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Rose AM, Krishan A, Chakarova CF, Moya L, Chambers SK, Hollands M, Illingworth JC, Williams SMG, McCabe HE, Shah AZ, Palmer CNA, Chakravarti A, Berg JN, Batra J, Bhattacharya SS. MSR1 repeats modulate gene expression and affect risk of breast and prostate cancer. Ann Oncol 2019; 29:1292-1303. [PMID: 29509840 DOI: 10.1093/annonc/mdy082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background MSR1 repeats are a 36-38 bp minisatellite element that have recently been implicated in the regulation of gene expression, through copy number variation (CNV). Patients and methods Bioinformatic and experimental methods were used to assess the distribution of MSR1 across the genome, evaluate the regulatory potential of such elements and explore the role of MSR1 elements in cancer, particularly non-familial breast cancer and prostate cancer. Results MSR1s are predominately located at chromosome 19 and are functionally enriched in regulatory regions of the genome, particularly regions implicated in short-range regulatory activities (H3K27ac, H3K4me1 and H3K4me3). MSR1-regulated genes were found to have specific molecular roles, such as serine-protease activity (P = 4.80 × 10-7) and ion channel activity (P = 2.7 × 10-4). The kallikrein locus was found to contain a large number of MSR1 clusters, and at least six of these showed CNV. An MSR1 cluster was identified within KLK14, with 9 and 11 copies being normal variants. A significant association with the 9-copy allele and non-familial breast cancer was found in two independent populations (P = 0.004; P = 0.03). In the white British population, the minor allele conferred an increased risk of 1.21-3.51 times for all non-familial disease, or 1.7-5.3 times in early-onset disease. The 9-copy allele was also found to be associated with increased risk of prostate cancer in an independent population (odds ratio = 1.27-1.56; P =0.009). Conclusions MSR1 repeats act as molecular switches that modulate gene expression. It is likely that CNV of MSR1 will affect risk of development of various forms of cancer, including that of breast and prostate. The MSR1 cluster at KLK14 represents the strongest risk factor identified to date in non-familial breast cancer and a significant risk factor for prostate cancer. Analysis of MSR1 genotype will allow development of precise stratification of disease risk and provide a novel target for therapeutic agents.
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Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.
| | - A Krishan
- Cell Therapy and Regenerative Medicine, CABIMER, Seville, Spain
| | - C F Chakarova
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK
| | - L Moya
- Australian Prostate Cancer Research Centre - Queensland, Translational Research Institute, Brisbane; Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane
| | - S K Chambers
- Menzies Health Institute Queensland, Griffith University, Southport; Cancer Research Centre, Cancer Council Queensland, Brisbane, Australia
| | - M Hollands
- UCL Medical School, University College London, London
| | | | | | - H E McCabe
- Clinical Genetics, Ninewells Hospital & Medical School, University of Dundee, Dundee
| | - A Z Shah
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK
| | - C N A Palmer
- Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and School of Medicine, University of Dundee, Dundee, UK
| | - A Chakravarti
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J N Berg
- Clinical Genetics, Ninewells Hospital & Medical School, University of Dundee, Dundee
| | - J Batra
- Australian Prostate Cancer Research Centre - Queensland, Translational Research Institute, Brisbane; Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK; Cell Therapy and Regenerative Medicine, CABIMER, Seville, Spain
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Kousal B, Skalicka P, Valesova L, Fletcher T, Hart-Holden N, O'Grady A, Chakarova CF, Michaelides M, Hardcastle AJ, Liskova P. Severe retinal degeneration in women with a c.2543del mutation in ORF15 of the RPGR gene. Mol Vis 2014; 20:1307-17. [PMID: 25352739 PMCID: PMC4169777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 09/18/2014] [Indexed: 11/11/2022] Open
Abstract
PURPOSE To describe the genotype-phenotype correlation and serial observations in a five-generation Czech family with X-linked retinitis pigmentosa (XLRP) associated with severe visual impairment in women. METHODS Comprehensive ophthalmological examination including spectral domain optical coherence tomography (SD-OCT) was performed. Based on the pedigree structure and women being severely affected, autosomal dominant inheritance was suspected, and screening for known mutations by genotyping microarray was performed. Subsequently, direct sequencing of ORF15 RPGR was undertaken. RESULTS Eighteen family members (nine women and nine men) were examined. A pathogenic variant, c.2543del in ORF15 of RPGR, was found to segregate with disease. The oldest woman and her two sisters had no perception of light in their sixth decade. Four women and five men had signs and symptoms of typical XLRP, including moderate to high myopia. Three other women also had moderate to high myopia and myopic astigmatism but without the presence of bone spicule-like formation. Severe disruption of macular architecture on SD-OCT was equally common in both sexes. Only one 32-year-old female carrier had clinically normal findings. Subfoveal choroidal thickness was decreased in all affected men and in all female carriers, except the only carrier with a normal fundus examination. CONCLUSIONS The c.2543del mutation in ORF15 of RPGR is associated with a severe phenotype in the women in this family. The presence of a significant myopic refractive error, in the absence of male-to-male transmission, may be indicative of X-linked inheritance. Measurements of choroidal thickness may help in clinically identifying carrier status.
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Affiliation(s)
- Bohdan Kousal
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic,Laboratory of the Biology and Pathology of the Eye, Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Lucie Valesova
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Tracy Fletcher
- Regional Molecular Genetics Service, St Mary's Hospital, Manchester, United Kingdom
| | - Niki Hart-Holden
- Regional Molecular Genetics Service, St Mary's Hospital, Manchester, United Kingdom
| | - Anna O'Grady
- Regional Molecular Genetics Service, St Mary's Hospital, Manchester, United Kingdom
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London, United Kingdom,Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | | | - Petra Liskova
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic,Laboratory of the Biology and Pathology of the Eye, Institute of Inherited Metabolic Disorders; First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic,UCL Institute of Ophthalmology, London, United Kingdom
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Ratnapriya R, Zhan X, Fariss RN, Branham KE, Zipprer D, Chakarova CF, Sergeev YV, Campos MM, Othman M, Friedman JS, Maminishkis A, Waseem NH, Brooks M, Rajasimha HK, Edwards AO, Lotery A, Klein BE, Truitt BJ, Li B, Schaumberg DA, Morgan DJ, Morrison MA, Souied E, Tsironi EE, Grassmann F, Fishman GA, Silvestri G, Scholl HPN, Kim IK, Ramke J, Tuo J, Merriam JE, Merriam JC, Park KH, Olson LM, Farrer LA, Johnson MP, Peachey NS, Lathrop M, Baron RV, Igo RP, Klein R, Hagstrom SA, Kamatani Y, Martin TM, Jiang Y, Conley Y, Sahel JA, Zack DJ, Chan CC, Pericak-Vance MA, Jacobson SG, Gorin MB, Klein ML, Allikmets R, Iyengar SK, Weber BH, Haines JL, Léveillard T, Deangelis MM, Stambolian D, Weeks DE, Bhattacharya SS, Chew EY, Heckenlively JR, Abecasis GR, Swaroop A. Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration. Hum Mol Genet 2014; 23:5827-37. [PMID: 24899048 DOI: 10.1093/hmg/ddu276] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neurodegenerative diseases affecting the macula constitute a major cause of incurable vision loss and exhibit considerable clinical and genetic heterogeneity, from early-onset monogenic disease to multifactorial late-onset age-related macular degeneration (AMD). As part of our continued efforts to define genetic causes of macular degeneration, we performed whole exome sequencing in four individuals of a two-generation family with autosomal dominant maculopathy and identified a rare variant p.Glu1144Lys in Fibrillin 2 (FBN2), a glycoprotein of the elastin-rich extracellular matrix (ECM). Sanger sequencing validated the segregation of this variant in the complete pedigree, including two additional affected and one unaffected individual. Sequencing of 192 maculopathy patients revealed additional rare variants, predicted to disrupt FBN2 function. We then undertook additional studies to explore the relationship of FBN2 to macular disease. We show that FBN2 localizes to Bruch's membrane and its expression appears to be reduced in aging and AMD eyes, prompting us to examine its relationship with AMD. We detect suggestive association of a common FBN2 non-synonymous variant, rs154001 (p.Val965Ile) with AMD in 10 337 cases and 11 174 controls (OR = 1.10; P-value = 3.79 × 10(-5)). Thus, it appears that rare and common variants in a single gene--FBN2--can contribute to Mendelian and complex forms of macular degeneration. Our studies provide genetic evidence for a key role of elastin microfibers and Bruch's membrane in maintaining blood-retina homeostasis and establish the importance of studying orphan diseases for understanding more common clinical phenotypes.
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Affiliation(s)
| | - Xiaowei Zhan
- Center for Statistical Genetics, Department of Biostatistics and
| | | | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Zipprer
- Neurobiology Neurodegeneration and Repair Laboratory
| | - Christina F Chakarova
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | | | | | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Naushin H Waseem
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | | | | | - Albert O Edwards
- Institute for Molecular Biology, University of Oregon and Oregon Retina, Eugene, OR 97401, USA
| | - Andrew Lotery
- Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Barbara E Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and, Public Health, Madison, WI 53726, USA
| | - Barbara J Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bingshan Li
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Debra A Schaumberg
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA, Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Denise J Morgan
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Margaux A Morrison
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Eric Souied
- Hôpital Intercommunal de Créteil, Hôpital Henri Mondor - Université Paris Est Créteil 94000, France
| | - Evangelia E Tsironi
- Department of Ophthalmology, University of Thessaly School of Medicine, Larissa, Greece
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg 93053, Germany
| | - Gerald A Fishman
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Hendrik P N Scholl
- Wilmer Eye Institute, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Ivana K Kim
- Retina Service and Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Jacqueline Ramke
- The Fred Hollows Foundation, Auckland, New Zealand, School of Social Sciences, University of New South Wales, Sydney, Australia
| | | | | | | | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul 463-707, Republic of Korea
| | - Lana M Olson
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Lindsay A Farrer
- Departments of Medicine (Section of Biomedical Genetics), Ophthalmology and Biostatistics, Neurology, Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA 02215, USA
| | | | - Neal S Peachey
- Cleveland Clinic Foundation, Cole Eye Institute, Cleveland, OH 44195, USA, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44195, USA
| | - Mark Lathrop
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | | | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and, Public Health, Madison, WI 53726, USA
| | | | - Yoichiro Kamatani
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Tammy M Martin
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Yingda Jiang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yvette Conley
- Health Promotion and Development, School of Nursing, 440 Victoria Building, 3500 Victoria St, Pittsburgh, PA 15261, USA
| | - Jose-Alan Sahel
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | | | - Margaret A Pericak-Vance
- Bascom Palmer Eye Institute and Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33125, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael B Gorin
- Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael L Klein
- Macular Degeneration Center, Casey Eye Institute, Oregon Health and Science, University, Portland, OR 97201, USA
| | - Rando Allikmets
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bernhard H Weber
- Institute of Human Genetics, University of Regensburg, Regensburg 93053, Germany
| | - Jonathan L Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Thierry Léveillard
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Margaret M Deangelis
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Dwight Stambolian
- Department of Ophthalmology, and Department of Genetics, University of Pennsylvania, Philadelphia, PA 9104, USA
| | - Daniel E Weeks
- Department of Human Genetics and Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shomi S Bhattacharya
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | - Emily Y Chew
- Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory,
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Valdés-Sánchez L, De la Cerda B, Diaz-Corrales FJ, Massalini S, Chakarova CF, Wright AF, Bhattacharya SS. ATR localizes to the photoreceptor connecting cilium and deficiency leads to severe photoreceptor degeneration in mice. Hum Mol Genet 2013; 22:1507-15. [DOI: 10.1093/hmg/dds563] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Rose AM, Shah AZ, Alfano G, Bujakowska KM, Barker AF, Robertson JL, Rahman S, Sánchez LV, Diaz-Corrales FJ, Chakarova CF, Krishna A, Bhattacharya SS. A Study into the Evolutionary Divergence of the Core Promoter Elements of PRPF31 and TFPT. J Mol Genet Med 2013; 7. [PMID: 25729402 PMCID: PMC4341892 DOI: 10.4172/1747-0862.1000067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutations in PRPF31 have been implicated in retinitis pigmentosa, a blinding disease caused by degeneration of rod photoreceptors. The disease mechanism in the majority of cases is haploinsufficiency. Crucially, attempts at generation of animal models of disease have proved unsuccessful, yielding animals with a visual phenotype that does not mirror human disease. This suggests that, in these animals, the transcriptional regulation of PRPF31 is different to humans and compared to other species. Study of the evolution of the PRPF31 core promoter has important implications for our understanding of human disease, as disease phenotype is modified by differentially expressed alleles in the population. PRPF31 lies in a head-to-head arrangement with TFPT, a gene involved in cellular apoptosis. The two genes were shown to share common regulatory elements in the human genome. In this study, the core promoters of PRPF31 and TFPT were characterised by dual-luciferase reporter assay using genomic DNA from the green monkey, domestic dog and house mouse. It was found that the core promoters were conserved between human and monkey. In dog, the TFPT core promoter was conserved, but different PRPF31 gene architecture meant the gene was controlled by a long-range promoter lying some 2000bp from the transcription start site. There was very low level of conservation (<20%) of the PRPF31 5′ region between mouse and human. It was shown that mouse populations did not show variable Prpf31 expression levels, revealing a potential explanation for the lack of phenotype observed in the Prpf31 knock-out mouse model.
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Affiliation(s)
- Anna M. Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
- Corresponding author: Anna M. Rose, Department of Genetics, UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK,
| | - Amna Z. Shah
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | - Giovanna Alfano
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | - Kinga M. Bujakowska
- Ocular Genomics Institute & Berman-Gund Laboratory, Department of Ophthalmology, Harvard Medical School, Boston, USA
| | - Amy F. Barker
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | - J Louis Robertson
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | - Sufia Rahman
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | - Lourdes Valdés Sánchez
- Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, 41092, Spain
| | | | | | - Abhay Krishna
- Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, 41092, Spain
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Rose AM, Shah AZ, Waseem NH, Chakarova CF, Alfano G, Coussa RG, Ajlan R, Koenekoop RK, Bhattacharya SS. Expression of PRPF31 and TFPT: regulation in health and retinal disease. Hum Mol Genet 2012; 21:4126-37. [PMID: 22723017 DOI: 10.1093/hmg/dds242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PRPF31, a gene located at chromosome 19q13.4, encodes the ubiquitous splicing factor PRPF31. The gene lies in a head-to-head arrangement with TFPT, a poorly characterized gene with a role in cellular apoptosis. Mutations in PRPF31 have been implicated in autosomal dominant retinitis pigmentosa (adRP), a frequent and important cause of blindness worldwide. Disease associated with PRPF31 mutations is unusual, in that there is often non-penetrance of the disease phenotype in affected families, caused by differential expression of PRPF31. This study aimed to characterize the basic promoter elements of PRPF31 and TFPT. Luciferase reporter constructs were made, using genomic DNA from an asymptomatic individual with a heterozygous deletion of the entire putative promoter region. Fragments were tested by the dual-luciferase reporter assay in HeLa and RPE-1 cell lines. A comparison was made between the promoter regions of symptomatic and asymptomatic mutation-carrying individuals. A patient (CAN493) with adRP was identified, harbouring a regulatory region mutation; both alleles were assayed by the dual-luciferase reporter assay. Luciferase assays led to the identification of core promoters for both PRPF31 and TFPT; despite their shared gene architecture, the two genes appear to be controlled by slightly different regulatory regions. One functional polymorphism was identified in the PRPF31 promoter that increased transcriptional activation. The change was not, however, consistent with the observed symptomatic-asymptomatic phenotypes in a family affected by PRPF31-adRP. Analysis of the mutant promoter fragment from CAN493 showed a >50% reduction in promoter activity, suggesting a disease mechanism of functional haploinsufficiency-the first report of this disease mechanism in adRP.
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London EC1V 9EL, UK.
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Maubaret C, Kosmaoglou M, Low S, Chakarova CF, Bidot S, Thauvin-Robinet C, Robson AG, Waseem N, Cheetham ME, Bhattacharya SS. Functional characterization of a novel c.614-622del rhodopsin mutation in a French pedigree with retinitis pigmentosa. Mol Vis 2012; 18:581-7. [PMID: 22419850 PMCID: PMC3298422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022] Open
Abstract
PURPOSE To identify and functionally characterize the mutation responsible for autosomal dominant retinitis pigmentosa (adRP) in a large, six-generation French family. METHODS Twenty individuals from this family participated in the genetic investigation. Six affected and 14 unaffected individuals from three-generations were available for linkage analysis using microsatellite markers flanking the rhodopsin (RHO) gene. A two-point logarithm of odds (LOD) score calculation was undertaken using GENEMARKER and MLINK software. Sanger sequencing of RHO was performed. Cellular localization of the mutant protein was performed by transforming SK-N-SH cells with pEGFP-N1-Rho, pEGFP-N1-Rho(P23H), and pEGFP-N1-Rho(c.614-622del). RESULTS The proband had nyctalopia, visual field constriction, peripheral bone spicule pigmentation of the fundus, central acuity (6/24 RE; 6/12 LE) at 55 years of age. Linkage analysis of this family suggested RHO as a possible candidate since the flanking marker D3S1292 yielded a LOD score of 2.43 at θ=0. Cloning of an exon 3 PCR product and direct sequencing of single clones identified a novel deletion in the third exon of RHO, c.614-622del (p.Y206-F208del). The deleted mutant protein localized to the endoplasmic reticulum and formed inclusion bodies. CONCLUSIONS This novel deletion in exon 3 of the RHO gene, c.614-622del results in a classical form of adRP in a multi-generation French family. Protein expression analyses confirmed that the deletion led to protein misfolding and suggest this is a class II mutation, similar to P23H, the most common class II mutation seen in North America.
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Affiliation(s)
| | | | - Sancy Low
- UCL Institute of Ophthalmology, London, United Kingdom,Moorfields Eye Hospital, London, United Kingdom
| | | | | | | | - Anthony G. Robson
- UCL Institute of Ophthalmology, London, United Kingdom,Moorfields Eye Hospital, London, United Kingdom
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Liskova P, Colclough T, Hart-Holden N, Chakarova CF, O'Grady A, Kondrova L, Skalicka P, Diblik P, Hardcastle AJ. Molecular genetic cause of X-linked retinitis pigmentosa in a Czech family. Acta Ophthalmol 2011; 89:e213-5. [PMID: 20064120 DOI: 10.1111/j.1755-3768.2009.01802.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chakarova CF, Khanna H, Shah AZ, Patil SB, Sedmak T, Murga-Zamalloa CA, Papaioannou MG, Nagel-Wolfrum K, Lopez I, Munro P, Cheetham M, Koenekoop RK, Rios RM, Matter K, Wolfrum U, Swaroop A, Bhattacharya SS. TOPORS, implicated in retinal degeneration, is a cilia-centrosomal protein. Hum Mol Genet 2010; 20:975-87. [PMID: 21159800 DOI: 10.1093/hmg/ddq543] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We recently reported that mutations in the widely expressed nuclear protein TOPORS (topoisomerase I-binding arginine/serine rich) are associated with autosomal dominant retinal degeneration. However, the precise localization and a functional role of TOPORS in the retina remain unknown. Here, we demonstrate that TOPORS is a novel component of the photoreceptor sensory cilium, which is a modified primary cilium involved with polarized trafficking of proteins. In photoreceptors, TOPORS localizes primarily to the basal bodies of connecting cilium and in the centrosomes of cultured cells. Morpholino-mediated silencing of topors in zebrafish embryos demonstrates in another species a comparable retinal problem as seen in humans, resulting in defective retinal development and failure to form outer segments. These defects can be rescued by mRNA encoding human TOPORS. Taken together, our data suggest that TOPORS may play a key role in regulating primary cilia-dependent photoreceptor development and function. Additionally, it is well known that mutations in other ciliary proteins cause retinal degeneration, which may explain why mutations in TOPORS result in the same phenotype.
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Wright AF, Chakarova CF, Abd El-Aziz MM, Bhattacharya SS. Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Nat Rev Genet 2010; 11:273-84. [PMID: 20212494 DOI: 10.1038/nrg2717] [Citation(s) in RCA: 434] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Schob C, Orth U, Gal A, Kindler S, Chakarova CF, Bhattacharya SS, Rüther K. Mutations inTOPORS: A Rare Cause of Autosomal Dominant Retinitis Pigmentosa in Continental Europe? Ophthalmic Genet 2009; 30:96-8. [DOI: 10.1080/13816810802695543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bujakowska K, Maubaret C, Chakarova CF, Tanimoto N, Beck SC, Fahl E, Humphries MM, Kenna PF, Makarov E, Makarova O, Paquet-Durand F, Ekström PA, van Veen T, Leveillard T, Humphries P, Seeliger MW, Bhattacharya SS. Study of gene-targeted mouse models of splicing factor gene Prpf31 implicated in human autosomal dominant retinitis pigmentosa (RP). Invest Ophthalmol Vis Sci 2009; 50:5927-33. [PMID: 19578015 DOI: 10.1167/iovs.08-3275] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Pre-mRNA processing factor 31 (PRPF31) is a ubiquitous protein needed for the assembly of the pre-mRNA splicing machinery. It has been shown that mutations in this gene cause autosomal dominant retinitis pigmentosa 11 (RP11), which is characterized by rod-cell degeneration. Interestingly, mutations in this ubiquitously expressed gene do not lead to phenotypes other than retinal malfunction. Furthermore, the dominant inheritance pattern has shown incomplete penetrance, which poses interesting questions about the disease mechanism of RP11. METHODS To characterize PRPF31 function in the rod cells, two animal models have been generated. One was a heterozygous knock-in mouse (Prpf31(A216P/+)) carrying a point mutation p.A216P, which has previously been identified in RP11 patients. The second was a heterozygous knockout mouse (Prpf31(+/-)). Retinal degeneration in RP11 mouse models was monitored by electroretinography and histology. RESULTS Generation of the mouse models is presented, as are results of ERGs and retinal morphology. No degenerative phenotype on fundus examination was found in Prpf31(A216P/+) and Prpf31(+/-) mice. Prpf31(A216P/A216P) and Prpf31(-/-) genotypes were embryonic lethal. CONCLUSIONS The results imply that Prpf31 is necessary for survival, and there is no compensation mechanism in mouse for the lack of this splicing factor. The authors suggest that p.A216P mutation in Prpf31 does not exert a dominant negative effect and that one Prpf31 wild-type allele is sufficient for maintenance of the healthy retina in mice.
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Affiliation(s)
- Kinga Bujakowska
- Institute of Ophthalmology, University College London, London, United Kingdom
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Friedman JS, Ray JW, Waseem N, Johnson K, Brooks MJ, Hugosson T, Breuer D, Branham KE, Krauth DS, Bowne SJ, Sullivan LS, Ponjavic V, Gränse L, Khanna R, Trager EH, Gieser LM, Hughbanks-Wheaton D, Cojocaru RI, Ghiasvand NM, Chakarova CF, Abrahamson M, Göring HH, Webster AR, Birch DG, Abecasis GR, Fann Y, Bhattacharya SS, Daiger SP, Heckenlively JR, Andréasson S, Swaroop A. Mutations in a BTB-Kelch protein, KLHL7, cause autosomal-dominant retinitis pigmentosa. Am J Hum Genet 2009; 84:792-800. [PMID: 19520207 DOI: 10.1016/j.ajhg.2009.05.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/19/2009] [Accepted: 05/20/2009] [Indexed: 01/08/2023] Open
Abstract
Retinitis pigmentosa (RP) refers to a genetically heterogeneous group of progressive neurodegenerative diseases that result in dysfunction and/or death of rod and cone photoreceptors in the retina. So far, 18 genes have been identified for autosomal-dominant (ad) RP. Here, we describe an adRP locus (RP42) at chromosome 7p15 through linkage analysis in a six-generation Scandinavian family and identify a disease-causing mutation, c.449G-->A (p.S150N), in exon 6 of the KLHL7 gene. Mutation screening of KLHL7 in 502 retinopathy probands has revealed three different missense mutations in six independent families. KLHL7 is widely expressed, including expression in rod photoreceptors, and encodes a 75 kDa protein of the BTB-Kelch subfamily within the BTB superfamily. BTB-Kelch proteins have been implicated in ubiquitination through Cullin E3 ligases. Notably, all three putative disease-causing KLHL7 mutations are within a conserved BACK domain; homology modeling suggests that mutant amino acid side chains can potentially fill the cleft between two helices, thereby affecting the ubiquitination complexes. Mutations in an identical region of another BTB-Kelch protein, gigaxonin, have previously been associated with giant axonal neuropathy. Our studies suggest an additional role of the ubiquitin-proteasome protein-degradation pathway in maintaining neuronal health and in disease.
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Chakarova CF, Papaioannou MG, Khanna H, Lopez I, Waseem N, Shah A, Theis T, Friedman J, Maubaret C, Bujakowska K, Veraitch B, Abd El-Aziz MM, Prescott DQ, Parapuram SK, Bickmore WA, Munro PMG, Gal A, Hamel CP, Marigo V, Ponting CP, Wissinger B, Zrenner E, Matter K, Swaroop A, Koenekoop RK, Bhattacharya SS. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa with perivascular retinal pigment epithelium atrophy. Am J Hum Genet 2007; 81:1098-103. [PMID: 17924349 DOI: 10.1086/521953] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 07/17/2007] [Indexed: 11/03/2022] Open
Abstract
We report mutations in the gene for topoisomerase I-binding RS protein (TOPORS) in patients with autosomal dominant retinitis pigmentosa (adRP) linked to chromosome 9p21.1 (locus RP31). A positional-cloning approach, together with the use of bioinformatics, identified TOPORS (comprising three exons and encoding a protein of 1,045 aa) as the gene responsible for adRP. Mutations that include an insertion and a deletion have been identified in two adRP-affected families--one French Canadian and one German family, respectively. Interestingly, a distinct phenotype is noted at the earlier stages of the disease, with an unusual perivascular cuff of retinal pigment epithelium atrophy, which was found surrounding the superior and inferior arcades in the retina. TOPORS is a RING domain-containing E3 ubiquitin ligase and localizes in the nucleus in speckled loci that are associated with promyelocytic leukemia bodies. The ubiquitous nature of TOPORS expression and a lack of mutant protein in patients are highly suggestive of haploinsufficiency, rather than a dominant negative effect, as the molecular mechanism of the disease and make rescue of the clinical phenotype amenable to somatic gene therapy.
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Chakarova CF, Cherninkova S, Tournev I, Waseem N, Kaneva R, Jordanova A, Veraitch BK, Gill B, Colclough T, Nakova A, Oscar A, Mihaylova V, Nikolova-Hill A, Wright AF, Black GCM, Ramsden S, Kremensky I, Bhattacharya SS. Molecular genetics of retinitis pigmentosa in two Romani (Gypsy) families. Mol Vis 2006; 12:909-14. [PMID: 16917484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
PURPOSE To identify the disease-causing mutations in two large Bulgarian Romani (Gypsy) pedigrees: one with autosomal dominant retinitis pigmentosa (adRP) with partial penetrance and the other with severe X-linked RP (xlRP). METHODS Detailed clinical investigations were undertaken and genomic DNA was extracted from blood samples. DNA was analyzed by PCR amplification with gene-specific primers and direct genomic sequencing. RESULTS Analysis of the complete coding sequence of PRPF31 in the adRP family led to the identification of a new heterozygous splice site mutation IVS6+1G>T. RPGR mutation screening in affected male individuals in the X-linked RP family identified a hemizygous c.ORF15+652_653delAG mutation. Interestingly this mutation was found in a homozygous state in one severely affected female from the family. CONCLUSIONS In this first report of molecular genetic analysis of retinitis pigmentosa in Romani families, we describe a novel PRPF31 mutation and present the first case of a homozygous mutation in the RPGR gene in a female individual.
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Papaioannou M, Chakarova CF, Prescott DQC, Waseem N, Theis T, Lopez I, Gill B, Koenekoop RK, Bhattacharya SS. A new locus (RP31) for autosomal dominant retinitis pigmentosa maps to chromosome 9p. Hum Genet 2005; 118:501-3. [PMID: 16189705 DOI: 10.1007/s00439-005-0063-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 08/24/2005] [Indexed: 11/28/2022]
Abstract
Retinitis pigmentosa (RP) is a debilitating disease of the retina affecting approximately 1.5 million people worldwide. RP shows remarkable heterogeneity both clinically and genetically, with more than 40 genetic loci implicated, 12 of which account for the autosomal dominant form (adRP) of inheritance. We have recently identified a French Canadian family that presents with early onset adRP. After exclusion of all known loci for adRP, a genome-wide search established firm linkage with a marker from the short arm of chromosome 9 (LOD score of 6.3 at recombination fraction theta=0). The linked region is flanked by markers D9S285 and D9S1874, corresponding to a genetic distance of 31 cM, in the region 9p22-p13.
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Affiliation(s)
- Myrto Papaioannou
- Department of Molecular Genetics, Institute of Ophthalmology, UCL, 11-43 Bath Street, London, EC1V 9EL, UK
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Kaneva RP, Chorbov VM, Milanova VK, Kostov CS, Nickolov KI, Chakarova CF, Stoyanova VS, Nikolova-Hill AN, Krastev SK, Onchev GN, Kremensky IM, Kalaydjieva LV, Jablensky AV. Linkage analysis in bipolar pedigrees adds support for a susceptibility locus on 21q22. Psychiatr Genet 2004; 14:101-6. [PMID: 15167697 DOI: 10.1097/01.ypg.0000128766.92096.ad] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Several studies provide suggestive evidence of a susceptibility locus for bipolar disorder at chromosome 21q22-23. In an attempt to replicate these findings, we have analyzed linkage to 11 polymorphic markers from this region in 18 Bulgarian pedigrees with affective disorder. Two-point linkage analysis under assumption of homogeneity and a dominant model with reduced penetrance produced modest positive values for some of the markers tested under a 'narrow' phenotype definition, including bipolar I and II, and schizoaffective disorder. The maximum two-point score (lod=1.76, theta=0.00) was at marker D21S1919. Non-parametric linkage analysis under the same phenotype model, yielded positive NPLall values (P<0.05) over the region between markers D21S211 and D21S416, with a peak at D21S1252 (NPL Zall=2.32, P=0.0003). The multipoint lod score (GENEHUNTER) reached a suggestive value for linkage (lod=2.10) also at marker D21S1252. The results under a recessive model were completely negative. These data add to the evidence for the existence of a susceptibility locus for bipolar affective disorder on chromosome 21q22.
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Affiliation(s)
- Radka P Kaneva
- Laboratory of Molecular Pathology, University Hospital of Obstetrics, Medical University Sofia, Bulgaria.
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Chakarova CF, Hims MM, Bolz H, Abu-Safieh L, Patel RJ, Papaioannou MG, Inglehearn CF, Keen TJ, Willis C, Moore AT, Rosenberg T, Webster AR, Bird AC, Gal A, Hunt D, Vithana EN, Bhattacharya SS. Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Hum Mol Genet 2002; 11:87-92. [PMID: 11773002 DOI: 10.1093/hmg/11.1.87] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Retinitis pigmentosa (RP), the commonest form of inherited retinal dystrophies is a clinically and genetically heterogeneous disorder. It is characterized by progressive degeneration of the peripheral retina leading to night blindness and loss of peripheral visual field. RP is inherited either in an autosomal dominant, autosomal recessive or X-linked mode. A locus (RP18) for autosomal dominant RP was previously mapped by linkage analysis in two large pedigrees to chromosome 1p13-q21. The human HPRP3 gene, the orthologue of the yeast pre-mRNA splicing factor (PRP3), localizes within the RP18 disease interval. The recent identification of mutations in human splicing factors, PRPF31 and PRPC8, led us to screen HPRP3 as a candidate in three chromosome 1q-linked families. So far, two different missense mutations in two English, a Danish family and in three RP individuals have been identified. Both mutations are clustered within a two-codon stretch in the 11th exon of the HPRP3 gene. Interestingly, one of the mutations (T494M) is seen repeatedly in apparently unlinked families raising the possibility of a mutation hot spot. This has been confirmed by haplotype analysis using SNPs spanning the HPRP3 gene region supporting multiple origins of the mutation. The altered HPRP3 amino acids, which are highly conserved in all known HPRP3 orthologues, indicate a major function of that domain in the splicing process. The identification of mutations in a third pre-mRNA splicing factor gene further highlights a novel mechanism of photoreceptor degeneration due to defects in the splicing process.
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Affiliation(s)
- Christina F Chakarova
- Department of Molecular Genetics, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EV, UK
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