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Duan R, Marafi D, Xia ZJ, Ng BG, Maroofian R, Sumya FT, Saad AK, Du H, Fatih JM, Hunter JV, Elbendary HM, Baig SM, Abdullah U, Ali Z, Efthymiou S, Murphy D, Mitani T, Withers MA, Jhangiani SN, Coban-Akdemir Z, Calame DG, Pehlivan D, Gibbs RA, Posey JE, Houlden H, Lupashin VV, Zaki MS, Freeze HH, Lupski JR. Biallelic missense variants in COG3 cause a congenital disorder of glycosylation with impairment of retrograde vesicular trafficking. J Inherit Metab Dis 2023; 46:1195-1205. [PMID: 37711075 PMCID: PMC10873070 DOI: 10.1002/jimd.12679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/16/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023]
Abstract
Biallelic variants in genes for seven out of eight subunits of the conserved oligomeric Golgi complex (COG) are known to cause recessive congenital disorders of glycosylation (CDG) with variable clinical manifestations. COG3 encodes a constituent subunit of the COG complex that has not been associated with disease traits in humans. Herein, we report two COG3 homozygous missense variants in four individuals from two unrelated consanguineous families that co-segregated with COG3-CDG presentations. Clinical phenotypes of affected individuals include global developmental delay, severe intellectual disability, microcephaly, epilepsy, facial dysmorphism, and variable neurological findings. Biochemical analysis of serum transferrin from one family showed the loss of a single sialic acid. Western blotting on patient-derived fibroblasts revealed reduced COG3 and COG4. Further experiments showed delayed retrograde vesicular recycling in patient cells. This report adds to the knowledge of the COG-CDG network by providing collective evidence for a COG3-CDG rare disease trait and implicating a likely pathology of the disorder as the perturbation of Golgi trafficking.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Zhi-Jie Xia
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Farhana Taher Sumya
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ahmed K. Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jill V. Hunter
- Department of Pediatric Radiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Hasnaa M. Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Shahid M. Baig
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
- Pakistan Science Foundation (PSF), Islamabad, Pakistan
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Zafar Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Daniel G. Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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2
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Yuan B, Liu P, Gupta A, Beck CR, Tejomurtula A, Campbell IM, Gambin T, Simmons AD, Withers MA, Harris RA, Rogers J, Schwartz DC, Lupski JR. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet 2015; 11:e1005686. [PMID: 26641089 PMCID: PMC4671654 DOI: 10.1371/journal.pgen.1005686] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022] Open
Abstract
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. Genomic instability due to the intrinsic sequence architecture of the genome, such as low copy repeats (LCRs), is a major contributor to de novo mutations that can occur in the process of human genome evolution. LCRs can mediate genomic rearrangements associated with genomic disorders by acting as substrates for nonallelic homologous recombination. Juvenile-onset nephronophthisis 1 is the most frequent genetic cause of renal failure in children. An LCR-mediated, homozygous common recurrent deletion encompassing NPHP1 is found in the majority of affected subjects, while heterozygous deletion representing the nephronophthisis 1 recessive carrier state is frequently observed amongst world populations. Interestingly, the human NPHP1 locus is located proximal to the head-to-head fusion site of two ancestral chromosomes that occurred in the great apes, which resulted in a reduction of chromosome number from 48 in nonhuman primates to the current 46 in humans. In this study, we characterized and provided evidence for the diverse genomic architecture at the NPHP1 locus and potential structural variant haplotypes in the human population. Furthermore, our analyses of primate genomes shed light on the massive changes of genomic architecture at the human NPHP1 locus and delineated a model for the emergence of the LCRs during primate evolution.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Aditya Gupta
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christine R. Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anusha Tejomurtula
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ian M. Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexandra D. Simmons
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and The UW-Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
- * E-mail:
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3
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Jensen PW, Falconi M, Kristoffersen EL, Simonsen AT, Cifuentes JB, Marcussen LB, Frøhlich R, Vagner J, Harmsen C, Juul S, Ho YP, Withers MA, Lupski JR, Koch J, Desideri A, Knudsen BR, Stougaard M. Real-time detection of TDP1 activity using a fluorophore-quencher coupled DNA-biosensor. Biosens Bioelectron 2013; 48:230-7. [PMID: 23693093 DOI: 10.1016/j.bios.2013.04.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/13/2013] [Indexed: 12/16/2022]
Abstract
Real-time detection of enzyme activities may present the easiest and most reliable way of obtaining quantitative analyses in biological samples. We present a new DNA-biosensor capable of detecting the activity of the potential anticancer drug target tyrosyl-DNA phosphodiesterase 1 (TDP1) in a very simple, high throughput, and real-time format. The biosensor is specific for Tdp1 even in complex biological samples, such as human cell extracts, and may consequently find future use in fundamental studies as well as a cancer predictive tool allowing fast analyses of diagnostic cell samples such as biopsies. TDP1 removes covalent 3'DNA adducts in DNA single-strand break repair. This enzymatic activity forms the basis of the design of the TDP1-biosensor, which consists of a short hairpin-forming oligonucleotide having a 5'fluorophore and a 3'quencher brought in close proximity by the secondary structure of the biosensor. The specific action of TDP1 removes the quencher, thereby enabling optical detection of the fluorophore. Since the enzymatic action of TDP1 is the only "signal amplification" the increase in fluorescence may easily be followed in real-time and allows quantitative analyses of TDP1 activity in pure enzyme fractions as well as in crude cell extracts. In the present study we demonstrate the specificity of the biosensor, its ability to quantitatively detect up- or down-regulated TDP1 activity, and that it may be used for measuring and for analyzing the mechanism of TDP1 inhibition.
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Affiliation(s)
- Pia W Jensen
- Department of Pathology, Aarhus University Hospital, Denmark
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4
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Sun Z, Liu P, Jia X, Withers MA, Jin L, Lupski JR, Zhang F. Replicative mechanisms of CNV formation preferentially occur as intrachromosomal events: evidence from Potocki-Lupski duplication syndrome. Hum Mol Genet 2012; 22:749-56. [PMID: 23161748 DOI: 10.1093/hmg/dds482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Copy number variations (CNVs) in the human genome contribute significantly to disease. De novo CNV mutations arise via genomic rearrangements, which can occur in 'trans', i.e. via interchromosomal events, or in 'cis', i.e. via intrachromosomal events. However, what molecular mechanisms occur between chromosomes versus between or within chromatids has not been systematically investigated. We hypothesized that distinct CNV mutational mechanisms, based on their intrinsic properties, may occur in a biased intrachromosomal versus interchromosomal manner. Here, we studied 62 genomic duplications observed in association with sporadic Potocki-Lupski syndrome (PTLS), in which multiple mutational mechanisms appear to be operative. Intriguingly, more interchromosomal than intrachromosomal events were identified in recurrent PTLS duplications mediated by non-allelic homologous recombination, whereas the reciprocal distribution was found for replicative mechanisms and non-homologous end-joining, likely reflecting the differences in spacial proximity of homologous chromosomes during different mutational processes.
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Affiliation(s)
- Zhe Sun
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
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5
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Liu P, Erez A, Nagamani SCS, Dhar SU, Kołodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernández-Almaguer D, Immken L, Lalani SR, McLean SD, Northrup H, Scaglia F, Strathearn L, Trapane P, Kang SHL, Patel A, Cheung SW, Hastings PJ, Stankiewicz P, Lupski JR, Bi W. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 2011; 146:889-903. [PMID: 21925314 DOI: 10.1016/j.cell.2011.07.042] [Citation(s) in RCA: 320] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 06/06/2011] [Accepted: 07/25/2011] [Indexed: 10/25/2022]
Abstract
Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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6
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Outwin E, Carpenter G, Bi W, Withers MA, Lupski JR, O'Driscoll M. Increased RPA1 gene dosage affects genomic stability potentially contributing to 17p13.3 duplication syndrome. PLoS Genet 2011; 7:e1002247. [PMID: 21901111 PMCID: PMC3161930 DOI: 10.1371/journal.pgen.1002247] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 07/03/2011] [Indexed: 11/18/2022] Open
Abstract
A novel microduplication syndrome involving various-sized contiguous duplications in 17p13.3 has recently been described, suggesting that increased copy number of genes in 17p13.3, particularly PAFAH1B1, is associated with clinical features including facial dysmorphism, developmental delay, and autism spectrum disorder. We have previously shown that patient-derived cell lines from individuals with haploinsufficiency of RPA1, a gene within 17p13.3, exhibit an impaired ATR-dependent DNA damage response (DDR). Here, we show that cell lines from patients with duplications specifically incorporating RPA1 exhibit a different although characteristic spectrum of DDR defects including abnormal S phase distribution, attenuated DNA double strand break (DSB)-induced RAD51 chromatin retention, elevated genomic instability, and increased sensitivity to DNA damaging agents. Using controlled conditional over-expression of RPA1 in a human model cell system, we also see attenuated DSB-induced RAD51 chromatin retention. Furthermore, we find that transient over-expression of RPA1 can impact on homologous recombination (HR) pathways following DSB formation, favouring engagement in aberrant forms of recombination and repair. Our data identifies unanticipated defects in the DDR associated with duplications in 17p13.3 in humans involving modest RPA1 over-expression.
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Affiliation(s)
- Emily Outwin
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Gillian Carpenter
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Medical Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Medical Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
- * E-mail:
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Zhang F, Potocki L, Sampson JB, Liu P, Sanchez-Valle A, Robbins-Furman P, Navarro AD, Wheeler PG, Spence JE, Brasington CK, Withers MA, Lupski JR. Identification of uncommon recurrent Potocki-Lupski syndrome-associated duplications and the distribution of rearrangement types and mechanisms in PTLS. Am J Hum Genet 2010; 86:462-70. [PMID: 20188345 DOI: 10.1016/j.ajhg.2010.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 10/19/2022] Open
Abstract
Nonallelic homologous recombination (NAHR) can mediate recurrent rearrangements in the human genome and cause genomic disorders. Smith-Magenis syndrome (SMS) and Potocki-Lupski syndrome (PTLS) are genomic disorders associated with a 3.7 Mb deletion and its reciprocal duplication in 17p11.2, respectively. In addition to these common recurrent rearrangements, an uncommon recurrent 5 Mb SMS-associated deletion has been identified. However, its reciprocal duplication predicted by the NAHR mechanism had not been identified. Here we report the molecular assays on 74 subjects with PTLS-associated duplications, 35 of whom are newly investigated. By both oligonucleotide-based comparative genomic hybridization and recombination hot spot analyses, we identified two cases of the predicted 5 Mb uncommon recurrent PTLS-associated duplication. Interestingly, the crossovers occur in proximity to a recently delineated allelic homologous recombination (AHR) hot spot-associated sequence motif, further documenting the common hot spot features shared between NAHR and AHR. An additional eight subjects with nonrecurrent PTLS duplications were identified. The smallest region of overlap (SRO) for all of the 74 PTLS duplications examined is narrowed to a 125 kb interval containing only RAI1, a gene recently further implicated in autism. Sequence complexities consistent with DNA replication-based mechanisms were identified in four of eight (50%) newly identified nonrecurrent PTLS duplications. Our findings of the uncommon recurrent PTLS-associated duplication at a relative prevalence reflecting the de novo mutation rate and the distribution of 17p11.2 duplication types in PTLS reveal insights into both the contributions of new mutations and the different underlying mechanisms that generate genomic rearrangements causing genomic disorders.
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8
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Ben-Shachar S, Khajavi M, Withers MA, Shaw CA, van Bokhoven H, Brunner HG, Lupski JR. Dominant versus recessive traits conveyed by allelic mutations - to what extent is nonsense-mediated decay involved? Clin Genet 2009; 75:394-400. [PMID: 19236432 DOI: 10.1111/j.1399-0004.2008.01114.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mutations in ROR2, encoding a receptor tyrosine kinase, can cause autosomal recessive Robinow syndrome (RRS), a severe skeletal dysplasia with limb shortening, brachydactyly, and a dysmorphic facial appearance. Other mutations in ROR2 result in the autosomal dominant disease, brachydactyly type B (BDB1). No functional mechanisms have been delineated to effectively explain the association between mutations and different modes of inheritance causing different phenotypes. BDB1-causing mutations in ROR2 result from heterozygous premature termination codons (PTCs) in downstream exons and the conveyed phenotype segregates as an autosomal dominant trait, whereas heterozygous missense mutations and PTCs in upstream exons result in carrier status for RRS. Given that the distribution of PTC mutations revealed a correlation between the phenotype and the mode of inheritance conveyed, we investigated the potential role for the nonsense-mediated decay (NMD) pathway in the abrogation of possible aberrant effects of selected mutant alleles. Our experiments show that triggering or escaping NMD may cause different phenotypes with a distinct mode of inheritance. We generalize these findings to other disease-associated genes by examining PTC mutation distribution correlation with conveyed phenotype and inheritance patterns. Indeed, NMD may explain distinct phenotypes and different inheritance patterns conveyed by allelic truncating mutations enabling better genotype-phenotype correlations in several other disorders.
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Affiliation(s)
- S Ben-Shachar
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Shaw CJ, Withers MA, Lupski JR. Uncommon deletions of the Smith-Magenis syndrome region can be recurrent when alternate low-copy repeats act as homologous recombination substrates. Am J Hum Genet 2004; 75:75-81. [PMID: 15148657 PMCID: PMC1182010 DOI: 10.1086/422016] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Accepted: 04/07/2004] [Indexed: 11/03/2022] Open
Abstract
Several homologous recombination "hotspots," or sites of positional preference for strand exchanges, associated with recurrent deletions and duplications have been reported within large low-copy repeats (LCRs). Recently, such a hotspot was identified in patients with the Smith-Magenis syndrome (SMS) common deletion of approximately 4 Mb or a reciprocal duplication within the KER gene cluster of the SMS-REP LCRs, in which 50% of analyzed strand exchanges resulting in deletion and 23% of those resulting in duplication occurred. Here, we report an additional recombination hotspot within LCR17pA and LCR17pD, which serve as alternative substrates for nonallelic homologous recombination that results in large (approximately 5 Mb) deletions of 17p11.2, which include the SMS region. Using polymerase-chain-reaction mapping of somatic cell hybrid lines, we refined the breakpoints of six deletions within these LCRs. Sequence analysis of the recombinant junctions revealed that all six strand exchanges occurred within a 524-bp interval, and four of them occurred within an AluSq/x element. This interval represents only 0.5% of the 124-kb stretch of 98.6% sequence identity between LCR17pA and LCR17pD. A search for potentially stimulating sequence motifs revealed short AT-rich segments flanking the recombination hotspot. Our findings indicate that alternative LCRs can mediate rearrangements, resulting in haploinsufficiency of the SMS critical region, and reimplicate homologous recombination as a major mechanism for genomic disorders.
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Affiliation(s)
- Christine J. Shaw
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - Marjorie A. Withers
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - James R. Lupski
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
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10
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Bi W, Park SS, Shaw CJ, Withers MA, Patel PI, Lupski JR. Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2. Am J Hum Genet 2003; 73:1302-15. [PMID: 14639526 PMCID: PMC1180396 DOI: 10.1086/379979] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Accepted: 09/16/2003] [Indexed: 01/15/2023] Open
Abstract
Smith-Magenis syndrome (SMS) is caused by an approximately 4-Mb heterozygous interstitial deletion on chromosome 17p11.2 in approximately 80%-90% of affected patients. Three large ( approximately 200 kb), complex, and highly homologous ( approximately 98%) low-copy repeats (LCRs) are located inside or flanking the SMS common deletion. These repeats, also known as "SMS-REPs," are termed "distal," "middle," and "proximal." The directly oriented distal and proximal copies act as substrates for nonallelic homologous recombination resulting in both the deletion associated with SMS and the reciprocal duplication: dup(17)(p11.2p11.2). Using restriction enzyme cis-morphism analyses and direct sequencing, we mapped the regions of strand exchange in 16 somatic-cell hybrids that harbor only the recombinant SMS-REP. Our studies showed that the sites of crossovers were distributed throughout the region of homology between the distal and proximal SMS-REPs. However, despite approximately 170 kb of high homology, 50% of the recombinant junctions occurred in a 12.0-kb region within the KER gene clusters. DNA sequencing of this hotspot (positional preference for strand exchange) in seven recombinant SMS-REPs narrowed the crossovers to an approximately 8-kb interval. Four of them occurred in a 1,655-bp region rich in polymorphic nucleotides that could potentially reflect frequent gene conversion. For further evaluation of the strand exchange frequency in patients with SMS, novel junction fragments from the recombinant SMS-REPs were identified. As predicted by the reciprocal-recombination model, junction fragments were also identified from this hotspot region in patients with dup(17)(p11.2p11.2), documenting reciprocity of the positional preference for strand exchange. Several potential cis-acting recombination-promoting sequences were identified within the hotspot. It is interesting that we found 2.1-kb AT-rich inverted repeats flanking the proximal and middle KER gene clusters but not the distal one. The role of any or all of these in stimulating double-strand breaks around this positional recombination hotspot remains to be explored.
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Affiliation(s)
- Weimin Bi
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - Sung-Sup Park
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - Christine J. Shaw
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - Marjorie A. Withers
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - Pragna I. Patel
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
| | - James R. Lupski
- Departments of Molecular and Human Genetics, Neurology, and Pediatrics, Baylor College of Medicine, and Texas Children’s Hospital, Houston
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Potocki L, Chen KS, Park SS, Osterholm DE, Withers MA, Kimonis V, Summers AM, Meschino WS, Anyane-Yeboa K, Kashork CD, Shaffer LG, Lupski JR. Molecular mechanism for duplication 17p11.2- the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat Genet 2000; 24:84-7. [PMID: 10615134 DOI: 10.1038/71743] [Citation(s) in RCA: 262] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recombination between repeated sequences at various loci of the human genome are known to give rise to DNA rearrangements associated with many genetic disorders. Perhaps the most extensively characterized genomic region prone to rearrangement is 17p12, which is associated with the peripheral neuropathies, hereditary neuropathy with liability to pressure palsies (HNPP) and Charcot-Marie-Tooth disease type 1A (CMT1A;ref. 2). Homologous recombination between 24-kb flanking repeats, termed CMT1A-REPs, results in a 1.5-Mb deletion that is associated with HNPP, and the reciprocal duplication product is associated with CMT1A (ref. 2). Smith-Magenis syndrome (SMS) is a multiple congenital anomalies, mental retardation syndrome associated with a chromosome 17 microdeletion, del(17)(p11.2p11.2) (ref. 3,4). Most patients (>90%) carry deletions of the same genetic markers and define a common deletion. We report seven unrelated patients with de novo duplications of the same region deleted in SMS. A unique junction fragment, of the same apparent size, was identified in each patient by pulsed field gel electrophoresis (PFGE). Further molecular analyses suggest that the de novo17p11.2 duplication is preferentially paternal in origin, arises from unequal crossing over due to homologous recombination between flanking repeat gene clusters and probably represents the reciprocal recombination product of the SMS deletion. The clinical phenotype resulting from duplication [dup(17)(p11.2p11.2)] is milder than that associated with deficiency of this genomic region. This mechanism of reciprocal deletion and duplication via homologous recombination may not only pertain to the 17p11.2 region, but may also be common to other regions of the genome where interstitial microdeletion syndromes have been defined.
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Affiliation(s)
- L Potocki
- Department of Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
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