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Chaudhary R, Rehman M, Agarwal V, Kumar A, Kaushik AS, Srivastava S, Srivastava S, Verma R, Rajinikanth PS, Mishra V. Terra incognita of glial cell dynamics in the etiology of leukodystrophies: Broadening disease and therapeutic perspectives. Life Sci 2024; 354:122953. [PMID: 39122110 DOI: 10.1016/j.lfs.2024.122953] [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: 02/05/2024] [Revised: 07/09/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Neuroglial cells, also known as glia, are primarily characterized as auxiliary cells within the central nervous system (CNS). The recent findings have shed light on their significance in numerous physiological processes and their involvement in various neurological disorders. Leukodystrophies encompass an array of rare and hereditary neurodegenerative conditions that were initially characterized by the deficiency, aberration, or degradation of myelin sheath within CNS. The primary cellular populations that experience significant alterations are astrocytes, oligodendrocytes and microglia. These glial cells are either structurally or metabolically impaired due to inherent cellular dysfunction. Alternatively, they may fall victim to the accumulation of harmful by-products resulting from metabolic disturbances. In either situation, the possible replacement of glial cells through the utilization of implanted tissue or stem cell-derived human neural or glial progenitor cells hold great promise as a therapeutic strategy for both the restoration of structural integrity through remyelination and the amelioration of metabolic deficiencies. Various emerging treatment strategies like stem cell therapy, ex-vivo gene therapy, infusion of adeno-associated virus vectors, emerging RNA-based therapies as well as long-term therapies have demonstrated success in pre-clinical studies and show promise for rapid clinical translation. Here, we addressed various leukodystrophies in a comprehensive and detailed manner as well as provide prospective therapeutic interventions that are being considered for clinical trials. Further, we aim to emphasize the crucial role of different glial cells in the pathogenesis of leukodystrophies. By doing so, we hope to advance our understanding of the disease, elucidate underlying mechanisms, and facilitate the development of potential treatment interventions.
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Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Mujeeba Rehman
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Anand Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Arjun Singh Kaushik
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Siddhi Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Sukriti Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Rajkumar Verma
- University of Connecticut School of Medicine, 200 Academic Way, Farmington, CT 06032, USA
| | - P S Rajinikanth
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Vikas Mishra
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India.
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Ghasemi A, Sadr Z, Babanejad M, Rohani M, Alavi A. Copy Number Variations in Hereditary Spastic Paraplegia-Related Genes: Evaluation of an Iranian Hereditary Spastic Paraplegia Cohort and Literature Review. Mol Syndromol 2023; 14:477-484. [PMID: 38058755 PMCID: PMC10697729 DOI: 10.1159/000531507] [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: 05/11/2023] [Accepted: 06/07/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction In human genetic disorders, copy number variations (CNVs) are considered a considerable underlying cause. CNVs are generally detected by array-based methods but can also be discovered by read-depth analysis of whole-exome sequencing (WES) data. We performed WES-based CNV identification in a cohort of 35 Iranian families with hereditary spastic paraplegia (HSP) patients. Methods Thirty-five patients whose routine single-nucleotide variants (SNVs) and insertion/deletion analyses from exome data were unrevealing underwent a pipeline of CNV analysis using the read-depth detection method. Subsequently, a comprehensive search about the existence of CNVs in all 84 known HSP-causing genes was carried out in all reported HSP cases, so far. Results and Discussion CNV analysis of exome data indicated that 1 patient harbored a heterozygous deletion in exon 17 of the SPAST gene. Multiplex ligation-dependent probe amplification analysis confirmed this deletion in the proband and his affected father. Literature review demonstrated that, to date, pathogenic CNVs have been identified in 30 out of 84 HSP-causing genes (∼36%). However, CNVs in only 17 of these genes were specifically associated with the HSP phenotype. Among them, CNVs were more common in L1CAM, PLP1, SPAST, SPG7, SPG11, and REEP1 genes. The identification of the CNV in 1 of our patients suggests that WES allows the detection of both SNVs and CNVs from a single method without additional costs and execution time. However, because of intrinsic issues of WES in the detection of large rearrangements, it may not yet be exploited to replace the CNV detection methods in standard clinical practice.
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Affiliation(s)
- Aida Ghasemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zahra Sadr
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Iran University of Medical Sciences, Hazrat Rasool Hospital, Tehran, Iran
| | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Hijazi H, Reis LM, Pehlivan D, Bernstein JA, Muriello M, Syverson E, Bonner D, Estiar MA, Gan-Or Z, Rouleau GA, Lyulcheva E, Greenhalgh L, Tessarech M, Colin E, Guichet A, Bonneau D, van Jaarsveld RH, Lachmeijer AMA, Ruaud L, Levy J, Tabet AC, Ploski R, Rydzanicz M, Kępczyński Ł, Połatyńska K, Li Y, Fatih JM, Marafi D, Rosenfeld JA, Coban-Akdemir Z, Bi W, Gibbs RA, Hobson GM, Hunter JV, Carvalho CMB, Posey JE, Semina EV, Lupski JR. TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am J Hum Genet 2022; 109:2270-2282. [PMID: 36368327 PMCID: PMC9748253 DOI: 10.1016/j.ajhg.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, WI, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael Muriello
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, WI, USA
| | - Erin Syverson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, WI, USA
| | - Devon Bonner
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montreal, QC, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, QC, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada; Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada; The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada; Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Ekaterina Lyulcheva
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Marine Tessarech
- Department of Medical Genetics, Angers University Hospital, Angers, France; Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Estelle Colin
- Department of Medical Genetics, Angers University Hospital, Angers, France; Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Agnès Guichet
- Department of Medical Genetics, Angers University Hospital, Angers, France; Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Dominique Bonneau
- Department of Medical Genetics, Angers University Hospital, Angers, France; Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - R H van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A M A Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lyse Ruaud
- INSERM UMR1141, Neurodiderot, University of Paris, 75019 Paris, France; APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Jonathan Levy
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Anne-Claude Tabet
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Łukasz Kępczyński
- Department of Genetics, Polish Mother's Memorial Hospital - Research Institute, Łódź, Poland
| | - Katarzyna Połatyńska
- Department of Developmental Neurology an Epileptology, Polish Mother's Memorial Hospital - Research Institute, Łódź, Poland
| | - Yidan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Grace M Hobson
- Department of Research, Nemours Children's Health, Wilmington, DE, USA
| | - Jill V Hunter
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, WI, USA; Departments of Ophthalmology and Visual Sciences and Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA.
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Bolotin E, Melamed D, Livnat A. Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis. Evol Biol 2022; 50:30-55. [PMID: 36816837 PMCID: PMC9925542 DOI: 10.1007/s11692-022-09579-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 09/11/2022] [Indexed: 12/05/2022]
Abstract
Cases of parallel or recurrent gene fusions in evolution as well as in genetic disease and cancer are difficult to explain, because unlike point mutations, they can require the repetition of a similar configuration of multiple breakpoints rather than the repetition of a single point mutation. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a specific context are more likely to undergo fusion mutation in the course of evolution for mechanistic reasons. This hypothesis offers to explain gene fusion in both evolution and disease under one umbrella. Using bioinformatic data, we tested this hypothesis against alternatives, including that all gene pairs can fuse by random mutation, but among pairs thus fused, those that had interacted previously are more likely to be favored by selection. Results show that across multiple measures of gene interaction, human genes whose orthologs are fused in one or more species are more likely to interact with each other than random pairs of genes of the same genomic distance between pair members; that an overlap exists between genes that fused in the course of evolution in non-human species and genes that undergo fusion in human cancers; and that across six primate species studied, fusions predominate over fissions and exhibit substantial evolutionary parallelism. Together, these results support the used-together-fused-together hypothesis over its alternatives. Multiple implications are discussed, including the relevance of mutational mechanisms to the evolution of genome organization, to the distribution of fitness effects of mutation, to evolutionary parallelism and more. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-022-09579-9.
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Affiliation(s)
- Evgeni Bolotin
- Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, 3498838 Israel
| | - Daniel Melamed
- Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, 3498838 Israel
| | - Adi Livnat
- Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, 3498838 Israel
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5
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Gasmi L, Baek S, Kim JC, Kim S, Lee MR, Park SE, Shin TY, Lee SJ, Parker BL, Kim JS. Gene diversity explains variation in biological features of insect killing fungus, Beauveria bassiana. Sci Rep 2021; 11:91. [PMID: 33420123 PMCID: PMC7794557 DOI: 10.1038/s41598-020-78910-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Beauveria bassiana is a species complex whose isolates show considerable natural genetic variability. However, little is known about how this genetic diversity affects the fungus performance. Herein, we characterized the diversity of genes involved in various mechanisms of the infective cycle of 42 isolates that have different growth rates, thermotolerance and virulence. The analysed genes showed general genetic diversity measured as non-synonymous changes (NSC) and copy number variation (CNV), with most of them being subjected to positive episodic diversifying selection. Correlation analyses between NSC or CNV and the isolate virulence, thermotolerance and growth rate revealed that various genes shaped the biological features of the fungus. Lectin-like, mucin signalling, Biotrophy associated and chitinase genes NSCs correlated with the three biological features of B. bassiana. In addition, other genes (i.e. DNA photolyase and cyclophilin B) that had relatively conserved sequences, had variable CNs across the isolates which were correlated with the variability of either virulence or thermotolerance of B. bassiana isolates. The data obtained is important for a better understanding of population structure, ecological and potential impact when isolates are used as mycoinsecticides and can justify industrialization of new isolates.
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Affiliation(s)
- Laila Gasmi
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Sehyeon Baek
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Jong Cheol Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Sihyeon Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Mi Rong Lee
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - So Eun Park
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Tae Young Shin
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea
| | - Se Jin Lee
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA
| | - Bruce L Parker
- Entomology Research Laboratory, University of Vermont, 661 Spear Street, Burlington, VT, 05405-0105, USA
| | - Jae Su Kim
- Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54596, Korea.
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54596, Korea.
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Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. Genome Med 2019; 11:80. [PMID: 31818324 PMCID: PMC6902434 DOI: 10.1186/s13073-019-0676-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. METHODS Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis. RESULTS High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches). CONCLUSIONS These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.
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Hijazi H, Coelho FS, Gonzaga-Jauregui C, Bernardini L, Mar SS, Manning MA, Hanson-Kahn A, Naidu S, Srivastava S, Lee JA, Jones JR, Friez MJ, Alberico T, Torres B, Fang P, Cheung SW, Song X, Davis-Williams A, Jornlin C, Wight PA, Patyal P, Taube J, Poretti A, Inoue K, Zhang F, Pehlivan D, Carvalho CMB, Hobson GM, Lupski JR. Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome. Hum Mutat 2019; 41:150-168. [PMID: 31448840 DOI: 10.1002/humu.23902] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023]
Abstract
Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernanda S Coelho
- Programa de Pós-Graduação em Genética Departmento de Biologia Geral, UFMG, Belo Horizonte, Minas Gerais, Brazil.,Instituto René Rachou, FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | | | - Laura Bernardini
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Melanie A Manning
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Andrea Hanson-Kahn
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Genetics, Stanford University School of Medicine, Palo Alto, California
| | - SakkuBai Naidu
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | | | - Jennifer A Lee
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Thomas Alberico
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Barbara Torres
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Ping Fang
- Clinical Genomics, WuXi NextCODE, Cambridge, Massachusetts
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angelique Davis-Williams
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Carly Jornlin
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Patricia A Wight
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Pankaj Patyal
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer Taube
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Andrea Poretti
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Grace M Hobson
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
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8
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Xie X, Chen C, Liang Q, Wu X, Wang X, Wu W, Ding Q. Characterization of two large duplications of
F9
associated with mild and severe haemophilia B, respectively. Haemophilia 2019; 25:475-483. [PMID: 30866119 DOI: 10.1111/hae.13704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 01/23/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoling Xie
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
| | - Wenman Wu
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
- Faculty of Medical Laboratory Science, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
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9
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Inoue K. Pelizaeus-Merzbacher Disease: Molecular and Cellular Pathologies and Associated Phenotypes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1190:201-216. [PMID: 31760646 DOI: 10.1007/978-981-32-9636-7_13] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Pelizaeus-Merzbacher disease (PMD) represents a group of disorders known as hypomyelinating leukodystrophies, which are characterized by abnormal development and maintenance of myelin in the central nervous system. PMD is caused by different types of mutations in the proteolipid protein 1 (PLP1) gene, which encodes a major myelin membrane lipoprotein. These mutations in the PLP1 gene result in distinct cellular and molecular pathologies and a spectrum of clinical phenotypes. In this chapter, I discuss the historical aspects and current understanding of the mechanisms underlying how different PLP1 mutations disrupt the normal process of myelination and result in PMD and other disorders.
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Affiliation(s)
- Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.
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10
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Abstract
Pelizaeus-Merzbacher disease (PMD) is an X-linked disorder caused by mutations in the PLP1 gene, which encodes the proteolipid protein of myelinating oligodendroglia. PMD exhibits phenotypic variability that reflects its considerable genotypic heterogeneity, but all forms of the disease result in central hypomyelination associated with early neurologic dysfunction, progressive deterioration, and ultimately death. PMD has been classified into three major subtypes, according to the age of presentation: connatal PMD, classic PMD, and transitional PMD, combining features of both connatal and classic forms. Two other less severe phenotypes were subsequently described, including the spastic paraplegia syndrome and PLP1-null disease. These disorders may be associated with duplications, as well as with point, missense, and null mutations within the PLP1 gene. A number of clinically similar Pelizaeus-Merzbacher-like disorders (PMLD) are considered in the differential diagnosis of PMD, the most prominent of which is PMLD-1, caused by misexpression of the GJC2 gene encoding connexin-47. No effective therapy for PMD exists. Yet, as a relatively pure central nervous system hypomyelinating disorder, with limited involvement of the peripheral nervous system and little attendant neuronal pathology, PMD is an attractive therapeutic target for neural stem cell and glial progenitor cell transplantation, efforts at which are now underway in a number of centers internationally.
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Affiliation(s)
- M Joana Osório
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY, United States; Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Steven A Goldman
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY, United States; Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark.
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11
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Reid ES, Papandreou A, Drury S, Boustred C, Yue WW, Wedatilake Y, Beesley C, Jacques TS, Anderson G, Abulhoul L, Broomfield A, Cleary M, Grunewald S, Varadkar SM, Lench N, Rahman S, Gissen P, Clayton PT, Mills PB. Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes. Brain 2017; 139:2844-2854. [PMID: 27604308 PMCID: PMC5091046 DOI: 10.1093/brain/aww221] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022] Open
Abstract
Neurometabolic disorders are markedly heterogeneous, both clinically and genetically, and are characterized by variable neurological dysfunction accompanied by suggestive neuroimaging or biochemical abnormalities. Despite early specialist input, delays in diagnosis and appropriate treatment initiation are common. Next-generation sequencing approaches still have limitations but are already enabling earlier and more efficient diagnoses in these patients. We designed a gene panel targeting 614 genes causing inborn errors of metabolism and tested its diagnostic efficacy in a paediatric cohort of 30 undiagnosed patients presenting with variable neurometabolic phenotypes. Genetic defects that could, at least partially, explain observed phenotypes were identified in 53% of cases. Where biochemical abnormalities pointing towards a particular gene defect were present, our panel identified diagnoses in 89% of patients. Phenotypes attributable to defects in more than one gene were seen in 13% of cases. The ability of in silico tools, including structure-guided prediction programmes to characterize novel missense variants were also interrogated. Our study expands the genetic, clinical and biochemical phenotypes of well-characterized (POMGNT1, TPP1) and recently identified disorders (PGAP2, ACSF3, SERAC1, AFG3L2, DPYS). Overall, our panel was accurate and efficient, demonstrating good potential for applying similar approaches to clinically and biochemically diverse neurometabolic disease cohorts.
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Affiliation(s)
- Emma S Reid
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Apostolos Papandreou
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Yehani Wedatilake
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Clare Beesley
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Developmental Biology and Cancer Programme, UCL Institute of Child Health, London, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lara Abulhoul
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alex Broomfield
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Maureen Cleary
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephanie Grunewald
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sophia M Varadkar
- Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nick Lench
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shamima Rahman
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Paul Gissen
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Peter T Clayton
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Philippa B Mills
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
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12
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Cardoso AR, Oliveira M, Amorim A, Azevedo L. Major influence of repetitive elements on disease-associated copy number variants (CNVs). Hum Genomics 2016; 10:30. [PMID: 27663310 PMCID: PMC5035501 DOI: 10.1186/s40246-016-0088-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/16/2016] [Indexed: 01/13/2023] Open
Abstract
Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements may guide genomic stability which will give rise to CNVs either by non-allelic homologous recombination (NAHR) or non-homologous end joining (NHEJ). Here, we present a short guide based on previously documented cases of disease-associated CNVs in order to provide a general view on the impact of repeated elements on the stability of the genomic sequence and consequently in the origin of the human pathogenic variome.
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Affiliation(s)
- Ana R Cardoso
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal.
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13
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Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication. PLoS Genet 2015; 11:e1005050. [PMID: 25749076 PMCID: PMC4352052 DOI: 10.1371/journal.pgen.1005050] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/02/2015] [Indexed: 02/07/2023] Open
Abstract
Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.
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14
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Rodriguez E, Sakowski L, Hobson GM, Armani MH, Kreiger PA, Zhu Y, Waldman SA, Shaffer TH. Plp1 gene duplication inhibits airway responsiveness and induces lung inflammation. Pulm Pharmacol Ther 2015; 30:22-31. [PMID: 25445931 PMCID: PMC6874309 DOI: 10.1016/j.pupt.2014.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/26/2014] [Accepted: 10/25/2014] [Indexed: 11/25/2022]
Abstract
Mice with Plp1 gene duplication model the most common form of Pelizaeus-Merzbacher disease (PMD), a CNS disease in which patients may suffer respiratory complications. We hypothesized that affected mice would lack airway responsiveness compared to wild-type and carrier mice during methacholine challenge. Wild-type (n = 10), carrier female (n = 6) and affected male (n = 8) mice were anesthetized-paralyzed, tracheostomized and ventilated. Respiratory mechanics were recorded at baseline and during escalating doses of nebulized methacholine followed by albuterol. Lung resistance (RL) was the primary endpoint. Lung tissues were assayed for inflammatory and histological differences. At baseline, phase angles were higher in carrier and affected mice than wild-type. Dose-response RL curves in affected and carrier mice indicated a lack of methacholine response. Albuterol reduced RL in wild-type and carrier, but not affected mice. Affected mice exhibited lower interleukin (IL)-6 tissue levels and alveolar inflammatory infiltrates. Affected and carrier mice, compared to wild-type, lacked airway reactivity during methacholine challenge, but only affected mice exhibited decreased lung tissue levels of IL-6 and inflammation.
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Affiliation(s)
- Elena Rodriguez
- Alfred I. duPont Hospital for Children, Nemours Lung Center, Wilmington, DE 19803, USA; Alfred I. duPont Hospital for Children, Nemours Biomedical Research, Wilmington, DE 19803, USA; Thomas Jefferson University, Division of Clinical Pharmacology, Dept. of Pharmacology and Experimental Therapeutics, Philadelphia, PA 19107, USA.
| | - Lauren Sakowski
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Wilmington, DE 19803, USA; University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA
| | - Grace M Hobson
- Alfred I. duPont Hospital for Children, Nemours Biomedical Research, Wilmington, DE 19803, USA; Center for Applied Clinical Genomics, Nemours Biomedical Research, Wilmington, DE 19803, USA; University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA; Thomas Jefferson University, Department of Pediatrics, Philadelphia, PA 19107, USA
| | - Milena Hirata Armani
- Alfred I. duPont Hospital for Children, Nemours Lung Center, Wilmington, DE 19803, USA
| | - Portia A Kreiger
- Nemours Alfred I. duPont Hospital for Children, Department of Pathology, Wilmington, DE 19803, USA
| | - Yan Zhu
- Alfred I. duPont Hospital for Children, Nemours Lung Center, Wilmington, DE 19803, USA; Alfred I. duPont Hospital for Children, Nemours Biomedical Research, Wilmington, DE 19803, USA
| | - Scott A Waldman
- Thomas Jefferson University, Division of Clinical Pharmacology, Dept. of Pharmacology and Experimental Therapeutics, Philadelphia, PA 19107, USA
| | - Thomas H Shaffer
- Alfred I. duPont Hospital for Children, Nemours Lung Center, Wilmington, DE 19803, USA; Alfred I. duPont Hospital for Children, Nemours Biomedical Research, Wilmington, DE 19803, USA
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15
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Carvalho CMB, Zuccherato LW, Williams CL, Neill NJ, Murdock DR, Bainbridge M, Jhangiani SN, Muzny DM, Gibbs RA, Ip W, Guillerman RP, Lupski JR, Bertuch AA. Structural variation and missense mutation in SBDS associated with Shwachman-Diamond syndrome. BMC MEDICAL GENETICS 2014; 15:64. [PMID: 24898207 PMCID: PMC4057820 DOI: 10.1186/1471-2350-15-64] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/29/2014] [Indexed: 12/18/2022]
Abstract
Background Shwachman–Diamond syndrome (SDS) is an autosomal recessive ribosomopathy caused mainly by compound heterozygous mutations in SBDS. Structural variation (SV) involving the SBDS locus has been rarely reported in association with the disease. We aimed to determine whether an SV contributed to the pathogenesis of a case lacking biallelic SBDS point mutations. Case presentation Whole exome sequencing was performed in a patient with SDS lacking biallelic SBDS point mutations. Array comparative genomic hybridization and Southern blotting were used to seek SVs across the SBDS locus. Locus-specific polymerase chain reaction (PCR) encompassing flanking intronic sequence was also performed to investigate mutation within the locus. RNA expression and Western blotting were performed to analyze allele and protein expression. We found the child harbored a single missense mutation in SBDS (c.98A > C; p.K33T), inherited from the mother, and an SV in the SBDS locus, inherited from the father. The missense allele and SV segregated in accordance with Mendelian expectations for autosomal recessive SDS. Complementary DNA and western blotting analysis and locus specific PCR support the contention that the SV perturbed SBDS protein expression in the father and child. Conclusion Our findings implicate genomic rearrangements in the pathogenesis of some cases of SDS and support patients lacking biallelic SBDS point mutations be tested for SV within the SBDS locus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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16
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Sahoo T, Wang JC, Elnaggar MM, Sanchez-Lara P, Ross LP, Mahon LW, Hafezi K, Deming A, Hinman L, Bruno Y, Bartley JA, Liehr T, Anguiano A, Jones M. Concurrent triplication and uniparental isodisomy: evidence for microhomology-mediated break-induced replication model for genomic rearrangements. Eur J Hum Genet 2014; 23:61-6. [PMID: 24713661 DOI: 10.1038/ejhg.2014.53] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/11/2022] Open
Abstract
Whole-genome oligonucleotide single-nucleotide polymorphism (oligo-SNP) arrays enable simultaneous interrogation of copy number variations (CNVs), copy neutral regions of homozygosity (ROH) and uniparental disomy (UPD). Structural variation in the human genome contributes significantly to genetic variation, and often has deleterious effects leading to disease causation. Co-occurrence of CNV and regions of allelic homozygosity in tandem involving the same chromosomal arm are extremely rare. Replication-based mechanisms such as microhomology-mediated break-induced replication (MMBIR) are recent models predicted to induce structural rearrangements and gene dosage aberrations; however, supportive evidence in humans for one-ended DNA break repair coupled with MMBIR giving rise to interstitial copy number gains and distal loss of heterozygosity has not been documented. We report on the identification and characterization of two cases with interstitial triplication followed by uniparental isodisomy (isoUPD) for remainder of the chromosomal arm. Case 1 has a triplication at 9q21.11-q21.33 and segmental paternal isoUPD for 9q21.33-qter, and presented with citrullinemia with a homozygous mutation in the argininosuccinate synthetase gene (ASS1 at 9q34.1). Case 2 has a triplication at 22q12.1-q12.2 and segmental maternal isoUPD 22q12.2-qter, and presented with hearing loss, mild dysmorphic features and bilateral iris coloboma. Interstitial triplication coupled with distal segmental isoUPD is a novel finding that provides human evidence for one-ended DNA break and replication-mediated repair. Both copy number gains and isoUPD may contribute to the phenotype. Significantly, these cases represent the first detailed genomic analysis that provides support for a MMBIR mechanism inducing copy number gains and segmental isoUPD in tandem.
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Affiliation(s)
- Trilochan Sahoo
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Jia-Chi Wang
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | | | - Pedro Sanchez-Lara
- Children's Hospital Los Angeles, Division of Medical Genetics, Los Angeles, CA, USA
| | - Leslie P Ross
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Loretta W Mahon
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Katayoun Hafezi
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Abigail Deming
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Lynne Hinman
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Yovana Bruno
- White Memorial Medical Center, Los Angeles, CA, USA
| | - James A Bartley
- Children's Hospital Los Angeles, Division of Medical Genetics, Los Angeles, CA, USA
| | | | - Arturo Anguiano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Marilyn Jones
- 1] Rady Children's Hospital, Division of Genetics/Dysmorphology, San Diego, CA, USA [2] University of California, San Diego, CA, USA
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17
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Bickhart DM, Liu GE. The challenges and importance of structural variation detection in livestock. Front Genet 2014; 5:37. [PMID: 24600474 PMCID: PMC3927395 DOI: 10.3389/fgene.2014.00037] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/31/2014] [Indexed: 01/25/2023] Open
Abstract
Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among individuals of each species. Many of these variants have been linked to debilitating diseases in humans, thereby cementing the importance of refining methods for their detection. Despite progress in the field, reliable detection of SVs still remains a problem even for human subjects. Many of the underlying problems that make SVs difficult to detect in humans are amplified in livestock species, whose lower quality genome assemblies and incomplete gene annotation can often give rise to false positive SV discoveries. Regardless of the challenges, SV detection is just as important for livestock researchers as it is for human researchers, given that several productive traits and diseases have been linked to copy number variations (CNVs) in cattle, sheep, and pig. Already, there is evidence that many beneficial SVs have been artificially selected in livestock such as a duplication of the agouti signaling protein gene that causes white coat color in sheep. In this review, we will list current SV and CNV discoveries in livestock and discuss the problems that hinder routine discovery and tracking of these polymorphisms. We will also discuss the impacts of selective breeding on CNV and SV frequencies and mention how SV genotyping could be used in the future to improve genetic selection.
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Affiliation(s)
- Derek M Bickhart
- Animal Improvement Programs Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
| | - George E Liu
- Bovine Functional Genomics Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
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18
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Enggaard Hoeffding LK, Hansen T, Ingason A, Doung L, Thygesen JH, Møller RS, Tommerup N, Kirov G, Rujescu D, Larsen LA, Werge T. Sequence analysis of 17 NRXN1 deletions. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:52-61. [PMID: 24339137 DOI: 10.1002/ajmg.b.32204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genome instability plays fundamental roles in human evolution and phenotypic variation within our population. This instability leads to genomic rearrangements that are involved in a wide variety of human disorders, including congenital and neurodevelopmental disorders, and cancers. Insight into the molecular mechanisms governing such genomic rearrangements may increase our understanding of disease pathology and evolutionary processes. Here we analyse 17 carriers of non-recurrent deletions in the NRXN1 gene, which have been associated with neurodevelopmental disorders, e.g. schizophrenia, autism and epilepsies. METHODS 17 non-recurrent NRXN1 deletions identified by GWA were sequenced to map the breakpoints of each. Meme … etc. was used to identify shared patterns between the deletions and compare these were previously studies on non-recurrent deletions. RESULTS We discovered two novel sequence motifs shared between all 17 NRXN1 deletions and a significantly higher AT nucleotide content at the breakpoints, compared to the overall nucleotide content on chromosome 2. We found different alteration of sequence at the breakpoint; small insertions and duplications giving rise to short microhomology sequences. CONCLUSIONS No single mechanism seems to be implicated in the deletion events, but the results suggest that NHEJ, FoSTeS or MMBIR is implicated. The two novel sequence motifs together with a high AT content in all in NRXN1 deletions may lead to increased instability leading to a increase susceptibility to a single stranded structures. This favours potentially repaired by NHEJ mechanism of double strand breaks or may leading to replication errors. © 2013 Wiley Periodicals, Inc.
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19
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Livnat A. Interaction-based evolution: how natural selection and nonrandom mutation work together. Biol Direct 2013; 8:24. [PMID: 24139515 PMCID: PMC4231362 DOI: 10.1186/1745-6150-8-24] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/26/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. PRESENTATION OF THE HYPOTHESIS Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation-while not Lamarckian, or "directed" to increase fitness-is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination's fitness. TESTING AND IMPLICATIONS OF THE HYPOTHESIS This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive potential than previously considered. Empirical evidence for the proposed mechanism from both molecular evolution and evolution at the organismal level is discussed, and multiple predictions are offered by which it may be tested. REVIEWERS This article was reviewed by Nigel Goldenfeld (nominated by Eugene V. Koonin), Jürgen Brosius and W. Ford Doolittle.
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Affiliation(s)
- Adi Livnat
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061,
USA
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20
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Gait abnormalities and progressive myelin degeneration in a new murine model of Pelizaeus-Merzbacher disease with tandem genomic duplication. J Neurosci 2013; 33:11788-99. [PMID: 23864668 DOI: 10.1523/jneurosci.1336-13.2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pelizaeus-Merzbacher disease (PMD) is a hypomyelinating leukodystrophy caused by mutations of the proteolipid protein 1 gene (PLP1), which is located on the X chromosome and encodes the most abundant protein of myelin in the central nervous sytem. Approximately 60% of PMD cases result from genomic duplications of a region of the X chromosome that includes the entire PLP1 gene. The duplications are typically in a head-to-tail arrangement, and they vary in size and gene content. Although rodent models with extra copies of Plp1 have been developed, none contains an actual genomic rearrangement that resembles those found in PMD patients. We used mutagenic insertion chromosome engineering resources to generate the Plp1dup mouse model by introducing an X chromosome duplication in the mouse genome that contains Plp1 and five neighboring genes that are also commonly duplicated in PMD patients. The Plp1dup mice display progressive gait abnormalities compared with wild-type littermates. The single duplication leads to increased transcript levels of Plp1 and four of the five other duplicated genes over wild-type levels in the brain beginning the second postnatal week. The Plp1dup mice also display altered transcript levels of other important myelin proteins leading to a progressive degeneration of myelin. Our results show that a single duplication of the Plp1 gene leads to a phenotype similar to the pattern seen in human PMD patients with duplications.
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Giorgio E, Rolyan H, Kropp L, Chakka AB, Yatsenko S, Gregorio ED, Lacerenza D, Vaula G, Talarico F, Mandich P, Toro C, Pierre EE, Labauge P, Capellari S, Cortelli P, Vairo FP, Miguel D, Stubbolo D, Marques LC, Gahl W, Boespflug-Tanguy O, Melberg A, Hassin-Baer S, Cohen OS, Pjontek R, Grau A, Klopstock T, Fogel B, Meijer I, Rouleau G, Bouchard JPL, Ganapathiraju M, Vanderver A, Dahl N, Hobson G, Brusco A, Brussino A, Padiath QS. Analysis of LMNB1 duplications in autosomal dominant leukodystrophy provides insights into duplication mechanisms and allele-specific expression. Hum Mutat 2013; 34:1160-71. [PMID: 23649844 PMCID: PMC3714349 DOI: 10.1002/humu.22348] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/19/2013] [Indexed: 02/05/2023]
Abstract
Autosomal dominant leukodystrophy (ADLD) is an adult onset demyelinating disorder that is caused by duplications of the lamin B1 (LMNB1) gene. However, as only a few cases have been analyzed in detail, the mechanisms underlying LMNB1 duplications are unclear. We report the detailed molecular analysis of the largest collection of ADLD families studied, to date. We have identified the minimal duplicated region necessary for the disease, defined all the duplication junctions at the nucleotide level and identified the first inverted LMNB1 duplication. We have demonstrated that the duplications are not recurrent; patients with identical duplications share the same haplotype, likely inherited from a common founder and that the duplications originated from intrachromosomal events. The duplication junction sequences indicated that nonhomologous end joining or replication-based mechanisms such fork stalling and template switching or microhomology-mediated break induced repair are likely to be involved. LMNB1 expression was increased in patients' fibroblasts both at mRNA and protein levels and the three LMNB1 alleles in ADLD patients show equal expression, suggesting that regulatory regions are maintained within the rearranged segment. These results have allowed us to elucidate duplication mechanisms and provide insights into allele-specific LMNB1 expression levels.
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Affiliation(s)
- Elisa Giorgio
- University of Torino, Department of Medical SciencesTorino, Italy
| | - Harshvardhan Rolyan
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
| | - Laura Kropp
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
| | - Anish Baswanth Chakka
- Department of Biomedical Informatics School of Medicine, University of PittsburghPittsburgh, Pennsylvania
| | - Svetlana Yatsenko
- Department of Obstetrics Gynecology and Reproductive Sciences, University of PittsburghPittsburgh, Pennsylvania
- Department of Pathology University of Pittsburgh, School of MedicinePittsburgh, Pennsylvania
| | - Eleonora Di Gregorio
- University of Torino, Department of Medical SciencesTorino, Italy
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | | | - Giovanna Vaula
- Department of Neuroscience, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | - Flavia Talarico
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | - Paola Mandich
- Department of Neurology, Ophthalmology and Genetics, di Bologna, Department of Biomedical and NeuroMotor Sciences (DIBINEM) Alma Mater StudiorumBologna, Italy
| | - Camilo Toro
- NIH Undiagnosed Diseases Program NIH Office of Rare Disease, Research and NHGRIBethesda, Maryland
| | | | - Pierre Labauge
- Neurologie Hopital Caremeau, Centre Hospitalo-Universitaire de NimesNimes, France
| | - Sabina Capellari
- University of Bologna IRCCS Istituto delle Scienze Neurologiche di Bologna Department of Biomedical and NeuroMotor Sciences (DIBINEM), Alma Mater StudiorumItaly
| | - Pietro Cortelli
- University of Bologna IRCCS Istituto delle Scienze Neurologiche di Bologna Department of Biomedical and NeuroMotor Sciences (DIBINEM), Alma Mater StudiorumItaly
| | - Filippo Pinto Vairo
- Hospital de Clínicas de Porto Alegre … Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Diego Miguel
- Hospital de Clínicas de Porto Alegre … Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Danielle Stubbolo
- Nemours Biomedical Research, Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Lourenco Charles Marques
- Department of Medical Genetics Clinics Hospital of Ribeirao Preto, University of Sao PauloSao Paulo, Brazil
| | - William Gahl
- NIH Undiagnosed Diseases Program NIH Office of Rare Disease, Research and NHGRIBethesda, Maryland
| | - Odile Boespflug-Tanguy
- Institut National de la Santé et de la Recherche Médicale (INSERM) – Paris Diderot Sorbonne Paris Cité University, Robert Debré HospitalParis, France
- Assistance Publique des Hopitaux de Paris Reference Center for Rare Diseases “Leukodystrophies”, Child Neurology and Metabolic Disorders DepartmentParis, France
| | - Atle Melberg
- Department of Neuroscience Neurology, Uppsala UniversityUppsala, Sweden
| | - Sharon Hassin-Baer
- Parkinson’s disease and Movement Disorders Clinic Department of Neurology, Chaim Sheba Medical CenterTel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Oren S Cohen
- Parkinson’s disease and Movement Disorders Clinic Department of Neurology, Chaim Sheba Medical CenterTel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Rastislav Pjontek
- Department of Neurology, University of HeidelbergHeidelberg, Germany
| | - Armin Grau
- Dept. of Neurology, Klinikum LudwigshafenLudwigshafen, Germany
| | - Thomas Klopstock
- Dept. of Neurology Friedrich-Baur-Institute, Ludwig-Maximilians-UniversityMunich, Germany
- German Center for Vertigo and Balance DisordersMunich, Germany
- DZNE – German Center for Neurodegenerative DiseasesMunich, Germany
- German Network for Mitochondrial Disorders(mitoNET), Germany
| | - Brent Fogel
- Department of Neurology David Geffen School of Medicine, University of CaliforniaLos Angeles, California
| | - Inge Meijer
- Montreal Neurological Institute, McGill UniversityMontreal, Canada
| | - Guy Rouleau
- Montreal Neurological Institute, McGill UniversityMontreal, Canada
| | | | - Madhavi Ganapathiraju
- Department of Biomedical Informatics School of Medicine, University of PittsburghPittsburgh, Pennsylvania
| | - Adeline Vanderver
- Department of Neurology, Childrens National Medical CenterWashington, District of Columbia
| | - Niklas Dahl
- Dept. of Immunology Genetics and Pathology Section of Clinical Genetics The Rudbeck laboratory, Uppsala University Children’s HospitalUppsala, Sweden
| | - Grace Hobson
- Nemours Biomedical Research, Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- University of Delaware, Department of BiologyNewark, Delaware
- Thomas Jefferson University, Jefferson Medical CollegePhiladelphia, Pennsylvania
| | - Alfredo Brusco
- University of Torino, Department of Medical SciencesTorino, Italy
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | | | - Quasar Saleem Padiath
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
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22
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Yamamoto T, Shimada S, Shimojima K. Fiber-fluorescence in situ hybridization analyses as a diagnostic application for orientation of microduplications. World J Med Genet 2013; 3:5-8. [DOI: 10.5496/wjmg.v3.i2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/14/2013] [Accepted: 06/04/2013] [Indexed: 02/06/2023] Open
Abstract
Microduplications are normally invisible under microscopy and were not recognized before chromosomal microarray testing was available. Although it is difficult to confirm the orientation of duplicated segments by standard fluorescence in situ hybridization (FISH), our data indicates that fiber-FISH analysis has the potential to reveal the orientation of duplicated and triplicated segments of chromosomes. Recurrent microduplications reciprocal to microdeletions show tandem orientations of the duplicated segments, which is consistent with a non-allelic homologous recombination mechanism. Several random duplications showed tandem configurations and inverted duplications are rare. Further analysis is required to fully elucidate the basic mechanisms underlying such duplications/triplications.
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Yamamoto T, Shimojima K. Pelizaeus-Merzbacher disease as a chromosomal disorder. Congenit Anom (Kyoto) 2013; 53:3-8. [PMID: 23480352 DOI: 10.1111/cga.12005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/04/2012] [Indexed: 12/29/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is a congenital hypomyelination disorder caused by alterations affecting the proteolipid protein 1 gene (PLP1) located on Xq22.2. Generally, patients with PLP1 missense mutations show the most severe form of PMD (connatal form); however, two-thirds of patients with PMD carry PLP1 duplications and present typical manifestations of the disorder, recognized as the classical form. Other rare PLP1 abnormalities have been also identified, including X-chromosome translocations, triplications, and a partial duplication, all involving PLP1. The genomic structure of the distal end of the PLP1 locus, characterized by repeated genomic segments, contributes to the chromosomal rearrangements around PLP1 and the manifestation of PMD. Thus, PMD is recognized as a chromosomal disorder.
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Affiliation(s)
- Toshiyuki Yamamoto
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan.
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24
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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] [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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25
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Froyen G, Belet S, Martinez F, Santos-Rebouças C, Declercq M, Verbeeck J, Donckers L, Berland S, Mayo S, Rosello M, Pimentel M, Fintelman-Rodrigues N, Hovland R, Rodrigues dos Santos S, Raymond F, Bose T, Corbett M, Sheffield L, van Ravenswaaij-Arts C, Dijkhuizen T, Coutton C, Satre V, Siu V, Marynen P. Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements. Am J Hum Genet 2012; 91:252-64. [PMID: 22840365 DOI: 10.1016/j.ajhg.2012.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/21/2012] [Accepted: 06/21/2012] [Indexed: 12/20/2022] Open
Abstract
We previously reported on nonrecurrent overlapping duplications at Xp11.22 in individuals with nonsyndromic intellectual disability (ID) harboring HSD17B10, HUWE1, and the microRNAs miR-98 and let-7f-2 in the smallest region of overlap. Here, we describe six additional individuals with nonsyndromic ID and overlapping microduplications that segregate in the families. High-resolution mapping of the 12 copy-number gains reduced the minimal duplicated region to the HUWE1 locus only. Consequently, increased mRNA levels were detected for HUWE1, but not HSD17B10. Marker and SNP analysis, together with identification of two de novo events, suggested a paternally derived intrachromosomal duplication event. In four independent families, we report on a polymorphic 70 kb recurrent copy-number gain, which harbors part of HUWE1 (exon 28 to 3' untranslated region), including miR-98 and let-7f-2. Our findings thus demonstrate that HUWE1 is the only remaining dosage-sensitive gene associated with the ID phenotype. Junction and in silico analysis of breakpoint regions demonstrated simple microhomology-mediated rearrangements suggestive of replication-based duplication events. Intriguingly, in a single family, the duplication was generated through nonallelic homologous recombination (NAHR) with the use of HUWE1-flanking imperfect low-copy repeats, which drive this infrequent NAHR event. The recurrent partial HUWE1 copy-number gain was also generated through NAHR, but here, the homologous sequences used were identified as TcMAR-Tigger DNA elements, a template that has not yet been reported for NAHR. In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements.
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26
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Shimojima K, Inoue T, Imai Y, Arai Y, Komoike Y, Sugawara M, Fujita T, Ideguchi H, Yasumoto S, Kanno H, Hirose S, Yamamoto T. Reduced PLP1 expression in induced pluripotent stem cells derived from a Pelizaeus-Merzbacher disease patient with a partial PLP1 duplication. J Hum Genet 2012; 57:580-6. [PMID: 22695888 DOI: 10.1038/jhg.2012.71] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive disorder characterized by dysmyelination of the central nervous system (CNS). We identified a rare partial duplication of the proteolipid protein 1 gene (PLP1) in a patient with PMD. To assess the underlying effect of this duplication, we examined PLP1 expression in induced pluripotent stem (iPS) cells generated from the patient's fibroblasts. Disease-specific iPS cells were generated from skin fibroblasts obtained from the indicated PMD patient and two other PMD patients having a 637-kb chromosomal duplication including entire PLP1 and a novel missense mutation (W212C) of PLP1, by transfections of OCT3/4, C-MYC, KLF4 and SOX2 using retro-virus vectors. PLP1 expressions in the generated iPS cells were examined by northern blot analysis. Although PLP1 expression was confirmed in iPS cells generated from two patients with the entire PLP1 duplication and the missense mutation of PLP1, iPS cells generated from the patient with the partial PLP1 duplication manifesting a milder form of PMD showed null expression. This indicated that the underlying effect of the partial PLP1 duplication identified in this study was different from other PLP1 alterations including a typical duplication and a missense mutation.
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Affiliation(s)
- Keiko Shimojima
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
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27
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Simmons AD, Carvalho CMB, Lupski JR. What have studies of genomic disorders taught us about our genome? Methods Mol Biol 2012; 838:1-27. [PMID: 22228005 DOI: 10.1007/978-1-61779-507-7_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The elucidation of genomic disorders began with molecular technologies that enabled detection of genomic changes which were (a) smaller than those resolved by traditional cytogenetics (less than 5 Mb) and (b) larger than what could be determined by conventional gel electrophoresis. Methods such as pulsed field gel electrophoresis (PFGE) and fluorescent in situ hybridization (FISH) could resolve such changes but were limited to locus-specific studies. The study of genomic disorders has rapidly advanced with the development of array-based techniques. These enabled examination of the entire human genome at a higher level of resolution, thus allowing elucidation of the basis of many new disorders, mechanisms that result in genomic changes that can result in copy number variation (CNV), and most importantly, a deeper understanding of the characteristics, features, and plasticity of our genome. In this chapter, we focus on the structural and architectural features of the genome, which can potentially result in genomic instability, delineate how mechanisms, such as NAHR, NHEJ, and FoSTeS/MMBIR lead to disease-causing rearrangements, and briefly describe the relationship between the leading methods presently used in studying genomic disorders. We end with a discussion on our new understanding about our genome including: the contribution of new mutation CNV to disease, the abundance of mosaicism, the extent of subtelomeric rearrangements, the frequency of de novo rearrangements associated with sporadic birth defects, the occurrence of balanced and unbalanced translocations, the increasing discovery of insertional translocations, the exploration of complex rearrangements and exonic CNVs. In the postgenomic era, our understanding of the genome has advanced very rapidly as the level of technical resolution has become higher. This leads to a greater understanding of the effects of rearrangements present both in healthy subjects and individuals with clinically relevant phenotypes.
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Bilir B, Yapici Z, Yalcinkaya C, Baris I, Carvalho CMB, Bartnik M, Ozes B, Eraksoy M, Lupski JR, Battaloglu E. High frequency of GJA12/GJC2 mutations in Turkish patients with Pelizaeus-Merzbacher disease. Clin Genet 2012; 83:66-72. [PMID: 22283455 DOI: 10.1111/j.1399-0004.2012.01846.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pelizaeus-Merzbacher disease is an early onset dysmyelinating leukodystrophy. About 80% of PMD cases have been associated with duplications and mutations of the proteolipid protein 1 (PLP1) gene. Pelizaeus-Merzbacher-like disease is a genetically heterogeneous autosomal recessive disease and rarely caused by mutations in gap junction protein α12 (GJA12/GJC2) gene. The molecular basis of the disease was investigated in a cohort of 19 Turkish families. This study identified novel chromosomal rearrangements proximal and distal to, and exclusive of the PLP1 gene, showed equal frequencies of PLP1 and GJA12/GJC2 mutations at least in our cohort, and suggested further genetic heterogeneity.
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Affiliation(s)
- B Bilir
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
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Abstract
Structural variation (SV) encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, and complex rearrangements, and is now recognized to be an abundant class of genetic variation in mammals. Different individuals, or strains, of a given species can differ by thousands of variants. However, despite a large number of studies over the past decade and impressive progress on many fronts, there remain significant gaps in our knowledge, particularly in species other than human. Arguably the most relevant among these are genetically tractable models such as mouse, rat, and dog. The emergence of efficient and affordable DNA sequencing technologies presents an opportunity to make rapid progress toward understanding the nature, origin, and function of SV in these, and other, domesticated species. Here, we summarize the current state of knowledge of SV in mammals, with a focus on the similarities and differences between domesticated species and human. We then present methods to identify SV breakpoints from next-generation sequence (NGS) data by paired-end mapping, split-read mapping, and local assembly, and discuss challenges that arise when interpreting these data in lineages with complex breeding histories and incomplete reference genomes. We further describe technical modifications that allow for identification of variants involving repetitive DNA elements such as transposons and segmental duplications. Finally, we explore a few of the key biological insights that can be gained by applying NGS methods to model organisms.
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Affiliation(s)
- Ira M Hall
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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30
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De Caris L, Cecceroni L, Tummala H. On a Break with the X: The Role of Repair of Double-Stranded DNA Breaks in X-Linked Disease. BIOTECHNOL BIOTEC EQ 2012. [DOI: 10.5504/bbeq.2012.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Laura De Caris
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
| | - Lucia Cecceroni
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
| | - Hemanth Tummala
- University of Abertay Dundee, School of Contemporary Sciences, Scotland, UK
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31
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Fusco F, Paciolla M, Napolitano F, Pescatore A, D'Addario I, Bal E, Lioi MB, Smahi A, Miano MG, Ursini MV. Genomic architecture at the Incontinentia Pigmenti locus favours de novo pathological alleles through different mechanisms. Hum Mol Genet 2011; 21:1260-71. [PMID: 22121116 DOI: 10.1093/hmg/ddr556] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IKBKG/NEMO gene mutations cause an X-linked, dominant neuroectodermal disorder named Incontinentia Pigmenti (IP). Located at Xq28, IKBKG/NEMO has a unique genomic organization, as it is part of a segmental duplication or low copy repeat (LCR1-LCR2, >99% identical) containing the gene and its pseudogene copy (IKBKGP). In the opposite direction and outside LCR1, IKBKG/NEMO partially overlaps G6PD, whose mutations cause a common X-linked human enzymopathy. The two LCRs in the IKBKG/NEMO locus are able to recombine through non-allelic homologous recombination producing either a pathological recurrent exon 4-10 IKBKG/NEMO deletion (IKBKGdel) or benign small copy number variations. We here report that the local high frequency of micro/macro-homologies, tandem repeats and repeat/repetitive sequences make the IKBKG/NEMO locus susceptible to novel pathological IP alterations. Indeed, we describe the first two independent instances of inter-locus gene conversion, occurring between the two LCRs, that copies the IKBKGP pseudogene variants into the functional IKBKG/NEMO, causing the de novo occurrence of p.Glu390ArgfsX61 and the IKBKGdel mutations, respectively. Subsequently, by investigating a group of 20 molecularly unsolved IP subjects using a high-density quantitative polymerase chain reaction assay, we have identified seven unique de novo deletions varying from 4.8 to ∼115 kb in length. Each deletion removes partially or completely both IKBKG/NEMO and the overlapping G6PD, thereby uncovering the first deletions disrupting the G6PD gene which were found in patients with IP. Interestingly, the 4.8 kb deletion removes the conserved bidirectional promoterB, shared by the two overlapping IKBKG/NEMO and G6PD genes, leaving intact the alternative IKBKG/NEMO unidirectional promoterA. This promoter, although active in the keratinocytes of the basal dermal layer, is down-regulated during late differentiation. Genomic analysis at the breakpoint sites indicated that other mutational forces, such as non-homologous end joining, Alu-Alu-mediated recombination and replication-based events, might enhance the vulnerability of the IP locus to produce de novo pathological IP alleles.
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Affiliation(s)
- Francesca Fusco
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, IGB-CNR, Naples 80131, Italy
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Takanashi JI, Saito S, Aoki I, Barkovich AJ, Ito Y, Inoue K. Increased N-acetylaspartate in model mouse of pelizaeus-merzbacher disease. J Magn Reson Imaging 2011; 35:418-25. [DOI: 10.1002/jmri.22817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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33
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Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nat Genet 2011; 43:1074-81. [PMID: 21964572 PMCID: PMC3235474 DOI: 10.1038/ng.944] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 08/23/2011] [Indexed: 01/17/2023]
Abstract
We identified complex genomic rearrangements consisting of intermixed duplications and triplications of genomic segments at the MECP2 and PLP1 loci. These complex rearrangements were characterized by a triplicated segment embedded within a duplication in 11 unrelated subjects. Notably, only two breakpoint junctions were generated during each rearrangement formation. All the complex rearrangement products share a common genomic organization, duplication-inverted triplication-duplication (DUP-TRP/INV-DUP), in which the triplicated segment is inverted and located between directly oriented duplicated genomic segments. We provide evidence that the DUP-TRP/INV-DUP structures are mediated by inverted repeats that can be separated by >300 kb, a genomic architecture that apparently leads to susceptibility to such complex rearrangements. A similar inverted repeat-mediated mechanism may underlie structural variation in many other regions of the human genome. We propose a mechanism that involves both homology-driven events, via inverted repeats, and microhomologous or nonhomologous events.
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34
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Carvalho CMB, Bartnik M, Pehlivan D, Fang P, Shen J, Lupski JR. Evidence for disease penetrance relating to CNV size: Pelizaeus-Merzbacher disease and manifesting carriers with a familial 11 Mb duplication at Xq22. Clin Genet 2011; 81:532-41. [PMID: 21623770 DOI: 10.1111/j.1399-0004.2011.01716.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potential causes for the incomplete penetrance of Pelizaeus-Merzbacher disease (PMD) in female carriers of PLP1 mutations are not well understood. We present a family with a boy having PMD in association with PLP1 duplication and three females who are apparent manifesting carriers. Custom high-resolution oligonucleotide array comparative genomic hybridization (aCGH) and breakpoint junction sequencing were performed and revealed a familial complex duplication consisting of a small duplicated genomic interval (∼56 kb) and a large segmental duplication (∼11 Mb) that resulted in a PLP1 copy number variation gain. Breakpoint junction analysis implicates a replication-based mechanism underlying the rearrangement formation. X-inactivation studies (XCI) showed a random to moderate advantageous skewing pattern in peripheral blood cells but a moderate to extremely skewed (≥90%) pattern in buccal cells. In conclusion, our data show that complex duplications involving PLP1 are not uncommon, can be detected at the level of genome resolution afforded by clinical aCGH and duplication and inversion can be produced in the same event. Furthermore, the observation of three manifesting carriers with a large genomic rearrangement supports the contention that duplication size along with genomic content can be an important factor for penetrance of the PMD phenotype in females.
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Affiliation(s)
- C M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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35
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Grossi S, Regis S, Biancheri R, Mort M, Lualdi S, Bertini E, Uziel G, Boespflug-Tanguy O, Simonati A, Corsolini F, Demir E, Marchiani V, Percesepe A, Stanzial F, Rossi A, Vaurs-Barrière C, Cooper DN, Filocamo M. Molecular genetic analysis of the PLP1 gene in 38 families with PLP1-related disorders: identification and functional characterization of 11 novel PLP1 mutations. Orphanet J Rare Dis 2011; 6:40. [PMID: 21679407 PMCID: PMC3125326 DOI: 10.1186/1750-1172-6-40] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/16/2011] [Indexed: 12/18/2022] Open
Abstract
Background The breadth of the clinical spectrum underlying Pelizaeus-Merzbacher disease and spastic paraplegia type 2 is due to the extensive allelic heterogeneity in the X-linked PLP1 gene encoding myelin proteolipid protein (PLP). PLP1 mutations range from gene duplications of variable size found in 60-70% of patients to intragenic lesions present in 15-20% of patients. Methods Forty-eight male patients from 38 unrelated families with a PLP1-related disorder were studied. All DNA samples were screened for PLP1 gene duplications using real-time PCR. PLP1 gene sequencing analysis was performed on patients negative for the duplication. The mutational status of all 14 potential carrier mothers of the familial PLP1 gene mutation was determined as well as 15/24 potential carrier mothers of the PLP1 duplication. Results and Conclusions PLP1 gene duplications were identified in 24 of the unrelated patients whereas a variety of intragenic PLP1 mutations were found in the remaining 14 patients. Of the 14 different intragenic lesions, 11 were novel; these included one nonsense and 7 missense mutations, a 657-bp deletion, a microdeletion and a microduplication. The functional significance of the novel PLP1 missense mutations, all occurring at evolutionarily conserved residues, was analysed by the MutPred tool whereas their potential effect on splicing was ascertained using the Skippy algorithm and a neural network. Although MutPred predicted that all 7 novel missense mutations would be likely to be deleterious, in silico analysis indicated that four of them (p.Leu146Val, p.Leu159Pro, p.Thr230Ile, p.Ala247Asp) might cause exon skipping by altering exonic splicing elements. These predictions were then investigated in vitro for both p.Leu146Val and p.Thr230Ile by means of RNA or minigene studies and were subsequently confirmed in the case of p.Leu146Val. Peripheral neuropathy was noted in four patients harbouring intragenic mutations that altered RNA processing, but was absent from all PLP1-duplication patients. Unprecedentedly, family studies revealed the de novo occurrence of the PLP1 duplication at a frequency of 20%.
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Affiliation(s)
- Serena Grossi
- SSD Lab, Diagnosi Pre-Postnatale Malattie Metaboliche, IRCCS G, Gaslini, Genova, Italy
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Carvalho CMB, Zhang F, Lupski JR. Structural variation of the human genome: mechanisms, assays, and role in male infertility. Syst Biol Reprod Med 2011; 57:3-16. [PMID: 21210740 DOI: 10.3109/19396368.2010.527427] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Genomic disorders are defined as diseases caused by rearrangements of the genome incited by a genomic architecture that conveys instability. Y-chromosome related dysfunctions such as male infertility are frequently associated with gross DNA rearrangements resulting from its peculiar genomic architecture. The Y-chromosome has evolved into a highly specialized chromosome to perform male functions, mainly spermatogenesis. Direct and inverted repeats, some of them palindromes with highly identical nucleotide sequences that can form DNA cruciform structures, characterize the genomic structure of the Y-chromosome long arm. Some particular Y chromosome genomic deletions can cause spermatogenic failure likely because of removal of one or more transcriptional units with a potential role in spermatogenesis. We describe mechanisms underlying the formation of human genomic rearrangements on autosomes and review Y-chromosome deletions associated with male infertility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3498, USA
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37
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van Binsbergen E. Origins and Breakpoint Analyses of Copy Number Variations: Up Close and Personal. Cytogenet Genome Res 2011; 135:271-6. [DOI: 10.1159/000330267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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38
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Whibley AC, Plagnol V, Tarpey PS, Abidi F, Fullston T, Choma MK, Boucher CA, Shepherd L, Willatt L, Parkin G, Smith R, Futreal PA, Shaw M, Boyle J, Licata A, Skinner C, Stevenson RE, Turner G, Field M, Hackett A, Schwartz CE, Gecz J, Stratton MR, Raymond FL. Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability. Am J Hum Genet 2010; 87:173-88. [PMID: 20655035 DOI: 10.1016/j.ajhg.2010.06.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 06/14/2010] [Accepted: 06/21/2010] [Indexed: 11/16/2022] Open
Abstract
Copy number variants and indels in 251 families with evidence of X-linked intellectual disability (XLID) were investigated by array comparative genomic hybridization on a high-density oligonucleotide X chromosome array platform. We identified pathogenic copy number variants in 10% of families, with mutations ranging from 2 kb to 11 Mb in size. The challenge of assessing causality was facilitated by prior knowledge of XLID-associated genes and the ability to test for cosegregation of variants with disease through extended pedigrees. Fine-scale analysis of rare variants in XLID families leads us to propose four additional genes, PTCHD1, WDR13, FAAH2, and GSPT2, as candidates for XLID causation and the identification of further deletions and duplications affecting X chromosome genes but without apparent disease consequences. Breakpoints of pathogenic variants were characterized to provide insight into the underlying mutational mechanisms and indicated a predominance of mitotic rather than meiotic events. By effectively bridging the gap between karyotype-level investigations and X chromosome exon resequencing, this study informs discussion of alternative mutational mechanisms, such as noncoding variants and non-X-linked disease, which might explain the shortfall of mutation yield in the well-characterized International Genetics of Learning Disability (IGOLD) cohort, where currently disease remains unexplained in two-thirds of families.
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Affiliation(s)
- Annabel C Whibley
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge CB2 0XY, UK
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39
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Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 2010; 20:623-35. [PMID: 20308636 DOI: 10.1101/gr.102970.109] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.
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Affiliation(s)
- Aaron R Quinlan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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40
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Comprehensive genetic analyses of PLP1 in patients with Pelizaeus-Merzbacher disease applied by array-CGH and fiber-FISH analyses identified new mutations and variable sizes of duplications. Brain Dev 2010; 32:171-9. [PMID: 19328639 DOI: 10.1016/j.braindev.2009.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 02/02/2009] [Accepted: 02/22/2009] [Indexed: 12/12/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD; MIM#312080) is a rare X-linked recessive neurodegenerative disorder. The main cause of PMD is alterations in the proteolipid protein 1 gene (PLP1) on chromosome Xq22.2. Duplications and point mutations of PLP1 have been found in 70% and 10-25% of all patients with PMD, respectively, with a wide clinical spectrum. Since the underlining genomic abnormalities are heterogeneous in patients with PMD, clarification of the genotype-phenotype correlation is the object of this study. Comprehensive genetic analyses using microarray-based comparative genomic hybridization (aCGH) analysis and genomic sequencing were applied to fifteen unrelated male patients with a clinical diagnosis of PMD. Duplicated regions were further analyzed by fiber-fluorescence in situ hybridization (FISH) analysis. Four novel and one known nucleotide alterations were identified in five patients. Five microduplications including PLP1 were identified by aCGH analysis with the sizes ranging from 374 to 951-kb. The directions of five PLP1 duplications were further investigated by fiber-FISH analysis, and all showed tandem duplications. The common manifestations of the disease in patients with PLP1 mutations or duplications in this study were nystagmus in early infancy, dysmyelination revealed by magnetic resonance imaging (MRI), and auditory brain response abnormalities. Although the grades of dysmyelination estimated by MRI findings were well correlated to the clinical phenotypes of the patients, there is no correlation between the size of the duplications and the phenotypic severity.
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Abstract
During the last quarter of the twentieth century, our knowledge about human genetic variation was limited mainly to the heterochromatin polymorphisms, large enough to be visible in the light microscope, and the single nucleotide polymorphisms (SNPs) identified by traditional PCR-based DNA sequencing. In the past five years, the rapid development and expanded use of microarray technologies, including oligonucleotide array comparative genomic hybridization and SNP genotyping arrays, as well as next-generation sequencing with “paired-end” methods, has enabled a whole-genome analysis with essentially unlimited resolution. The discovery of submicroscopic copy-number variations (CNVs) present in our genomes has changed dramatically our perspective on DNA structural variation and disease. It is now thought that CNVs encompass more total nucleotides and arise more frequently than SNPs. CNVs, to a larger extent than SNPs, have been shown to be responsible for human evolution, genetic diversity between individuals, and a rapidly increasing number of traits or susceptibility to traits; such conditions have been referred to as genomic disorders. In addition to well-known sporadic chromosomal microdeletion syndromes and Mendelian diseases, many common complex traits including autism and schizophrenia can result from CNVs. Both recombination- and replication-based mechanisms for CNV formation have been described.
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Affiliation(s)
| | - James R. Lupski
- Departments of Molecular and Human Genetics, Houston, Texas 77030
- Departments of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
- Departments of Texas Children's Hospital, Houston, Texas 77030
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Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci U S A 2010; 107 Suppl 1:1765-71. [PMID: 20080665 DOI: 10.1073/pnas.0906222107] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events.
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Padiath QS, Fu YH. Autosomal dominant leukodystrophy caused by lamin B1 duplications a clinical and molecular case study of altered nuclear function and disease. Methods Cell Biol 2010; 98:337-57. [PMID: 20816241 DOI: 10.1016/s0091-679x(10)98014-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Autosomal dominant leukodystrophy (ADLD) is an adult-onset demyelinating disorder that has recently shown to be caused by duplications of the nuclear lamina gene, lamin B1. This chapter attempts to collate and summarize the current knowledge about the disease and the clinical, pathological, and radiological presentations of the different ADLD families described till date. It also provides an overview of the molecular genetics underlying the disease and the mechanisms that may cause the duplication mutation event. ADLD is the first disease that has ever been linked to lamin B1 mutations and it expands the pathological role of the nuclear lamia to include disorders of the brain. The chapter also speculates on the different mechanisms that may link an important and ubiquitous structure like the nuclear lamina with the complex and cell-specific functions of myelin formation and maintenance. Understanding these mechanisms may not only prove helpful in understanding ADLD pathology but can also help in identifying new pathways that may be involved in myelin biology that can have implications for common demyelinating diseases like multiple sclerosis.
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Affiliation(s)
- Quasar Saleem Padiath
- Department of Neurology, University of California, San Francisco, San Francisco, California 94158, USA
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44
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Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10:551-64. [PMID: 19597530 DOI: 10.1038/nrg2593] [Citation(s) in RCA: 857] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deletions and duplications of chromosomal segments (copy number variants, CNVs) are a major source of variation between individual humans and are an underlying factor in human evolution and in many diseases, including mental illness, developmental disorders and cancer. CNVs form at a faster rate than other types of mutation, and seem to do so by similar mechanisms in bacteria, yeast and humans. Here we review current models of the mechanisms that cause copy number variation. Non-homologous end-joining mechanisms are well known, but recent models focus on perturbation of DNA replication and replication of non-contiguous DNA segments. For example, cellular stress might induce repair of broken replication forks to switch from high-fidelity homologous recombination to non-homologous repair, thus promoting copy number change.
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Affiliation(s)
- P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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45
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Zahir FR, Langlois S, Gall K, Eydoux P, Marra MA, Friedman JM. A novel de novo 1.1 Mb duplication of 17q21.33 associated with cognitive impairment and other anomalies. Am J Med Genet A 2009; 149A:1257-62. [PMID: 19449402 DOI: 10.1002/ajmg.a.32827] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on a 14-year-old girl with mild cognitive impairment, deafness, and an unusual pattern of anomalies associated with a previously unreported de novo duplication of chromosome 17q21.33. The 1.1 Mb duplication was detected by Affymetrix 100K GeneChip array genome hybridization and involves the genomic region between 45,093,544 and 46,196,038 base pairs on chromosome 17 (NCBI build 36.1). The patient has microcephaly, unusual cup-shaped ears, scoliosis and other skeletal defects. Two genes involved in the duplicated region, PPP1R9B and COL1A1, are strong candidates for producing her phenotype.
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Affiliation(s)
- Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Children's and Women's Hospital, Vancouver, British Columbia, Canada.
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46
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Carvalho CMB, Zhang F, Liu P, Patel A, Sahoo T, Bacino CA, Shaw C, Peacock S, Pursley A, Tavyev YJ, Ramocki MB, Nawara M, Obersztyn E, Vianna-Morgante AM, Stankiewicz P, Zoghbi HY, Cheung SW, Lupski JR. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum Mol Genet 2009; 18:2188-203. [PMID: 19324899 DOI: 10.1093/hmg/ddp151] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from approximately 250 kb to approximately 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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47
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Gu W, Lupski JR. CNV and nervous system diseases--what's new? Cytogenet Genome Res 2009; 123:54-64. [PMID: 19287139 DOI: 10.1159/000184692] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2008] [Indexed: 11/19/2022] Open
Abstract
Several new genomic disorders caused by copy number variation (CNV) of genes whose dosage is critical for the physiological function of the nervous system have been recently identified. Dup(7)(q11.23) patients carry duplications of the genomic region deleted in Williams-Beuren syndrome, they are characterized by prominent speech delay. The phenotypes of Potocki-Lupski syndrome and MECP2 duplication syndrome were neuropsychologically examined in detail, which revealed autism as an endophenotype and a prominent behavioral feature of these disorders. Tandem duplication of LMNB1 was reported to cause adult-onset autosomal dominant leukodystrophy. PAFAH1B1/LIS1 and YWHAE, which were deleted in isolated lissencephaly (PAFAH1B1/LIS1 alone) and Miller-Dieker syndrome (both genes), were found to be duplicated in patients with developmental delay. Finally, two novel microdeletion syndromes affecting 17q21.31 and 15q13.3, as well as their reciprocal duplications, were also identified. In this review, we provide an overview of the phenotypic manifestation of these syndromes and the rearrangements causing them.
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Affiliation(s)
- W Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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48
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A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet 2009; 5:e1000327. [PMID: 19180184 PMCID: PMC2621351 DOI: 10.1371/journal.pgen.1000327] [Citation(s) in RCA: 615] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
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Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. PATHOGENETICS 2008; 1:4. [PMID: 19014668 PMCID: PMC2583991 DOI: 10.1186/1755-8417-1-4] [Citation(s) in RCA: 432] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 11/03/2008] [Indexed: 02/08/2023]
Abstract
Genomic rearrangements describe gross DNA changes of the size ranging from a couple of hundred base pairs, the size of an average exon, to megabases (Mb). When greater than 3 to 5 Mb, such changes are usually visible microscopically by chromosome studies. Human diseases that result from genomic rearrangements have been called genomic disorders. Three major mechanisms have been proposed for genomic rearrangements in the human genome. Non-allelic homologous recombination (NAHR) is mostly mediated by low-copy repeats (LCRs) with recombination hotspots, gene conversion and apparent minimal efficient processing segments. NAHR accounts for most of the recurrent rearrangements: those that share a common size, show clustering of breakpoints, and recur in multiple individuals. Non-recurrent rearrangements are of different sizes in each patient, but may share a smallest region of overlap whose change in copy number may result in shared clinical features among different patients. LCRs do not mediate, but may stimulate non-recurrent events. Some rare NAHRs can also be mediated by highly homologous repetitive sequences (for example, Alu, LINE); these NAHRs account for some of the non-recurrent rearrangements. Other non-recurrent rearrangements can be explained by non-homologous end-joining (NHEJ) and the Fork Stalling and Template Switching (FoSTeS) models. These mechanisms occur both in germ cells, where the rearrangements can be associated with genomic disorders, and in somatic cells in which such genomic rearrangements can cause disorders such as cancer. NAHR, NHEJ and FoSTeS probably account for the majority of genomic rearrangements in our genome and the frequency distribution of the three at a given locus may partially reflect the genomic architecture in proximity to that locus. We provide a review of the current understanding of these three models.
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Affiliation(s)
- Wenli Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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50
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Gaudio DD, Yang Y, Boggs BA, Schmitt ES, Lee JA, Sahoo T, Pham HT, Wiszniewska J, Craig Chinault A, Beaudet AL, Eng CM. Molecular diagnosis of Duchenne/Becker muscular dystrophy: enhanced detection of dystrophin gene rearrangements by oligonucleotide array-comparative genomic hybridization. Hum Mutat 2008; 29:1100-7. [DOI: 10.1002/humu.20841] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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