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Tajeddin N, Arabfard M, Alizadeh S, Salesi M, Khamse S, Delbari A, Ohadi M. Novel islands of GGC and GCC repeats coincide with human evolution. Gene 2024; 902:148194. [PMID: 38262548 DOI: 10.1016/j.gene.2024.148194] [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: 08/21/2023] [Revised: 10/29/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored. RESULTS In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions. CONCLUSION We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.
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Affiliation(s)
- N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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2
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [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: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Alizadeh S, Khamse S, Tajeddin N, Khorram Khorshid HR, Delbari A, Ohadi M. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 2024; 893:147968. [PMID: 37931854 DOI: 10.1016/j.gene.2023.147968] [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: 08/26/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.
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Affiliation(s)
- S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Annear DJ, Kooy RF. Unravelling the link between neurodevelopmental disorders and short tandem CGG-repeat expansions. Emerg Top Life Sci 2023; 7:265-275. [PMID: 37768318 PMCID: PMC10754333 DOI: 10.1042/etls20230021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Neurodevelopmental disorders (NDDs) encompass a diverse group of disorders characterised by impaired cognitive abilities and developmental challenges. Short tandem repeats (STRs), repetitive DNA sequences found throughout the human genome, have emerged as potential contributors to NDDs. Specifically, the CGG trinucleotide repeat has been implicated in a wide range of NDDs, including Fragile X Syndrome (FXS), the most common inherited form of intellectual disability and autism. This review focuses on CGG STR expansions associated with NDDs and their impact on gene expression through repeat expansion-mediated epigenetic silencing. We explore the molecular mechanisms underlying CGG-repeat expansion and the resulting epigenetic modifications, such as DNA hypermethylation and gene silencing. Additionally, we discuss the involvement of other CGG STRs in neurodevelopmental diseases. Several examples, including FMR1, AFF2, AFF3, XYLT1, FRA10AC1, CBL, and DIP2B, highlight the complex relationship between CGG STR expansions and NDDs. Furthermore, recent advancements in this field are highlighted, shedding light on potential future research directions. Understanding the role of STRs, particularly CGG-repeats, in NDDs has the potential to uncover novel diagnostic and therapeutic strategies for these challenging disorders.
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Affiliation(s)
- Dale J Annear
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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Panoyan MA, Wendt FR. The role of tandem repeat expansions in brain disorders. Emerg Top Life Sci 2023; 7:249-263. [PMID: 37401564 DOI: 10.1042/etls20230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
The human genome contains numerous genetic polymorphisms contributing to different health and disease outcomes. Tandem repeat (TR) loci are highly polymorphic yet under-investigated in large genomic studies, which has prompted research efforts to identify novel variations and gain a deeper understanding of their role in human biology and disease outcomes. We summarize the current understanding of TRs and their implications for human health and disease, including an overview of the challenges encountered when conducting TR analyses and potential solutions to overcome these challenges. By shedding light on these issues, this article aims to contribute to a better understanding of the impact of TRs on the development of new disease treatments.
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Affiliation(s)
- Mary Anne Panoyan
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
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Liao X, Zhu W, Zhou J, Li H, Xu X, Zhang B, Gao X. Repetitive DNA sequence detection and its role in the human genome. Commun Biol 2023; 6:954. [PMID: 37726397 PMCID: PMC10509279 DOI: 10.1038/s42003-023-05322-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Wufei Zhu
- Department of Endocrinology, Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, 443000, Yichang, P.R. China
| | - Juexiao Zhou
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Haoyang Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xiaopeng Xu
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Bin Zhang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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