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Havrylov S, Chrystal P, van Baarle S, French CR, MacDonald IM, Avasarala J, Rogers RC, Berry FB, Kume T, Waskiewicz AJ, Lehmann OJ. Pleiotropy in FOXC1-attributable phenotypes involves altered ciliation and cilia-dependent signaling. Sci Rep 2024; 14:20278. [PMID: 39217245 PMCID: PMC11365983 DOI: 10.1038/s41598-024-71159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
Alterations to cilia are responsible for a wide range of severe disease; however, understanding of the transcriptional control of ciliogenesis remains incomplete. In this study we investigated whether altered cilia-mediated signaling contributes to the pleiotropic phenotypes caused by the Forkhead transcription factor FOXC1. Here, we show that patients with FOXC1-attributable Axenfeld-Rieger Syndrome (ARS) have a prevalence of ciliopathy-associated phenotypes comparable to syndromic ciliopathies. We demonstrate that altering the level of Foxc1 protein, via shRNA mediated inhibition, CRISPR/Cas9 mutagenesis and overexpression, modifies cilia length in vitro. These structural changes were associated with substantially perturbed cilia-dependent signaling [Hedgehog (Hh) and PDGFRα], and altered ciliary compartmentalization of the Hh pathway transcription factor, Gli2. Consistent with these data, in primary cultures of murine embryonic meninges, cilia length was significantly reduced in heterozygous and homozygous Foxc1 mutants compared to controls. Meningeal expression of the core Hh signaling components Gli1, Gli3 and Sufu was dysregulated, with comparable dysregulation of Pdgfrα signaling evident from significantly altered Pdgfrα and phosphorylated Pdgfrα expression. On the basis of these clinical and experimental findings, we propose a model that altered cilia-mediated signaling contributes to some FOXC1-induced phenotypes.
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Affiliation(s)
- Serhiy Havrylov
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Paul Chrystal
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Suey van Baarle
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Curtis R French
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
- Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Ian M MacDonald
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Jagannadha Avasarala
- Department of Neurology, University of Kentucky Medical Center, Lexington, KY, USA
| | | | - Fred B Berry
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Surgery, 3002D Li Ka Shing Centre, University of Alberta, Edmonton, AB, Canada
| | - Tsutomu Kume
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ordan J Lehmann
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada.
- Department of Ophthalmology, 829 Medical Sciences Building, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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2
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Maxwell G, Souzeau E. Childhood glaucoma: Implications for genetic counselling. Clin Genet 2024. [PMID: 39206700 DOI: 10.1111/cge.14603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Childhood glaucoma is a heterogeneous group of ocular disorders defined by an age of onset from birth to 18 years. These vision-threatening disorders require early diagnosis, timely treatment, and lifelong management to maintain vision and minimise irreversible blindness. The genetics of childhood glaucoma is complex with both phenotypic and genetic heterogeneity. The purpose of this review is to summarise the different types of childhood glaucoma and their genetic architecture to aid in the genetic counselling process with patients and their families. We provide an overview of associated syndromes and discuss implications for genetic counselling, including genetic testing strategies, cascade genetic testing, and reproductive options.
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Affiliation(s)
- Giorgina Maxwell
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
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3
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Reis LM, Seese SE, Costakos D, Semina EV. Congenital anterior segment ocular disorders: Genotype-phenotype correlations and emerging novel mechanisms. Prog Retin Eye Res 2024; 102:101288. [PMID: 39097141 DOI: 10.1016/j.preteyeres.2024.101288] [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: 03/30/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Development of the anterior segment of the eye requires reciprocal sequential interactions between the arising tissues, facilitated by numerous genetic factors. Disruption of any of these processes results in congenital anomalies in the affected tissue(s) leading to anterior segment disorders (ASD) including aniridia, Axenfeld-Rieger anomaly, congenital corneal opacities (Peters anomaly, cornea plana, congenital primary aphakia), and primary congenital glaucoma. Current understanding of the genetic factors involved in ASD remains incomplete, with approximately 50% overall receiving a genetic diagnosis. While some genes are strongly associated with a specific clinical diagnosis, the majority of known factors are linked with highly variable phenotypic presentations, with pathogenic variants in FOXC1, CYP1B1, and PITX2 associated with the broadest spectrum of ASD conditions. This review discusses typical clinical presentations including associated systemic features of various forms of ASD; the latest functional data and genotype-phenotype correlations related to 25 ASD factors including newly identified genes; promising novel candidates; and current and emerging treatments for these complex conditions. Recent developments of interest in the genetics of ASD include identification of phenotypic expansions for several factors, discovery of multiple modes of inheritance for some genes, and novel mechanisms including a growing number of non-coding variants and alleles affecting specific domains/residues and requiring further studies.
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Affiliation(s)
- Linda M Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Sarah E Seese
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Elena V Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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4
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Syu YM, Ma JY, Ou TH, Lee CL, Lin HY, Lin SP, Lee CJ, Chen CP. De Novo Mosaic 6p23-p25.3 Tetrasomy Caused by a Small Supernumerary Marker Chromosome Presenting Trisomy Distal 6p Phenotype: A Case Report and Literature Review. Diagnostics (Basel) 2022; 12:2306. [PMID: 36291995 PMCID: PMC9600663 DOI: 10.3390/diagnostics12102306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) derived from the chromosome 6 short arm are rare and their clinical significance remains unknown. No case with sSMC(6) without centromeric DNA has been reported. Partial trisomy and tetrasomy of distal 6p is a rare but clinically distinct syndrome. We report on a de novo mosaic sSMC causing partial tetrasomy for 6p23-p25.3 in a male infant with symptoms of being small for gestational age, microcephaly, facial dysmorphism, congenital eye defects, and multi-system malformation. Conventional cytogenetic analysis revealed a karyotype of 47,XY,+mar [25]/46,XY [22]. Array comparative genomic hybridization (aCGH) revealed mosaic tetrasomy of distal 6p. This is the first case of mosaic tetrasomy 6p23-p25.3 caused by an inverted duplicated neocentric sSMC with characteristic features of trisomy distal 6p. Comparison of phenotypes in cases with trisomy and tetrasomy of 6p23-p25.3 could facilitate a genotype-phenotype correlation and identification of candidate genes contributing to their presentation. The presentation of anterior segment dysgenesis and anomaly of the renal system suggest triplosensitivity of the FOXC1 gene. In patients with microcephaly growth retardation, and malformation of the cardiac and renal systems, presentation of anterior segment dysgenesis might be indicative of chromosome 6p duplication, and aCGH evaluation should be performed for associated syndromic disease.
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Affiliation(s)
- Yu-Min Syu
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Juine-Yih Ma
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Tzu-Hsuen Ou
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Chung-Lin Lee
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Hsiang-Yu Lin
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medical Research, Division of Genetics and Metabolism, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Childhood Care and Education, MacKay Junior College of Medicine, Nursing and Management, Taipei 11260, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Shuan-Pei Lin
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medical Research, Division of Genetics and Metabolism, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
| | - Chia-Jung Lee
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei 10449, Taiwan
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei 11230, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11230, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41346, Taiwan
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5
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Elian FA, Are U, Ghosh S, Nuin P, Footz T, McMullen TPW, Brindley DN, Walter MA. FOXQ1 is Differentially Expressed Across Breast Cancer Subtypes with Low Expression Associated with Poor Overall Survival. BREAST CANCER-TARGETS AND THERAPY 2021; 13:171-188. [PMID: 33688250 PMCID: PMC7935334 DOI: 10.2147/bctt.s282860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
Purpose Forkhead box Q1 (FOXQ1) has been shown to contribute to the development and progression of cancers, including ovarian and breast cancer (BC). However, research exploring FOXQ1 expression, copy number variation (CNV), and prognostic value across different BC subtypes is limited. Our purpose was to evaluate FOXQ1 mRNA expression, CNV, and prognostic value across BC subtypes. Materials and Methods We determined FOXQ1 expression and CNV in BC patient tumors using RT-qPCR and qPCR, respectively. We also analyzed FOXQ1 expression and CNV in BC cell lines in the CCLE database using K-means clustering. The prognostic value of FOXQ1 expression in the TCGA-BRCA database was assessed using univariate and multivariate Cox's regression analysis as well as using the online tools OncoLnc, GEPIA, and UALCAN. Results Our analyses reveal that FOXQ1 mRNA is differentially expressed between different subtypes of BC and is significantly decreased in luminal BC and HER2 patients when compared to normal breast tissue samples. Furthermore, analysis of BC cell lines showed that FOXQ1 mRNA expression was independent of CNV. Moreover, patients with low FOXQ1 mRNA expression had significantly poorer overall survival compared to those with high FOXQ1 mRNA expression. Finally, low FOXQ1 expression had a critical impact on the prognostic values of BC patients and was an independent predictor of overall survival when it was adjusted for BC subtypes and to two other FOX genes, FOXF2 and FOXM1. Conclusion Our study reveals for the first time that FOXQ1 is differentially expressed across BC subtypes and that low expression of FOXQ1 is indicative of poor prognosis in patients with BC.
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Affiliation(s)
- Fahed A Elian
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ubah Are
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Sunita Ghosh
- Department of Medical Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Mathematical and Statistical Sciences, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Paulo Nuin
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tim Footz
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Todd P W McMullen
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - David N Brindley
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael A Walter
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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6
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Walter MA, Rezaie T, Hufnagel RB, Arno G. Ocular genetics in the genomics age. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:860-868. [PMID: 32896097 DOI: 10.1002/ajmg.c.31844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/29/2022]
Abstract
Current genetic screening methods for inherited eye diseases are concentrated on the coding exons of known disease genes (gene panels, clinical exome). These tests have a variable and often limited diagnostic rate depending on the clinical presentation, size of the gene panel and our understanding of the inheritance of the disorder (with examples described in this issue). There are numerous possible explanations for the missing heritability of these cases including undetected variants within the relevant gene (intronic, up/down-stream and structural variants), variants harbored in genes outside the targeted panel, intergenic variants, variants undetectable by the applied technology, complex/non-Mendelian inheritance, and nongenetic phenocopies. In this article we further explore and review methods to investigate these sources of missing heritability.
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Affiliation(s)
- Michael A Walter
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tayebeh Rezaie
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
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7
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Lang E, Koller S, Bähr L, Töteberg-Harms M, Atac D, Roulez F, Bahr A, Steindl K, Feil S, Berger W, Gerth-Kahlert C. Exome Sequencing in a Swiss Childhood Glaucoma Cohort Reveals CYP1B1 and FOXC1 Variants as Most Frequent Causes. Transl Vis Sci Technol 2020; 9:47. [PMID: 32832252 PMCID: PMC7414719 DOI: 10.1167/tvst.9.7.47] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose The aim of this study was to investigate the molecular basis of childhood glaucoma in Switzerland to recommend future targeted genetic analysis in the Swiss population. Methods Whole-exome sequencing and copy number variation (CNV) analysis was performed in a Swiss cohort of 18 patients from 14 unrelated families. Identified variants were validated by Sanger sequencing and multiplex ligation-dependent probe amplification. Breakpoints of structural variants were determined by a microarray. A minigene assay was conducted for functional analysis of a splice site variant. Results A diagnosis of primary congenital glaucoma was made in 14 patients, of which six (43%) harbored pathogenic variants in CYP1B1, one (7%) a frameshift variant in FOXC1, and seven (50%) remained without a genetic diagnosis. Three patients were diagnosed with glaucoma associated with nonacquired ocular anomalies, of which two patients with mild ocular features of Axenfeld-Rieger syndrome harbored a FOXC1 duplication plus an additional FOXC1 missense variant, and one patient with a Barkan membrane remained without genetic diagnosis. A diagnosis of juvenile open-angle glaucoma was made in one patient, and genetic analysis revealed a FOXC1 duplication. Conclusions Sequencing of CYP1B1 and FOXC1, as well as analysis of CNVs in FOXC1, should be performed before extended gene panel sequencing. Translational Relevance The identification of the molecular cause of childhood glaucoma is a prerequisite for genetic counseling and personalized care for patients and families.
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Affiliation(s)
- Elena Lang
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Marc Töteberg-Harms
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - David Atac
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Françoise Roulez
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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8
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Seifi M, Footz T, Taylor SAM, Elhady GM, Abdalla EM, Walter MA. Novel PITX2 gene mutations in patients with Axenfeld-Rieger syndrome. Acta Ophthalmol 2016; 94:e571-e579. [PMID: 27009473 DOI: 10.1111/aos.13030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/23/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE Mutations in the bicoid-like transcription factor PITX2 gene often result in Axenfeld-Rieger syndrome (ARS), an autosomal-dominant inherited disorder. We report here the discovery and characterization of novel PITX2 deletions in a small kindred with ARS. METHODS Two familial patients (father and son) from a consanguineous family were examined in the present study. Patient DNA samples were screened for PITX2 mutations by DNA sequencing and for copy number variation by SYBR Green quantitative polymerase chain reaction (PCR) analysis. RESULTS We report a novel deletion involving the coding region of PITX2 in both patients. The minimum size of the deletion is 1 421 914 bp that spans one upstream regulatory element (CE4), PITX2 and a minimum of 13 neighbouring genes. The maximum size of the deletion is 3 789 983 bp. The proband (son) additionally possesses a novel 2-bp deletion in a non-coding exon of the remaining PITX2 allele predicted to alter correct splicing. CONCLUSION Our findings implicate a novel deletion of the PITX2 gene in the pathogenesis of ARS in the affected family. This ARS family presented with an atypical and extremely severe phenotype that resulted in four miscarriages and the death at 10 months of age of a sib of the proband. As the phenotypic manifestations in the proband are more severe than that of the father, we hypothesize that the deletion of the entire PITX2 allele plus a novel 2-bp deletion (observed in the proband) within the remaining PITX2 allele together contributed to the atypical ARS presentation in this family. This is the first study reporting on bi-allelic changes of PITX2 potentially contributing to a more severe ARS phenotype.
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Affiliation(s)
- Morteza Seifi
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tim Footz
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Sherry A M Taylor
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ghada M Elhady
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ebtesam M Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Michael A Walter
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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9
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de Vos IJHM, Stegmann APA, Webers CAB, Stumpel CTRM. The 6p25 deletion syndrome: An update on a rare neurocristopathy. Ophthalmic Genet 2016; 38:101-107. [DOI: 10.3109/13816810.2016.1164191] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ivo J. H. M. de Vos
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Alexander P. A. Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Carroll A. B. Webers
- Department of Ophthalmology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Constance T. R. M. Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, the Netherlands
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10
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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11
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Hsiao MC, Piotrowski A, Callens T, Fu C, Wimmer K, Claes KBM, Messiaen L. Decoding NF1 Intragenic Copy-Number Variations. Am J Hum Genet 2015; 97:238-49. [PMID: 26189818 DOI: 10.1016/j.ajhg.2015.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 11/30/2022] Open
Abstract
Genomic rearrangements can cause both Mendelian and complex disorders. Currently, several major mechanisms causing genomic rearrangements, such as non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), fork stalling and template switching (FoSTeS), and microhomology-mediated break-induced replication (MMBIR), have been proposed. However, to what extent these mechanisms contribute to gene-specific pathogenic copy-number variations (CNVs) remains understudied. Furthermore, few studies have resolved these pathogenic alterations at the nucleotide-level. Accordingly, our aim was to explore which mechanisms contribute to a large, unique set of locus-specific non-recurrent genomic rearrangements causing the genetic neurocutaneous disorder neurofibromatosis type 1 (NF1). Through breakpoint-spanning PCR as well as array comparative genomic hybridization, we have identified the breakpoints in 85 unrelated individuals carrying an NF1 intragenic CNV. Furthermore, we characterized the likely rearrangement mechanisms of these 85 CNVs, along with those of two additional previously published NF1 intragenic CNVs. Unlike the most typical recurrent rearrangements mediated by flanking low-copy repeats (LCRs), NF1 intragenic rearrangements vary in size, location, and rearrangement mechanisms. We propose the DNA-replication-based mechanisms comprising both FoSTeS and/or MMBIR and serial replication stalling to be the predominant mechanisms leading to NF1 intragenic CNVs. In addition to the loop within a 197-bp palindrome located in intron 40, four Alu elements located in introns 1, 2, 3, and 50 were also identified as intragenic-rearrangement hotspots within NF1.
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Affiliation(s)
- Meng-Chang Hsiao
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Arkadiusz Piotrowski
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Tom Callens
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chuanhua Fu
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria
| | - Kathleen B M Claes
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan, 185 9000 Gent, Belgium
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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12
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Pasutto F, Mauri L, Popp B, Sticht H, Ekici A, Piozzi E, Bonfante A, Penco S, Schlötzer-Schrehardt U, Reis A. Whole exome sequencing reveals a novel de novo FOXC1 mutation in a patient with unrecognized Axenfeld–Rieger syndrome and glaucoma. Gene 2015; 568:76-80. [DOI: 10.1016/j.gene.2015.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/17/2015] [Accepted: 05/07/2015] [Indexed: 02/03/2023]
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13
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Allen KF, Gaier ED, Wiggs JL. Genetics of Primary Inherited Disorders of the Optic Nerve: Clinical Applications. Cold Spring Harb Perspect Med 2015; 5:a017277. [PMID: 26134840 DOI: 10.1101/cshperspect.a017277] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inherited disorders of the optic nerve significantly impact vision in children and adults. The optic nerve disorders most commonly encountered clinically are glaucoma and primary optic neuropathy including Leber's hereditary optic neuropathy (LHON) and autosomal dominant or Kjer's optic atrophy. Current knowledge of the genetics of optic neuropathy and glaucoma makes it possible to test for mutations in disease-causing genes allowing for presymptomatic testing and risk assessment, and recent advances have revealed important disease mechanisms that may suggest potential therapeutic targets. In this perspective, we describe the current approaches and limitations to genetic testing for these disorders and provide an update on the development of gene-based therapies.
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Affiliation(s)
- Keri F Allen
- Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114
| | - Eric D Gaier
- Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114
| | - Janey L Wiggs
- Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114
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14
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French CR, Seshadri S, Destefano AL, Fornage M, Arnold CR, Gage PJ, Skarie JM, Dobyns WB, Millen KJ, Liu T, Dietz W, Kume T, Hofker M, Emery DJ, Childs SJ, Waskiewicz AJ, Lehmann OJ. Mutation of FOXC1 and PITX2 induces cerebral small-vessel disease. J Clin Invest 2014; 124:4877-81. [PMID: 25250569 PMCID: PMC4347243 DOI: 10.1172/jci75109] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/21/2014] [Indexed: 01/24/2023] Open
Abstract
Patients with cerebral small-vessel disease (CSVD) exhibit perturbed end-artery function and have an increased risk for stroke and age-related cognitive decline. Here, we used targeted genome-wide association (GWA) analysis and defined a CSVD locus adjacent to the forkhead transcription factor FOXC1. Moreover, we determined that the linked SNPs influence FOXC1 transcript levels and demonstrated that patients as young as 1 year of age with altered FOXC1 function exhibit CSVD. MRI analysis of patients with missense and nonsense mutations as well as FOXC1-encompassing segmental duplication and deletion revealed white matter hyperintensities, dilated perivascular spaces, and lacunar infarction. In a zebrafish model, overexpression or morpholino-induced suppression of foxc1 induced cerebral hemorrhage. Inhibition of foxc1 perturbed platelet-derived growth factor (Pdgf) signaling, impairing neural crest migration and the recruitment of mural cells, which are essential for vascular stability. GWA analysis also linked the FOXC1-interacting transcription factor PITX2 to CSVD, and both patients with PITX2 mutations and murine Pitx2-/- mutants displayed brain vascular phenotypes. Together, these results extend the genetic etiology of stroke and demonstrate an increasing developmental basis for human cerebrovascular disease.
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Affiliation(s)
- Curtis R. French
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Sudha Seshadri
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Anita L. Destefano
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Myriam Fornage
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Corey R. Arnold
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Philip J. Gage
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan M. Skarie
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - William B. Dobyns
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Kathleen J. Millen
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ting Liu
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - William Dietz
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Tsutomu Kume
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Marten Hofker
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Derek J. Emery
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Sarah J. Childs
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J. Waskiewicz
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ordan J. Lehmann
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada. Department of Neurology and School of Public Health, Boston University, Boston, Massachusetts, USA. Institute of Molecular Medicine and School of Public Health, University of Texas Health Sciences Center, Houston, Texas, USA. Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada. Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA. Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. Department of Pediatrics and the Center for Integrative Brain Research, University of Washington, Seattle, Washington, USA. Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA. Department of Genetics, University of Groningen, Groningen, The Netherlands. Department of Radiology and Diagnostic Imaging, Department of Biological Sciences, and Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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15
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Kaurani L, Vishal M, Kumar D, Sharma A, Mehani B, Sharma C, Chakraborty S, Jha P, Ray J, Sen A, Dash D, Ray K, Mukhopadhyay A. Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins. Invest Ophthalmol Vis Sci 2014; 55:3258-64. [PMID: 24764060 DOI: 10.1167/iovs.14-14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Large copy number variations (CNV) can contribute to increased burden for neurodegenerative diseases. In this study, we analyzed the genome-wide burden of large CNVs > 100 kb in primary open angle glaucoma (POAG), a neurodegenerative disease of the eye that is the largest cause of irreversible blindness. METHODS Genome-wide analysis of CNVs > 100 kb were analyzed in a total of 1720 individuals, including an Indian cohort (347 POAG cases and 345 controls) and a Caucasian cohort (624 cases and 404 controls). All the CNV data were obtained from experiments performed on Illumina 660W-Quad (infinium) arrays. RESULTS We observed that for both the populations CNVs > 1 Mb was significantly enriched for gene-rich regions unique to the POAG cases (P < 10(-11)). In the Indian cohort CNVs > 1 Mb (39 calls) in patients influenced 125 genes while in controls 31 such CNVs influenced only 5 genes with no overlap. In both cohorts we observed 1.9-fold gene enrichment in patients for deletions compared to duplications, while such a bias was not observed in controls (0.3-fold). Overall duplications > 1 Mb were more than deletions (Del/Dup = 0.82) confirming that the enrichment of gene-rich deletions in patients was associated with the disease. Of the 39 CNVs > 1 Mb from Indian patients, 28 (72%) also were implicated in other neurodegenerative disorders, like autism, schizophrenia, sensorineural hearing loss, and so forth. We found one large duplication encompassing CNTN4 gene in Indian and Caucasian POAG patients that was absent in the controls. CONCLUSIONS To our knowledge, our study is the first report on large CNV bias for gene-rich regions in glaucomatous neurodegeneration, implicating its impact across populations of contrasting ethnicities. We identified CNTN4 as a novel candidate gene for POAG.
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Affiliation(s)
- Lalit Kaurani
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mansi Vishal
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Dhirendra Kumar
- G. N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anchal Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Bharati Mehani
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Charu Sharma
- Mathematics Department, Shiv Nadar University, Uttar Pradesh, India
| | - Subhadip Chakraborty
- Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | - Pankaj Jha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Jharna Ray
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | | | - Debasis Dash
- G. N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Kunal Ray
- Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Arijit Mukhopadhyay
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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16
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Rosenberg RE, Egan M, Rodgers S, Harter D, Burnside RD, Milla S, Pappas J. Complex chromosome rearrangement of 6p25.3->p23 and 12q24.32->qter in a child with moyamoya. Pediatrics 2013; 131:e1996-2001. [PMID: 23713105 DOI: 10.1542/peds.2012-0749] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A 7-year-old white girl presented with left hemiparesis and ischemic stroke secondary to moyamoya syndrome, a progressive cerebrovascular occlusive disorder of uncertain but likely multifactorial etiology. Past medical history revealed hearing loss and developmental delay/intellectual disability. Routine karyotype demonstrated extra chromosomal material on 6p. Single nucleotide polymorphism microarray revealed a previously unreported complex de novo genetic rearrangement involving subtelomeric segments on chromosomes 6p and 12q. The duplicated/deleted regions included several known OMIM-annotated genes. This novel phenotype and genotype provides information about a possible association of genomic copy number variation and moyamoya syndrome. Dosage-sensitive genes in the deleted and duplicated segments may be involved in aberrant vascular proliferation. Our case also emphasizes the importance of comprehensive evaluation of both developmental delay and congenital anomalies such as moyamoya.
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Affiliation(s)
- Rebecca E Rosenberg
- Department of Pediatrics, New York University School of Medicine, New York, NY, USA.
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17
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Verdin H, D'haene B, Beysen D, Novikova Y, Menten B, Sante T, Lapunzina P, Nevado J, Carvalho CMB, Lupski JR, De Baere E. Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PLoS Genet 2013; 9:e1003358. [PMID: 23516377 PMCID: PMC3597517 DOI: 10.1371/journal.pgen.1003358] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022] Open
Abstract
Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)—were described in the etiology of non-recurrent CNVs in human disease. In addition, their formation may be stimulated by genomic architectural features. It is, however, largely unexplored to what extent these mechanisms contribute to rare, locus-specific pathogenic CNVs. Here, fine-mapping of 42 microdeletions of the FOXL2 locus, encompassing FOXL2 (32) or its regulatory domain (10), serves as a model for rare, locus-specific CNVs implicated in genetic disease. These deletions lead to blepharophimosis syndrome (BPES), a developmental condition affecting the eyelids and the ovary. For breakpoint mapping we used targeted array-based comparative genomic hybridization (aCGH), quantitative PCR (qPCR), long-range PCR, and Sanger sequencing of the junction products. Microhomology, ranging from 1 bp to 66 bp, was found in 91.7% of 24 characterized breakpoint junctions, being significantly enriched in comparison with a random control sample. Our results show that microhomology-mediated repair mechanisms underlie at least 50% of these microdeletions. Moreover, genomic architectural features, like sequence motifs, non-B DNA conformations, and repetitive elements, were found in all breakpoint regions. In conclusion, the majority of these microdeletions result from microhomology-mediated mechanisms like MMEJ, FoSTeS, MMBIR, SRS, or BISRS. Moreover, we hypothesize that the genomic architecture might drive their formation by increasing the susceptibility for DNA breakage or promote replication fork stalling. Finally, our locus-centered study, elucidating the etiology of a large set of rare microdeletions involved in a monogenic disorder, can serve as a model for other clustered, non-recurrent microdeletions in genetic disease. Genomic disorder is a general term describing conditions caused by genomic aberrations leading to a copy number change of one or more genes. Copy number changes with the same length and clustered breakpoints for a group of patients with the same disorder are named recurrent rearrangements. These originate mostly from a well-studied mechanism, namely nonallelic homologous recombination (NAHR). In contrast, non-recurrent rearrangements vary in size, have scattered breakpoints, and can originate from several different mechanisms that are not fully understood. Here we tried to gain further insight into the extent to which these mechanisms contribute to non-recurrent rearrangements and into the possible role of the surrounding genomic architecture. To this end, we investigated a unique group of patients with non-recurrent deletions of the FOXL2 region causing blepharophimosis syndrome. We observed that the majority of these deletions can result from several mechanisms mediated by microhomology. Furthermore, our data suggest that rare pathogenic microdeletions do not occur at random genome sequences, but are possibly guided by the surrounding genomic architecture. Finally, our study, elucidating the etiology of a unique cohort of locus-specific microdeletions implicated in genetic disease, can serve as a model for the formation of genomic aberrations in other genetic disorders.
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Affiliation(s)
- Hannah Verdin
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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18
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Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics 2012; 130:e1085-95. [PMID: 23071206 DOI: 10.1542/peds.2012-0568] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To test the hypothesis that chromosomal microarray analysis frequently diagnoses conditions that require specific medical follow-up and that referring physicians respond appropriately to abnormal test results. METHODS A total of 46,298 postnatal patients were tested by chromosomal microarray analysis for a variety of indications, most commonly intellectual disability/developmental delay, congenital anomalies, dysmorphic features, and neurobehavioral problems. The frequency of detection of abnormalities associated with actionable clinical features was tallied, and the rate of physician response to a subset of abnormal tests results was monitored. RESULTS A total of 2088 diagnoses were made of more than 100 different disorders that have specific clinical features that warrant follow-up. The detection rate for these conditions using high-resolution whole-genome microarrays was 5.4%, which translates to 35% of all clinically significant abnormal test results identified in our laboratory. In a subset of cases monitored for physician response, appropriate clinical action was taken more than 90% of the time as a direct result of the microarray finding. CONCLUSIONS The disorders diagnosed by chromosomal microarray analysis frequently have clinical features that need medical attention, and physicians respond to the diagnoses with specific clinical actions, thus arguing that microarray testing provides clinical utility for a significant number of patients tested.
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Affiliation(s)
- Jay W Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington 99207, USA.
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Delahaye A, Khung-Savatovsky S, Aboura A, Guimiot F, Drunat S, Alessandri JL, Gérard M, Bitoun P, Boumendil J, Robin S, Huel C, Guilherme R, Serero S, Gressens P, Elion J, Verloes A, Benzacken B, Delezoide AL, Pipiras E. Pre- and postnatal phenotype of 6p25 deletions involving the FOXC1 gene. Am J Med Genet A 2012; 158A:2430-8. [PMID: 22903608 DOI: 10.1002/ajmg.a.35548] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 06/06/2012] [Indexed: 01/14/2023]
Abstract
FOXC1 deletion, duplication, and mutations are associated with Axenfeld-Rieger anomaly, and Dandy-Walker malformation spectrum. We describe the clinical history, physical findings, and available brain imaging studies in three fetuses, two children, and one adult with 6p25 deletions encompassing FOXC1. Various combinations of ocular and cerebellar malformations were found. In all three fetuses, necropsy including detailed microscopic assessments of the eyes and brains showed ocular anterior segment dysgenesis suggestive of Axenfeld-Rieger anomaly. Five 6p25 deletions were terminal, including two derived from inherited reciprocal translocations; the remaining 6p25 deletion was interstitial. The size and breakpoints of these deletions were characterized using comparative genomic hybridization arrays. All six deletions included FOXC1. Our data confirm that FOXC1 haploinsufficiency plays a major role in the phenotype of patients with 6p25 deletions. Histopathological features of Axenfeld-Rieger anomaly were clearly identifiable before the beginning of the third-trimester of gestation.
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Affiliation(s)
- Andrée Delahaye
- AP-HP, Hôpital Jean Verdier, Service d'Histologie, Embryologie, et Cytogénétique, Bondy, France.
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20
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Reply to Chakrabarti et al.: Corneal angiogenesis in patients with null
FOXC1
variants. Proc Natl Acad Sci U S A 2012. [DOI: 10.1073/pnas.1204931109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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21
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Cellini E, Disciglio V, Novara F, Barkovich JA, Mencarelli MA, Hayek J, Renieri A, Zuffardi O, Guerrini R. Periventricular heterotopia with white matter abnormalities associated with 6p25 deletion. Am J Med Genet A 2012; 158A:1793-7. [DOI: 10.1002/ajmg.a.35416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 03/19/2012] [Indexed: 11/07/2022]
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22
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Abstract
PURPOSE OF REVIEW Anterior segment dysgenesis (ASD) disorders encompass a spectrum of developmental conditions affecting the cornea, iris, and lens and are generally associated with an approximate 50% risk for glaucoma. These conditions are characterized by both autosomal dominant and recessive patterns of inheritance often with incomplete penetrance/variable expressivity. This article summarizes what is known about the genetics of ASD disorders and reviews recent developments. RECENT FINDINGS Mutations in Collagen type IV alpha-1 (COL4A1) and Beta-1,3-galactosyltransferase-like (B3GALTL) have been reported in ASD patients. Novel findings in other well known ocular genes are also presented, among which regulatory region deletions in PAX6 and PITX2 are most notable. SUMMARY Although a number of genetic causes have been identified, many ASD conditions are still awaiting genetic elucidation. The majority of characterized ASD genes encode transcription factors; several other genes represent extracellular matrix-related proteins. All of the involved genes play active roles in ocular development and demonstrate conserved functions across species. The use of novel technologies, such as whole genome sequencing/comparative genomic hybridization, is likely to broaden the mutation spectrums in known genes and assist in the identification of novel causative genes as well as modifiers explaining the phenotypic variability of ASD conditions.
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23
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Forkhead box transcription factor FoxC1 preserves corneal transparency by regulating vascular growth. Proc Natl Acad Sci U S A 2011; 109:2015-20. [PMID: 22171010 DOI: 10.1073/pnas.1109540109] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Normal vision requires the precise control of vascular growth to maintain corneal transparency. Here we provide evidence for a unique mechanism by which the Forkhead box transcription factor FoxC1 regulates corneal vascular development. Murine Foxc1 is essential for development of the ocular anterior segment, and in humans, mutations have been identified in Axenfeld-Rieger syndrome, a disorder characterized by anterior segment dysgenesis. We show that FOXC1 mutations also lead to corneal angiogenesis, and that mice homozygous for either a global (Foxc1(-/-)) or neural crest (NC)-specific (NC-Foxc1(-/-)) null mutation display excessive growth of corneal blood and lymphatic vessels. This is associated with disorganization of the extracellular matrix and increased expression of multiple matrix metalloproteinases. Heterozygous mutants (Foxc1(+/-) and NC-Foxc1(+/-)) exhibit milder phenotypes, such as disrupted limbal vasculature. Moreover, environmental exposure to corneal injury significantly increases growth of both blood and lymphatic vessels in both Foxc1(+/-) and NC-Foxc1(+/-) mice compared with controls. Notably, this amplification of the angiogenic response is abolished by inhibition of VEGF receptor 2. Collectively, these findings identify a role for FoxC1 in inhibiting corneal angiogenesis, thereby maintaining corneal transparency by regulating VEGF signaling.
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24
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McKeone R, Vieira H, Gregory-Evans K, Gregory-Evans CY, Denny P. Foxf2: a novel locus for anterior segment dysgenesis adjacent to the Foxc1 gene. PLoS One 2011; 6:e25489. [PMID: 22022403 PMCID: PMC3192754 DOI: 10.1371/journal.pone.0025489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/05/2011] [Indexed: 12/12/2022] Open
Abstract
Anterior segment dysgenesis (ASD) is characterised by an abnormal migration of neural crest cells or an aberrant differentiation of the mesenchymal cells during the formation of the eye's anterior segment. These abnormalities result in multiple tissue defects affecting the iris, cornea and drainage structures of the iridocorneal angle including the ciliary body, trabecular meshwork and Schlemm's canal. In some cases, abnormal ASD development leads to glaucoma, which is usually associated with increased intraocular pressure. Haploinsufficiency through mutation or chromosomal deletion of the human FOXC1 transcription factor gene or duplications of the 6p25 region is associated with a spectrum of ocular abnormalities including ASD. However, mapping data and phenotype analysis of human deletions suggests that an additional locus for this condition may be present in the same chromosomal region as FOXC1. DHPLC screening of ENU mutagenised mouse archival tissue revealed five novel mouse Foxf2 mutations. Re-derivation of one of these (the Foxf2W174R mouse lineage) resulted in heterozygote mice that exhibited thinning of the iris stroma, hyperplasia of the trabecular meshwork, small or absent Schlemm's canal and a reduction in the iridocorneal angle. Homozygous E18.5 mice showed absence of ciliary body projections, demonstrating a critical role for Foxf2 in the developing eye. These data provide evidence that the Foxf2 gene, separated from Foxc1 by less than 70 kb of genomic sequence (250 kb in human DNA), may explain human abnormalities in some cases of ASD where FOXC1 has been excluded genetically.
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Affiliation(s)
- Richard McKeone
- MRC Mammalian Genetics Unit, Harwell, Oxford, United Kingdom
| | - Helena Vieira
- Department of Cell and Molecular Biology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kevin Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl Y. Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul Denny
- MRC Mammalian Genetics Unit, Harwell, Oxford, United Kingdom
- * E-mail:
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25
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Davis LK, Meyer KJ, Schindler EI, Beck JS, Rudd DS, Grundstad AJ, Scheetz TE, Braun TA, Fingert JH, Alward WLM, Kwon YH, Folk JC, Russell SR, Wassink TH, Sheffield VC, Stone EM. Copy number variations and primary open-angle glaucoma. Invest Ophthalmol Vis Sci 2011; 52:7122-33. [PMID: 21310917 DOI: 10.1167/iovs.10-5606] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE This study sought to investigate the role of rare copy number variation (CNV) in age-related disorders of blindness, with a focus on primary open-angle glaucoma (POAG). Data are reported from a whole-genome copy number screen in a large cohort of 400 individuals with POAG and 500 age-matched glaucoma-free subjects. METHODS DNA samples from patients and controls were tested for CNVs using a combination of two microarray platforms. The signal intensity data generated from these arrays were then analyzed with multiple CNV detection programs including CNAG version 2.0, PennCNV, and dChip. RESULTS A total of 11 validated CNVs were identified as recurrent in the POAG set and absent in the age-matched control set. This set included CNVs on 5q23.1 (DMXL1, DTWD2), 20p12 (PAK7), 12q14 (C12orf56, XPOT, TBK1, and RASSF3), 12p13.33 (TULP3), and 10q34.21 (PAX2), among others. The CNVs presented here are exceedingly rare and are not found in the Database of Genomic Variants. Moreover, expression data from ocular tissue support the role of these CNV-implicated genes in vision-related processes. In addition, CNV locations of DMXL1 and PAK7 overlap previously identified linkage signals for glaucoma on 5p23.1 and 20p12, respectively. CONCLUSIONS The data are consistent with the hypothesis that rare CNV plays a role in the development of POAG.
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Affiliation(s)
- Lea K Davis
- Department of Psychiatry, University of Illinois, Chicago, Illinois, USA
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26
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Acharya M, Huang L, Fleisch VC, Allison WT, Walter MA. A complex regulatory network of transcription factors critical for ocular development and disease. Hum Mol Genet 2011; 20:1610-24. [PMID: 21282189 DOI: 10.1093/hmg/ddr038] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The PITX2 'homeobox' and FOXC1 and FOXC2 'forkhead box' transcription factors are critical for eye development and cause human ocular diseases when mutated. We have identified biochemical and genetic links between these transcription factors and a transcriptional regulator protein PRKC apoptosis Wilms' tumor 1 regulator (PAWR) that we propose to functionally connect all these proteins in a common pathway critically involved in eye development. We discovered all binary physical interactions between FOXC1, PITX2, FOXC2 and PAWR. Importantly, PAWR modulates the abilities of PITX2, FOXC1 and FOXC2 to activate their genetic targets. Together with either FOXC1 or FOXC2, PAWR increases PITX2 activity. PAWR reduces PITX2 activity in the absence of FOXC1 or FOXC2. At the same time, PAWR also exerts different regulatory effects on different FOXC target sites. Furthermore, morpholino knockdown of pitx2, foxc1 and pawr in zebrafish indicate that PAWR, FOXC1 and PITX2 genetically interact, and are in the same developmental pathway. These data for the first time tie PITX2, FOXC1, FOXC2 and PAWR into a common regulatory pathway. We have therefore identified a functional link between three transcription factors, modulated by PAWR, which we propose underlies the similar ocular phenotypes and glaucoma pathology caused by mutations of these genes.
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Affiliation(s)
- Moulinath Acharya
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7.
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27
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Zhang A, Skaar DA, Li Y, Huang D, Price TM, Murphy SK, Jirtle RL. Novel retrotransposed imprinted locus identified at human 6p25. Nucleic Acids Res 2011; 39:5388-400. [PMID: 21421564 PMCID: PMC3141237 DOI: 10.1093/nar/gkr108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Differentially methylated regions (DMRs) are stable epigenetic features within or in proximity to imprinted genes. We used this feature to identify candidate human imprinted loci by quantitative DNA methylation analysis. We discovered a unique DMR at the 5′-end of FAM50B at 6p25.2. We determined that sense transcripts originating from the FAM50B locus are expressed from the paternal allele in all human tissues investigated except for ovary, in which expression is biallelic. Furthermore, an antisense transcript, FAM50B-AS, was identified to be monoallelically expressed from the paternal allele in a variety of tissues. Comparative phylogenetic analysis showed that FAM50B orthologs are absent in chicken and platypus, but are present and biallelically expressed in opossum and mouse. These findings indicate that FAM50B originated in Therians after divergence from Prototherians via retrotransposition of a gene on the X chromosome. Moreover, our data are consistent with acquisition of imprinting during Eutherian evolution after divergence of Glires from the Euarchonta mammals. FAM50B expression is deregulated in testicular germ cell tumors, and loss of imprinting occurs frequently in testicular seminomas, suggesting an important role for FAM50B in spermatogenesis and tumorigenesis. These results also underscore the importance of accounting for parental origin in understanding the mechanism of 6p25-related diseases.
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Affiliation(s)
- Aiping Zhang
- Department of Radiation Oncology, Department of Community and Family Medicine and Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
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28
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Lehman AM, du Souich C, Chai D, Eydoux P, Huang JL, Fok AK, Avila L, Swingland J, Delaney AD, McGillivray B, Goldowitz D, Argiropoulos B, Kobor MS, Boerkoel CF. 19p13.2 microduplication causes a Sotos syndrome-like phenotype and alters gene expression. Clin Genet 2011; 81:56-63. [PMID: 21204797 DOI: 10.1111/j.1399-0004.2010.01615.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Up to 90% of individuals affected by Sotos syndrome have a pathogenic alteration of NSD1 (encodes nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1), a histone methyltransferase that functions as both a transcriptional activator and a repressor. Genomic copy number variations may also cause a Sotos-like phenotype. We evaluated a three-generation family segregating a Sotos-like disorder characterized by typical facial features, overgrowth, learning disabilities, and advanced bone age. Affected individuals did not have a detectable NSD1 mutation, but rather were found to have a 1.9 Mb microduplication of 19p13.2 with breakpoints in two highly homologous Alu elements. Because the duplication included the DNA methyltransferase gene (DNMT1), we assessed DNA methylation of peripheral blood and buccal cell DNA and detected no alterations. We also examined peripheral blood gene expression and found evidence for increased expression of genes within the duplicated region. We conclude that microduplication of 19p13.2 is a novel genomic disorder characterized by variable neurocognitive disability, overgrowth, and facial dysmorphism similar to Sotos syndrome. Failed compensation of gene duplication at the transcriptional level, as seen in peripheral blood, supports gene dosage as the cause of this disorder.
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Affiliation(s)
- A M Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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29
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Bedoyan JK, Lesperance MM, Ackley T, Iyer RK, Innis JW, Misra VK. A complex 6p25 rearrangement in a child with multiple epiphyseal dysplasia. Am J Med Genet A 2010; 155A:154-63. [PMID: 21204225 DOI: 10.1002/ajmg.a.33751] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 09/12/2010] [Indexed: 11/08/2022]
Abstract
Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic hybridization arrays (aCGH) of different resolutions (44 and 244K) as well as a 1 M single nucleotide polymorphism (SNP) array to analyze this complex rearrangement. Our analyses reveal a complex rearrangement involving a ∼2.21 Mb interstitial deletion, a ∼240 kb terminal deletion, and a 70-80 kb region in between these two deletions that shows maintenance of genomic copy number. The interstitial deletion contains eight known genes, including three Forkhead box containing (FOX) transcription factors (FOXQ1, FOXF2, and FOXC1). The region maintaining genomic copy number partly overlaps the dual specificity protein phosphatase 22 (DUSP22) gene. Array analyses suggest a homozygous loss of genomic material at the 5' end of DUSP22, which was corroborated using TaqMan® copy number analysis. It is possible that this homozygous genomic loss may render both copies of DUSP22 or its products non-functional. Our analysis suggests a rearrangement mechanism distinct from a previously reported replication-based error-prone mechanism without template switching for a specific 6p25 rearrangement with a 1.22 Mb interstitial deletion. Our study demonstrates the utility and limitations of using oligonucleotide-based aCGH and SNP array technologies of increasing resolutions in order to identify complex DNA rearrangements and gene disruptions.
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Affiliation(s)
- Jirair K Bedoyan
- Department of Pediatrics, The University of Michigan Medical School, Ann Arbor, USA.
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30
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Pasic I, Shlien A, Durbin AD, Stavropoulos DJ, Baskin B, Ray PN, Novokmet A, Malkin D. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res 2010; 70:160-71. [PMID: 20048075 DOI: 10.1158/0008-5472.can-09-1902] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Osteosarcomas are copy number alteration (CNA)-rich malignant bone tumors. Using microarrays, fluorescence in situ hybridization, and quantitative PCR, we characterize a focal region of chr3q13.31 (osteo3q13.31) harboring CNAs in 80% of osteosarcomas. As such, osteo3q13.31 is the most altered region in osteosarcoma and contests the view that CNAs in osteosarcoma are nonrecurrent. Most (67%) osteo3q13.31 CNAs are deletions, with 75% of these monoallelic and frequently accompanied by loss of heterozygosity (LOH) in flanking DNA. Notably, these CNAs often involve the noncoding RNAs LOC285194 and BC040587 and, in some cases, a tumor suppressor gene that encodes the limbic system-associated membrane protein (LSAMP). Ubiquitous changes occur in these genes in osteosarcoma, usually involving loss of expression. Underscoring their functional significance, expression of these genes is correlated with the presence of osteo3q13.31 CNAs. Focal osteo3q13.31 CNAs and LOH are also common in cell lines from other cancers, identifying osteo3q13.31 as a generalized candidate region for tumor suppressor genes. Osteo3q13.31 genes may function as a unit, given significant correlation in their expression despite the great genetic distances between them. In support of this notion, depleting either LSAMP or LOC285194 promoted proliferation of normal osteoblasts by regulation of apoptotic and cell-cycle transcripts and also VEGF receptor 1. Moreover, genetic deletions of LOC285194 or BC040587 were also associated with poor survival of osteosarcoma patients. Our findings identify osteo3q13.31 as a novel region of cooperatively acting tumor suppressor genes.
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Affiliation(s)
- Ivan Pasic
- Institute of Medical Science, Department of Medical Biophysics, University of Toronto, and Program in Genetics and Genome Biology, Department of Pediatric Laboratory Medicine, Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
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31
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Tümer Z, Bach-Holm D. Axenfeld-Rieger syndrome and spectrum of PITX2 and FOXC1 mutations. Eur J Hum Genet 2009; 17:1527-39. [PMID: 19513095 PMCID: PMC2987033 DOI: 10.1038/ejhg.2009.93] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 01/23/2009] [Accepted: 03/17/2009] [Indexed: 01/09/2023] Open
Abstract
Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant disorder, which encompasses a range of congential malformations affecting the anterior segment of the eye. ARS shows genetic heterogeneity and mutations of the two genes, PITX2 and FOXC1, are known to be associated with the pathogenesis. There are several excellent reviews dealing with the complexity of the phenotype and genotype of ARS. In this study, we will attempt to give a brief review of the clinical features and the relevant diagnostic approaches, together with a detailed review of published PITX2 and FOXC1 mutations.
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Affiliation(s)
- Zeynep Tümer
- The Kennedy Center, Medical Genetics Laboratory, Glostrup, Denmark.
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32
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Catelani ALPM, Krepischi ACV, Kim CA, Kok F, Otto PA, Auricchio MTBM, Mazzeu JF, Uehara DT, Costa SS, Knijnenburg J, Tabith A, Vianna-Morgante AM, Mingroni-Netto RC, Rosenberg C. Chromosome imbalances in syndromic hearing loss. Clin Genet 2009; 76:458-64. [DOI: 10.1111/j.1399-0004.2009.01276.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Yang XR, Ng D, Alcorta DA, Liebsch NJ, Sheridan E, Li S, Goldstein AM, Parry DM, Kelley MJ. T (brachyury) gene duplication confers major susceptibility to familial chordoma. Nat Genet 2009; 41:1176-8. [PMID: 19801981 DOI: 10.1038/ng.454] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 08/17/2009] [Indexed: 01/20/2023]
Abstract
Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex families with at least three cases of chordoma, a cancer of presumed notochordal origin. The duplicated region contains only the T (brachyury) gene, which is important in notochord development and is expressed in most sporadic chordomas. Our findings highlight the value of screening for complex genomic rearrangements in searches for cancer-susceptibility genes.
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Affiliation(s)
- Xiaohong R Yang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
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34
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Bibliography. Current world literature. Curr Opin Ophthalmol 2009; 20:417-22. [PMID: 19684489 DOI: 10.1097/icu.0b013e32833079c5] [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]
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35
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FOXC1 is required for normal cerebellar development and is a major contributor to chromosome 6p25.3 Dandy-Walker malformation. Nat Genet 2009; 41:1037-42. [PMID: 19668217 DOI: 10.1038/ng.422] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 06/29/2009] [Indexed: 12/22/2022]
Abstract
Dandy-Walker malformation (DWM), the most common human cerebellar malformation, has only one characterized associated locus. Here we characterize a second DWM-linked locus on 6p25.3, showing that deletions or duplications encompassing FOXC1 are associated with cerebellar and posterior fossa malformations including cerebellar vermis hypoplasia (CVH), mega-cisterna magna (MCM) and DWM. Foxc1-null mice have embryonic abnormalities of the rhombic lip due to loss of mesenchyme-secreted signaling molecules with subsequent loss of Atoh1 expression in vermis. Foxc1 homozygous hypomorphs have CVH with medial fusion and foliation defects. Human FOXC1 heterozygous mutations are known to affect eye development, causing a spectrum of glaucoma-associated anomalies (Axenfeld-Rieger syndrome, ARS; MIM no. 601631). We report the first brain imaging data from humans with FOXC1 mutations and show that these individuals also have CVH. We conclude that alteration of FOXC1 function alone causes CVH and contributes to MCM and DWM. Our results highlight a previously unrecognized role for mesenchyme-neuroepithelium interactions in the mid-hindbrain during early embryogenesis.
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