic strategies to the scientific audience. Several highlighted ALS research topics discussed in this article include the 2023 FDA approved drug for SOD1 ALS, the updated C9orf72 GGGGCC repeat-expansion-related mechanisms and therapeutic targets, TDP-43-mediated cryptic splicing and disease markers and diagnostic and therapeutic options offered by these recent discoveries.
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Affiliation(s)
- Lien Nguyen
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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33
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Sasako T, Ilboudo Y, Liang KYH, Chen Y, Yoshiji S, Richards JB. The influence of trinucleotide repeats in the androgen receptor gene on androgen-related traits and diseases. J Clin Endocrinol Metab 2024:dgae302. [PMID: 38701087 DOI: 10.1210/clinem/dgae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/05/2024]
Abstract
CONTEXT Trinucleotide repeats in the androgen receptor have been proposed to influence testosterone signaling in men, but the clinical relevance of these trinucleotide repeats remains controversial. OBJECTIVE To examine how androgen receptor trinucleotide repeat lengths affect androgen-related traits and disease risks and whether they influence the clinical importance of circulating testosterone levels. METHODS We quantified CAG and GGC repeat lengths in the androgen receptor (AR) gene of European-ancestry male participants in UK Biobank from whole-genome and whole-exome sequence data using ExpansionHunter, and tested associations with androgen-related traits and diseases. We also examined whether the associations between testosterone levels and these outcomes were affected by adjustment for the repeat lengths. RESULTS We successfully quantified the repeat lengths from whole-genome and/or whole-exome sequence data in 181,217 males. Both repeat lengths were shown to be positively associated with circulating total testosterone level and bone mineral density, whereas CAG repeat length was negatively associated with male-pattern baldness, but their effects were relatively small and were not associated with most of the other outcomes. Circulating total testosterone level was associated with various outcomes, but this relationship was not affected by adjustment for the repeat lengths. CONCLUSION In this large-scale study, we found that longer CAG and GGC repeats in the AR gene influence androgen resistance, elevate circulating testosterone level via a feedback loop and play a role in some androgen-targeted tissues. Generally, however, circulating testosterone level is a more important determinant of androgen action in males than repeat lengths.
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Affiliation(s)
- Takayoshi Sasako
- McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Tanaka Diabetes Clinic Omiya, Saitama, Japan
| | - Yann Ilboudo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Québec, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Five Prime Sciences Inc, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King's College London, London, UK
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Van Deynze K, Mumm C, Maltby CJ, Switzenberg JA, Todd PK, Boyle AP. Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306681. [PMID: 38746091 PMCID: PMC11092683 DOI: 10.1101/2024.05.01.24306681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization of disease-associated repeat loci remains resource intensive and often lacks high resolution genotype calls. We introduce a multiplexed, targeted nanopore sequencing panel and HMMSTR, a sequence-based tandem repeat copy number caller. HMMSTR outperforms current signal- and sequence-based callers relative to two assemblies and we show it performs with high accuracy in heterozygous regions and at low read coverage. The flexible panel allows us to capture disease associated regions at an average coverage of >150x. Using these tools, we successfully characterize known or suspected repeat expansions in patient derived samples. In these samples we also identify unexpected expanded alleles at tandem repeat loci not previously associated with the underlying diagnosis. This genotyping approach for tandem repeat expansions is scalable, simple, flexible, and accurate, offering significant potential for diagnostic applications and investigation of expansion co-occurrence in neurodegenerative disorders. Abstract Figure
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35
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Currò R, Dominik N, Facchini S, Vegezzi E, Sullivan R, Galassi Deforie V, Fernández-Eulate G, Traschütz A, Rossi S, Garibaldi M, Kwarciany M, Taroni F, Brusco A, Good JM, Cavalcanti F, Hammans S, Ravenscroft G, Roxburgh RH, Parolin Schnekenberg R, Rugginini B, Abati E, Manini A, Quartesan I, Ghia A, Lòpez de Munaìn A, Manganelli F, Kennerson M, Santorelli FM, Infante J, Marques W, Jokela M, Murphy SM, Mandich P, Fabrizi GM, Briani C, Gosal D, Pareyson D, Ferrari A, Prados F, Yousry T, Khurana V, Kuo SH, Miller J, Troakes C, Jaunmuktane Z, Giunti P, Hartmann A, Basak N, Synofzik M, Stojkovic T, Hadjivassiliou M, Reilly MM, Houlden H, Cortese A. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 2024; 147:1887-1898. [PMID: 38193360 PMCID: PMC11068103 DOI: 10.1093/brain/awad436] [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: 10/06/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson's coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P < 0.001; larger allele HR = 1.53, P < 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P < 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P < 0.001; larger allele HR = 1.60; P < 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P < 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I-V β = -1.06, P < 0.001; lobules VI-VII β = -0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
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Affiliation(s)
- Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stefano Facchini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Gorka Fernández-Eulate
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Andreas Traschütz
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Salvatore Rossi
- Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Facoltà di Medicina e Chirurgia, Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Center, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sant'Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdańsk, 80-952 Gdańsk, Poland
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy
| | - Simon Hammans
- Wessex Neurological Centre, Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedland, WA 6009, Australia
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, New Zealand and the Centre for Brain Research, University of Auckland, Auckland 1142, New Zealand
| | | | - Bianca Rugginini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Arianna Manini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Arianna Ghia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Adolfo Lòpez de Munaìn
- Neurology Department, Donostia University Hospital, University of the Basque Country-Osakidetza-CIBERNED-Biodonostia, 20014 Donostia-San Sebastián, Spain
| | - Fiore Manganelli
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Marina Kennerson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, 56128 Pisa, Italy
| | - Jon Infante
- University Hospital Marquès de Valdecilla-IDIVAL, University of Cantabria, 39008 Santander, Spain
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University of São Paulo, 2650 Ribeirão Preto, Brazil
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland
- Neurocenter, Department of Neurology, Clinical Neurosciences, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino-UOC Genetica Medica, 16132 Genova, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Chiara Briani
- Department of Neurosciences, ERN Neuromuscular Unit, University of Padova, 35100 Padova, Italy
| | - David Gosal
- Manchester Centre for Clinical Neurosciences, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Greater Manchester, M6 8HD, UK
| | - Davide Pareyson
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Ferran Prados
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, WC1V 6LJ, UK
- NMR Research Unit, Institute of Neurology, University College London (UCL), London, WC1N 3BG, UK
- e-Health Centre, Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Tarek Yousry
- Neuroradiological Academic Unit, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James Miller
- Department of Neurology, Royal Victoria Hospitals, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE21 8EA, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paola Giunti
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Annette Hartmann
- Division of General Psychiatry, Medical University of Vienna, 1090 Vienna, Austria
| | - Nazli Basak
- Koç University, School of Medicine, Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine, 34010 Istanbul, Turkey
| | - Matthis Synofzik
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Tanya Stojkovic
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, S10 2JF, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
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Bhattacharyya N, Chai N, Hafford-Tear NJ, Sadan AN, Szabo A, Zarouchlioti C, Jedlickova J, Leung SK, Liao T, Dudakova L, Skalicka P, Parekh M, Moghul I, Jeffries AR, Cheetham ME, Muthusamy K, Hardcastle AJ, Pontikos N, Liskova P, Tuft SJ, Davidson AE. Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease. PLoS Genet 2024; 20:e1011230. [PMID: 38713708 PMCID: PMC11101122 DOI: 10.1371/journal.pgen.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/17/2024] [Accepted: 03/19/2024] [Indexed: 05/09/2024] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) is an age-related cause of vision loss, and the most common repeat expansion-mediated disease in humans characterised to date. Up to 80% of European FECD cases have been attributed to expansion of a non-coding CTG repeat element (termed CTG18.1) located within the ubiquitously expressed transcription factor encoding gene, TCF4. The non-coding nature of the repeat and the transcriptomic complexity of TCF4 have made it extremely challenging to experimentally decipher the molecular mechanisms underlying this disease. Here we comprehensively describe CTG18.1 expansion-driven molecular components of disease within primary patient-derived corneal endothelial cells (CECs), generated from a large cohort of individuals with CTG18.1-expanded (Exp+) and CTG 18.1-independent (Exp-) FECD. We employ long-read, short-read, and spatial transcriptomic techniques to interrogate expansion-specific transcriptomic biomarkers. Interrogation of long-read sequencing and alternative splicing analysis of short-read transcriptomic data together reveals the global extent of altered splicing occurring within Exp+ FECD, and unique transcripts associated with CTG18.1-expansions. Similarly, differential gene expression analysis highlights the total transcriptomic consequences of Exp+ FECD within CECs. Furthermore, differential exon usage, pathway enrichment and spatial transcriptomics reveal TCF4 isoform ratio skewing solely in Exp+ FECD with potential downstream functional consequences. Lastly, exome data from 134 Exp- FECD cases identified rare (minor allele frequency <0.005) and potentially deleterious (CADD>15) TCF4 variants in 7/134 FECD Exp- cases, suggesting that TCF4 variants independent of CTG18.1 may increase FECD risk. In summary, our study supports the hypothesis that at least two distinct pathogenic mechanisms, RNA toxicity and TCF4 isoform-specific dysregulation, both underpin the pathophysiology of FECD. We anticipate these data will inform and guide the development of translational interventions for this common triplet-repeat mediated disease.
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Affiliation(s)
- Nihar Bhattacharyya
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Niuzheng Chai
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Amanda N. Sadan
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Anita Szabo
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Jana Jedlickova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Szi Kay Leung
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Tianyi Liao
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Mohit Parekh
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Ismail Moghul
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Aaron R. Jeffries
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michael E. Cheetham
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Alison J. Hardcastle
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Nikolas Pontikos
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Stephen J. Tuft
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Alice E. Davidson
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
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Leitão E, Schröder C, Depienne C. Identification and characterization of repeat expansions in neurological disorders: Methodologies, tools, and strategies. Rev Neurol (Paris) 2024; 180:383-392. [PMID: 38594146 DOI: 10.1016/j.neurol.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Tandem repeats are a common, highly polymorphic class of variation in human genomes. Their expansion beyond a pathogenic threshold is a process that contributes to a wide range of neurological and neuromuscular genetic disorders, of which over 60 have been identified to date. The last few years have seen a resurgence in repeat expansion discovery propelled by technological advancements, enabling the identification of over 20 novel repeat expansion disorders. These expansions can occur in coding or non-coding regions of genes, resulting in a range of pathogenic mechanisms. In this article, we review strategies, tools and methods that can be used for efficient detection and characterization of known repeat expansions and identification of new expansion disorders. Features that can be used to prioritize repeat expansions include anticipation, which is characterized by increased severity or earlier onset of symptoms across generations, and founder effects, which contribute to higher prevalence rates in certain populations. Classical technologies such as Southern blotting, repeat-primed polymerase chain reaction (PCR) and long-range PCR can still be used to detect known repeat expansions, although they usually have significant limitations linked to the absence of sequence context. Targeted sequencing of known expansions using either long-range PCR or CRISPR-Cas9 enrichment combined with long-read sequencing or adaptive nanopore sampling are usually better but more expensive alternatives. The development of new bioinformatics tools applied to short-read genome data can now be used to detect repeat expansions either in a targeted manner or at the genome-wide level. In addition, technological advances, particularly long-read technologies such as optical genome mapping (Bionano Genomics), Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) HiFi sequencing, offer promising avenues for the detection of repeat expansions. Despite challenges in specific DNA extraction requirements, computation resources needed and data interpretation, these technologies have an immense potential to advance our understanding of repeat expansion disorders and improve diagnostic accuracy.
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Affiliation(s)
- E Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - C Schröder
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - C Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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Yoon JG, Lee S, Cho J, Kim N, Kim S, Kim MJ, Kim SY, Moon J, Chae JH. Diagnostic uplift through the implementation of short tandem repeat analysis using exome sequencing. Eur J Hum Genet 2024; 32:584-587. [PMID: 38308084 PMCID: PMC11061289 DOI: 10.1038/s41431-024-01542-w] [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: 09/14/2023] [Revised: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024] Open
Abstract
To date, approximately 50 short tandem repeat (STR) disorders have been identified; yet, clinical laboratories rarely conduct STR analysis on exomes. To assess its diagnostic value, we analyzed STRs in 6099 exomes from 2510 families with mostly suspected neurogenetic disorders. We employed ExpansionHunter and REViewer to detect pathogenic repeat expansions, confirming them using orthogonal methods. Genotype-phenotype correlations led to the diagnosis of thirteen individuals in seven previously undiagnosed families, identifying three autosomal dominant disorders: dentatorubral-pallidoluysian atrophy (n = 3), spinocerebellar ataxia type 7 (n = 2), and myotonic dystrophy type 1 (n = 2), resulting in a diagnostic gain of 0.28% (7/2510). Additionally, we found expanded ATXN1 alleles (≥39 repeats) with varying patterns of CAT interruptions in twelve individuals, accounting for approximately 0.19% in the Korean population. Our study underscores the importance of integrating STR analysis into exome sequencing pipeline, broadening the application of exome sequencing for STR assessments.
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Affiliation(s)
- Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jaeso Cho
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sheehyun Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Neurology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea.
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Sureshkumar S, Bandaranayake C, Lv J, Dent CI, Bhagat PK, Mukherjee S, Sarwade R, Atri C, York HM, Tamizhselvan P, Shamaya N, Folini G, Bergey BG, Yadav AS, Kumar S, Grummisch OS, Saini P, Yadav RK, Arumugam S, Rosonina E, Sadanandom A, Liu H, Balasubramanian S. SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana. NATURE PLANTS 2024; 10:749-759. [PMID: 38641663 DOI: 10.1038/s41477-024-01672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me2/3. Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me3 to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing.
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Affiliation(s)
- Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia.
| | - Champa Bandaranayake
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Junqing Lv
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Craig I Dent
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Sourav Mukherjee
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Rucha Sarwade
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Chhaya Atri
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Harrison M York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prashanth Tamizhselvan
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Giulia Folini
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Subhasree Kumar
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Oliver S Grummisch
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Prince Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Ram K Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- European Molecular Biology Laboratory, Australia (EMBL Australia), Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Ari Sadanandom
- Department of Biosciences, Durham University, Durham, UK
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nat Biotechnol 2024:10.1038/s41587-024-02225-z. [PMID: 38671154 DOI: 10.1038/s41587-024-02225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes. However, they are often excluded from at-scale studies because of challenges with variant calling and representation, as well as a lack of a genome-wide standard. Here, to promote the development of TR methods, we created a catalog of TR regions and explored TR properties across 86 haplotype-resolved long-read human assemblies. We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 'truth-set' TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies.
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Affiliation(s)
- Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | | | - Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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41
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Cui Y, Ye W, Li JS, Li JJ, Vilain E, Sallam T, Li W. A genome-wide spectrum of tandem repeat expansions in 338,963 humans. Cell 2024; 187:2336-2341.e5. [PMID: 38582080 PMCID: PMC11065452 DOI: 10.1016/j.cell.2024.03.004] [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: 09/08/2023] [Revised: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/08/2024]
Abstract
The Genome Aggregation Database (gnomAD), widely recognized as the gold-standard reference map of human genetic variation, has largely overlooked tandem repeat (TR) expansions, despite the fact that TRs constitute ∼6% of our genome and are linked to over 50 human diseases. Here, we introduce the TR-gnomAD (https://wlcb.oit.uci.edu/TRgnomAD), a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries (39.5% non-European samples). TR-gnomAD offers critical insights into ancestry-specific disease prevalence using disparities in TR unit number frequencies among ancestries. Moreover, TR-gnomAD is able to differentiate between common, presumably benign TR expansions, which are prevalent in TR-gnomAD, from those potentially pathogenic TR expansions, which are found more frequently in disease groups than within TR-gnomAD. Together, TR-gnomAD is an invaluable resource for researchers and physicians to interpret TR expansions in individuals with genetic diseases.
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Affiliation(s)
- Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| | - Wenbin Ye
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, Irvine, CA 92697, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA 92697, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
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Uppili B, Faruq M. STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. Database (Oxford) 2024; 2024:baae020. [PMID: 38602506 PMCID: PMC11008502 DOI: 10.1093/database/baae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/10/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Short Tandem Repeats (STRs) are genetic markers made up of repeating DNA sequences. The variations of the STRs are widely studied in forensic analysis, population studies and genetic testing for a variety of neuromuscular disorders. Understanding polymorphic STR variation and its cause is crucial for deciphering genetic information and finding links to various disorders. In this paper, we present STRIDE-DB, a novel and unique platform to explore STR Instability and its Phenotypic Relevance, and a comprehensive database of STRs in the human genome. We utilized RepeatMasker to identify all the STRs in the human genome (hg19) and combined it with frequency data from the 1000 Genomes Project. STRIDE-DB, a user-friendly resource, plays a pivotal role in investigating the relationship between STR variation, instability and phenotype. By harnessing data from genome-wide association studies (GWAS), ClinVar database, Alu loci, Haploblocks in genome and Conservation of the STRs, it serves as an important tool for researchers exploring the variability of STRs in the human genome and its direct impact on phenotypes. STRIDE-DB has its broad applicability and significance in various research domains like forensic sciences and other repeat expansion disorders. Database URL: https://stridedb.igib.res.in.
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Affiliation(s)
- Bharathram Uppili
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
- CSIR-HRDC Campus, Academy for Scientific and Innovative Research, Ghaziabad 201002, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India
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43
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Maity H, Nguyen HT, Hori N, Thirumalai D. Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. J Phys Chem Lett 2024; 15:3820-3827. [PMID: 38557079 DOI: 10.1021/acs.jpclett.3c03553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (GS) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, CS, increases, ΔGS and GS increase, which decreases the rates of dimer formation. In contrast, ΔGS for shuffled sequences, with the same length and sequence composition as (CAG)31, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.
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Affiliation(s)
- Hiranmay Maity
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung T Nguyen
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
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Kudo K, Hori K, Asamitsu S, Maeda K, Aida Y, Hokimoto M, Matsuo K, Yabuki Y, Shioda N. Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with the neurological disorder CANVAS. J Biol Chem 2024; 300:107138. [PMID: 38447794 PMCID: PMC10999818 DOI: 10.1016/j.jbc.2024.107138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Short tandem repeats are inherently unstable during DNA replication depending on repeat length, and the expansion of the repeat length in the human genome is responsible for repeat expansion disorders. Pentanucleotide AAGGG and ACAGG repeat expansions in intron 2 of the gene encoding replication factor C subunit 1 (RFC1) cause cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and other phenotypes of late-onset cerebellar ataxia. Herein, we reveal the structural polymorphism of the RFC1 repeats associated with CANVAS in vitro. Single-stranded AAGGG repeat DNA formed a hybrid-type G-quadruplex, whereas its RNA formed a parallel-type G-quadruplex with three layers. The RNA of the ACAGG repeat formed hairpin structure comprising C-G and G-C base pairs with A:A and GA:AG mismatched repeats. Furthermore, both pathogenic repeat RNAs formed more rigid structures than those of the nonpathogenic repeat RNAs. These findings provide novel insights into the structural polymorphism of the RFC1 repeats, which may be closely related to the disease mechanism of CANVAS.
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Affiliation(s)
- Kenta Kudo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Sefan Asamitsu
- Laboratory for Functional Non-coding Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Kohei Maeda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yukari Aida
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mei Hokimoto
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
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Ouyang R, Wan L, Pellerin D, Long Z, Hu J, Jiang Q, Wang C, Peng L, Peng H, He L, Qiu R, Wang J, Guo J, Shen L, Brais B, Danzi MC, Zuchner S, Tang B, Chen Z, Jiang H. The genetic landscape and phenotypic spectrum of GAA-FGF14 ataxia in China: a large cohort study. EBioMedicine 2024; 102:105077. [PMID: 38513302 PMCID: PMC10960143 DOI: 10.1016/j.ebiom.2024.105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND An intronic GAA repeat expansion in FGF14 was recently identified as a cause of GAA-FGF14 ataxia. We aimed to characterise the frequency and phenotypic profile of GAA-FGF14 ataxia in a large Chinese ataxia cohort. METHODS A total of 1216 patients that included 399 typical late-onset cerebellar ataxia (LOCA), 290 early-onset cerebellar ataxia (EOCA), and 527 multiple system atrophy with predominant cerebellar ataxia (MSA-c) were enrolled. Long-range and repeat-primed PCR were performed to screen for GAA expansions in FGF14. Targeted long-read and whole-genome sequencing were performed to determine repeat size and sequence configuration. A multi-modal study including clinical assessment, MRI, and neurofilament light chain was conducted for disease assessment. FINDINGS 17 GAA-FGF14 positive patients with a (GAA)≥250 expansion (12 patients with a GAA-pure expansion, five patients with a (GAA)≥250-[(GAA)n (GCA)m]z expansion) and two possible patients with biallelic (GAA)202/222 alleles were identified. The clinical phenotypes of the 19 positive and possible positive cases covered LOCA phenotype, EOCA phenotype and MSA-c phenotype. Five of six patients with EOCA phenotype were found to have another genetic disorder. The NfL levels of patients with EOCA and MSA-c phenotypes were significantly higher than patients with LOCA phenotype and age-matched controls (p < 0.001). NfL levels of pre-ataxic GAA-FGF14 positive individuals were lower than pre-ataxic SCA3 (p < 0.001) and similar to controls. INTERPRETATION The frequency of GAA-FGF14 expansion in a large Chinese LOCA cohort was low (1.3%). Biallelic (GAA)202/222 alleles and co-occurrence with other acquired or hereditary diseases may contribute to phenotypic variation and different progression. FUNDING This study was funded by the National Key R&D Program of China (2021YFA0805200 to H.J.), the National Natural Science Foundation of China (81974176 and 82171254 to H.J.; 82371272 to Z.C.; 82301628 to L.W.; 82301438 to Z.L.; 82201411 to L.H.), the Innovation Research Group Project of Natural Science Foundation of Hunan Province (2020JJ1008 to H.J.), the Key Research and Development Program of Hunan Province (2020SK2064 to H.J.), the Innovative Research and Development Program of Development and Reform Commission of Hunan Province to H.J., the Natural Science Foundation of Hunan Province (2024JJ3050 to H.J.; 2022JJ20094 and 2021JJ40974 to Z.C.; 2022JJ40783 to L.H.; 2022JJ40703 to Z.L.), the Project Program of National Clinical Research Center for Geriatric Disorders (Xiangya Hospital, 2020LNJJ12 to H.J.), the Central South University Research Programme of Advanced Interdisciplinary Study (2023QYJC010 to H.J.) and the Science and Technology Innovation Program of Hunan Province (2022RC1027 to Z.C.). D.P. holds a Fellowship award from the Canadian Institutes of Health Research (CIHR).
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Affiliation(s)
- Riwei Ouyang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - David Pellerin
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and the National Hospital for Neurology and Neurosurgery, University College London, London, United Kingdom
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Jian Hu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Qian Jiang
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linliu Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Huirong Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lang He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, China; Bioinformatics Center & National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China; Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China; National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China; Furong Laboratory, Central South University, Changsha, Hunan, 410008, China; Brain Research Center, Central South University, Changsha, Hunan, 410008, China.
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Fehlings DL, Zarrei M, Engchuan W, Sondheimer N, Thiruvahindrapuram B, MacDonald JR, Higginbotham EJ, Thapa R, Behlim T, Aimola S, Switzer L, Ng P, Wei J, Danthi PS, Pellecchia G, Lamoureux S, Ho K, Pereira SL, de Rijke J, Sung WWL, Mowjoodi A, Howe JL, Nalpathamkalam T, Manshaei R, Ghaffari S, Whitney J, Patel RV, Hamdan O, Shaath R, Trost B, Knights S, Samdup D, McCormick A, Hunt C, Kirton A, Kawamura A, Mesterman R, Gorter JW, Dlamini N, Merico D, Hilali M, Hirschfeld K, Grover K, Bautista NX, Han K, Marshall CR, Yuen RKC, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Maxwell G, Shevell M, Costain G, Michaud JL, Hamdan FF, Gauthier J, Uguen K, Stavropoulos DJ, Wintle RF, Oskoui M, Scherer SW. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy. Nat Genet 2024; 56:585-594. [PMID: 38553553 DOI: 10.1038/s41588-024-01686-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
We performed whole-genome sequencing (WGS) in 327 children with cerebral palsy (CP) and their biological parents. We classified 37 of 327 (11.3%) children as having pathogenic/likely pathogenic (P/LP) variants and 58 of 327 (17.7%) as having variants of uncertain significance. Multiple classes of P/LP variants included single-nucleotide variants (SNVs)/indels (6.7%), copy number variations (3.4%) and mitochondrial mutations (1.5%). The COL4A1 gene had the most P/LP SNVs. We also analyzed two pediatric control cohorts (n = 203 trios and n = 89 sib-pair families) to provide a baseline for de novo mutation rates and genetic burden analyses, the latter of which demonstrated associations between de novo deleterious variants and genes related to the nervous system. An enrichment analysis revealed previously undescribed plausible candidate CP genes (SMOC1, KDM5B, BCL11A and CYP51A1). A multifactorial CP risk profile and substantial presence of P/LP variants combine to support WGS in the diagnostic work-up across all CP and related phenotypes.
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Affiliation(s)
- Darcy L Fehlings
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Neal Sondheimer
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ritesh Thapa
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Tarannum Behlim
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sabrina Aimola
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Lauren Switzer
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Pamela Ng
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Prakroothi S Danthi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jill de Rijke
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mowjoodi
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roozbeh Manshaei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shannon Knights
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Dawa Samdup
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
| | - Anna McCormick
- Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Carolyn Hunt
- Grandview Children's Centre, Oshawa, Ontario, Canada
| | - Adam Kirton
- Department of Pediatrics, Department of Clinical Neuroscience, University of Calgary, Calgary, Alberta, Canada
| | - Anne Kawamura
- Division of Developmental Paediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ronit Mesterman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Jan Willem Gorter
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Nomazulu Dlamini
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Neurosciences and Mental Health Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Deep Genomics Inc., Toronto, Ontario, Canada
- Vevo Therapeutics Inc., San Francisco, CA, USA
| | - Murto Hilali
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Hirschfeld
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kritika Grover
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nelson X Bautista
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kara Han
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan K C Yuen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piush Mandhane
- Faculty of Medicine & Dentistry, Pediatrics Department, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - George Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Michael Shevell
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Gregory Costain
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jacques L Michaud
- Departments of Pediatrics and Neurosciences, Université de Montréal, Montréal, Québec, Canada
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Julie Gauthier
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada
| | - Kevin Uguen
- CHU Sainte-Justine Azrieli Research Center, Montréal, Québec, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maryam Oskoui
- Centre for Outcomes Research and Evaluation, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Departments of Pediatrics and Department of Neurology and Neurosurgery, McGill University, Montréal, Québec, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.
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Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, Wheeler MT, Battle A. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304565. [PMID: 38585781 PMCID: PMC10996727 DOI: 10.1101/2024.03.22.24304565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.
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48
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Chen X, Zhang F, Shi Y, Wang H, Chen M, Yang D, Wang L, Liu P, Xie F, Chen J, Fu A, Hu B, Wang B, Ouyang Z, Wu S, Lin Z, Cen Z, Luo W. Origin and evolution of pentanucleotide repeat expansions at the familial cortical myoclonic tremor with epilepsy type1 - SAMD12 locus. Eur J Hum Genet 2024:10.1038/s41431-024-01586-y. [PMID: 38467733 DOI: 10.1038/s41431-024-01586-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
Familial cortical myoclonic tremor with epilepsy type 1 (FCMTE1) is caused by (TTTTA)exp(TTTCA)exp repeat expansions in SAMD12, while pure (TTTTA)exp is polymorphic. Our investigation focused on the origin and evolution of pure (TTTTA)exp and (TTTTA)exp(TTTCA)exp at this locus. We observed a founder effect between them. The phylogenetic analysis suggested that the (TTTTA)exp(TTTCA)exp might be generated from pure (TTTTA)exp through infrequent transformation events. Long-read sequencing revealed somatic generation of (TTTTA)exp(TTTCA)exp from pure (TTTTA)exp, likely via long segment (TTTCA) repeats insertion. Our findings indicate close relationships between the non-pathogenic (TTTTA)exp and the pathogenic (TTTTA)exp(TTTCA)exp, with dynamic interconversions. This sheds light on the genesis of pathogenic repeat expansions from ancestral premutation alleles. Our results may guide future studies in detecting novel repeat expansion disorders and elucidating repeat expansion mutational processes, thereby enhancing our understanding of human genomic variation.
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Affiliation(s)
- Xinhui Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Fan Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yihua Shi
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Haotian Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Miao Chen
- Department of Neurology, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Dehao Yang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Lebo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Peng Liu
- Department of Neurology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, Zhejiang, China
| | - Jiawen Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co., Ltd. Wuhan, Wuhan, 430075, China
| | - Ben Hu
- Center for Tumor Precision Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430062, China
| | - Bo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiyuan Ouyang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Sheng Wu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiru Lin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhidong Cen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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49
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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Fritz J. Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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50
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Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
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Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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