51
|
Genetic Association Study of KCNQ5 Polymorphisms with High Myopia. BIOMED RESEARCH INTERNATIONAL 2017; 2017:3024156. [PMID: 28884119 PMCID: PMC5572591 DOI: 10.1155/2017/3024156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/10/2017] [Accepted: 07/17/2017] [Indexed: 02/05/2023]
Abstract
Identification of genetic variations related to high myopia may advance our knowledge of the etiopathogenesis of refractive error. This study investigated the role of potassium channel gene (KCNQ5) polymorphisms in high myopia. We performed a case-control study of 1563 unrelated Han Chinese subjects (809 cases of high myopia and 754 emmetropic controls). Five tag single-nucleotide polymorphisms (SNPs) of KCNQ5 were genotyped, and association testing with high myopia was conducted using logistic regression analysis adjusted for sex and age to give Pasym values, and multiple comparisons were corrected by permutation test to give Pemp values. All five noncoding SNPs were associated with high myopia. The SNP rs7744813, previously shown to be associated with refractive error and myopia in two GWAS, showed an odds ratio of 0.75 (95% CI 0.63-0.90; Pemp = 0.0058) for the minor allele. The top SNP rs9342979 showed an odds ratio of 0.75 (95% CI 0.64-0.89; Pemp = 0.0045) for the minor allele. Both SNPs are located within enhancer histone marks and DNase-hypersensitive sites. Our data support the involvement of KCNQ5 gene polymorphisms in the genetic susceptibility to high myopia and further exploration of KCNQ5 as a risk factor for high myopia.
Collapse
|
52
|
Mutational screening of SLC39A5, LEPREL1 and LRPAP1 in a cohort of 187 high myopia patients. Sci Rep 2017; 7:1120. [PMID: 28442722 PMCID: PMC5430800 DOI: 10.1038/s41598-017-01285-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/24/2017] [Indexed: 12/13/2022] Open
Abstract
High myopia (HM) is a leading cause of mid-way blindness with a high heritability in East Asia. Although only a few disease genes have been reported, a small proportion of patients could be identified with genetic predispositions. In order to expand the mutation spectrum of the causative genes in Chinese adult population, we investigated three genes, SLC39A5, LEPREL1 and LRPAP1, in a cohort of 187 independent Chinese patients with high myopia. Sanger sequencing was used to find possible pathogenic mutations, which were further screened in normal controls. After a pipeline of database and predictive assessments filtering, we, thereby, identified totally seven heterozygous mutations in the three genes. Among them, three novel missense mutations, c.860C > T, p.Pro287Leu and c.956G > C, p.Arg319Thr in SLC39A5, c.1982A > G, p.Lys661Arg in LEPREL1, were identified as potentially causative mutations. Additionally, the two heterozygous mutations (c.1582G > A, p.Ala528Thr; c.1982A > G, p.Lys661Arg) in one patient in LEPREL1 gene were reported in this study. Our findings will not only augment the mutation spectrum of these three genes, but also provide insights of the contribution of these genes to adult high myopia in Chinese. However, further studies are still needed to address the pathogenicity of each of the mutations reported in this study.
Collapse
|
53
|
Zhang D, Zeng G, Hu J, McCormick K, Shi Y, Gong B. Association of IGF1 polymorphism rs6214 with high myopia: A systematic review and meta-analysis. Ophthalmic Genet 2017; 38:434-439. [PMID: 28135889 DOI: 10.1080/13816810.2016.1253105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE To conduct a comprehensive evaluation of the association of Insulin-like growth factor 1 (IGF1) polymorphism rs6214 with high myopia through a systematic review and meta-analysis of candidate genetic association study. METHODS All case-control association studies on IGF1 and high myopia reported up to 15 June 2016 in PubMed, Embase, Web of Science, and the Chinese Biomedical Database were retrieved. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for single-nucleotide polymorphism (SNP) using fixed and random effects models according to between study heterogeneity. Publication bias analyses were conducted using Begg's test. RESULTS A total of eight studies from published articles were included in our analysis. The meta-analyses for IGF1 rs6214, composed of 4242 high myopia patients and 4430 controls, showed low heterogeneity for the included populations in all the genetic models, except that of the allelic genetic model in the pooled populations. The analyses of all the genetic models in Chinese, Japanese, and overall pooled populations did not identify any significant association between high myopia and IGF1 rs6214. CONCLUSIONS This meta-analysis showed there was no association detected between IGF1 rs6214 and high myopia. Given the limited sample size, further investigations including more ethnic groups are required to validate the association.
Collapse
Affiliation(s)
- Dingding Zhang
- a Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Guangqun Zeng
- b Department of Clinical Laboratory , People's Hospital of Pengzhou , Pengzhou , Sichuan , China
| | - Jinliang Hu
- c Institute of Health Policy and Hospital Management, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital , Chengdu , Sichuan , China.,d School of Public Health , Sichuan University , Chengdu , Sichuan , China
| | - Kerry McCormick
- e College of Science and Mathematics , California Polytechnic State University , San Luis Obispo , California , USA
| | - Yi Shi
- a Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Bo Gong
- a Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| |
Collapse
|
54
|
Chen Y, Wang W, Han X, Yan W, He M. What Twin Studies Have Taught Us About Myopia. Asia Pac J Ophthalmol (Phila) 2017; 5:411-414. [PMID: 27898444 DOI: 10.1097/apo.0000000000000238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Myopia has become epidemic, particularly in East Asia, and is a major cause of visual impairment worldwide. Twin studies are an important resource to investigate the genetics and the gene-environment interaction in myopia. This article aims to provide an overview of major findings regarding myopia from different types of twin studies, from the heritability of myopia-related traits to novel findings of genome-wide association studies. In the postgenomic era, twin studies will continue to serve as a unique method in the investigation of gene-environment interaction.
Collapse
Affiliation(s)
- Yanxian Chen
- From the *State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China; and †Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | | | | | | | | |
Collapse
|
55
|
Tideman JWL, Fan Q, Polling JR, Guo X, Yazar S, Khawaja A, Höhn R, Lu Y, Jaddoe VWV, Yamashiro K, Yoshikawa M, Gerhold-Ay A, Nickels S, Zeller T, He M, Boutin T, Bencic G, Vitart V, Mackey DA, Foster PJ, MacGregor S, Williams C, Saw SM, Guggenheim JA, Klaver CCW. When do myopia genes have their effect? Comparison of genetic risks between children and adults. Genet Epidemiol 2016; 40:756-766. [PMID: 27611182 DOI: 10.1002/gepi.21999] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 01/10/2023]
Abstract
Previous studies have identified many genetic loci for refractive error and myopia. We aimed to investigate the effect of these loci on ocular biometry as a function of age in children, adolescents, and adults. The study population consisted of three age groups identified from the international CREAM consortium: 5,490 individuals aged <10 years; 5,000 aged 10-25 years; and 16,274 aged >25 years. All participants had undergone standard ophthalmic examination including measurements of axial length (AL) and corneal radius (CR). We examined the lead SNP at all 39 currently known genetic loci for refractive error identified from genome-wide association studies (GWAS), as well as a combined genetic risk score (GRS). The beta coefficient for association between SNP genotype or GRS versus AL/CR was compared across the three age groups, adjusting for age, sex, and principal components. Analyses were Bonferroni-corrected. In the age group <10 years, three loci (GJD2, CHRNG, ZIC2) were associated with AL/CR. In the age group 10-25 years, four loci (BMP2, KCNQ5, A2BP1, CACNA1D) were associated; and in adults 20 loci were associated. Association with GRS increased with age; β = 0.0016 per risk allele (P = 2 × 10-8 ) in <10 years, 0.0033 (P = 5 × 10-15 ) in 10- to 25-year-olds, and 0.0048 (P = 1 × 10-72 ) in adults. Genes with strongest effects (LAMA2, GJD2) had an early effect that increased with age. Our results provide insights on the age span during which myopia genes exert their effect. These insights form the basis for understanding the mechanisms underlying high and pathological myopia.
Collapse
Affiliation(s)
- J Willem L Tideman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Qiao Fan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Jan Roelof Polling
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Orthoptics, School of Applied Science Utrecht, Rotterdam, The Netherlands
| | - Xiaobo Guo
- Department of Statistical Science, School of Mathematics & Computational Science, Sun Yat-Sen University, Guangzhou, GD, China
- SYSU-CMU Shunde International Joint Research Institute, Guangzhou, GD, China
- Southern China Research Center of Statistical Science, Sun Yat-Sen University, Guangzhou, GD, China
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Anthony Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - René Höhn
- Department of Ophthalmology, University Medical Center, Mainz, Germany
- Department of Ophthalmology, Inselspital, Bern, Switzerland
| | - Yi Lu
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Munemitsu Yoshikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Aslihan Gerhold-Ay
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center Mainz, Mainz, Germany
| | - Stefan Nickels
- Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Mingguang He
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Thibaud Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Seang Mei Saw
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- National University of Singapore Saw Swee Hock School of Public Health, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
56
|
Gong Q, Janowski M, Xie M, Yang G, Liu L. Rasgrf1 mRNA expression in myopic eyes of guinea pigs. Clin Exp Optom 2016; 100:174-178. [PMID: 27723119 DOI: 10.1111/cxo.12476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/08/2016] [Accepted: 07/17/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genome-wide association studies of patients have linked the Rasgrf1 gene with myopia. The aim of this study was to investigate the messenger RNA (mRNA) expression of Rasgrf1 in the eyes of guinea pigs with induced myopia. METHODS The myopia was induced by form deprivation in 24 guinea pigs, while additional 12 animals served as a control. Biometric measurements were used to monitor myopic progression. The animals were sacrificed at two, three and four weeks after beginning of the monocular form deprivation, followed by dissection of the retina, and the sclera, as well as mRNA isolation from both layers. A quantitative reverse transcriptase-polymerase chain reaction was performed to detect the expression of Rasgrf1. RESULTS The spherical equivalent in eyes subjected to form deprivation differed from the fellow eyes, with measurements of -3.80 ± 0.08 D, -3.96 ± 0.94 D and -4.00 ± 0.94 D at the two-, three- and four-week times, respectively, significantly more myopia than the inter-ocular difference in the control group (p < 0.05). The form-deprived eyes also had a longer axial length compared with the fellow eye: 1.37 ± 0.76 mm, 1.32 ± 0.65 mm and 0.92 ± 0.80 mm at two, three and four weeks, respectively, significantly different from the control group (p < 0.05). In contrast, there was no difference in the corneal curvature, anterior chamber depth or lens thickness between the two eyes at any time (p > 0.05). The increase of Rasgrf1 expression was observed in the sclera, with a fold change of 6.596, 4.379 after three weeks and 6.788, 5.711 after four weeks of treatment, compared with the fellow eyes and the control group, respectively (p < 0.05). CONCLUSION Rasgrf1 up-regulation was found in the sclera of myopic eyes; however, further investigation is needed to determine whether Rasgrf1 plays a causative role or is a consequence of myopia-induced scleral remodelling.
Collapse
Affiliation(s)
- Qianwen Gong
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Miroslaw Janowski
- Department of Radiology and Radiological Science, Division of MR Research, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,NeuroRepair Department, Mossakowski Medical Research Centre PAS, Warsaw, Poland
| | - Mingkun Xie
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Guoyuan Yang
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Longqian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
57
|
Cai YL, Zou YC, Lei JH, Zeng GP, Wang Y. The investigation on the role of mitochondrial fusion protein 1 in the development of myopia. Indian J Ophthalmol 2016; 64:500-3. [PMID: 27609161 PMCID: PMC5026074 DOI: 10.4103/0301-4738.190137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Purpose: The aim of this study is to preliminarily investigate the expression of mitochondrial fusion protein 1 (MFN1) in a lens-induced animal myopia (LIM) model and to explore the relationship between MFN1 and the visual development. Materials and Methods: MFN1 gene expression in guinea pigs was examined during the development of minus LIM, 15 tri-colored guinea pigs were obtained, and one eye of each pig was randomly selected and treated with −7.00D lenses. Ocular refraction and axial length were collected before intervention and 1, 2, and 3 weeks after intervention. After the refraction and axial length measurements at 1, 2, and 3 weeks of lens intervention, five guinea pigs were randomly selected. MFN1 expression in the retina of both eyes was tested by immunohistochemistry technique. Results: MFN1-positive cells could be observed in the retina of both eyes. The positive cells in the LIM eyes were staining deeper, and much more positive cells could be observed. Furthermore, MFN1-positive expression could be seen mainly in ganglion cells after 1 week of minus lens intervention, and with time extension, more and more positive cells appeared in the rod-cone cell and bipolar cell layer, and this phenomenon could not be found in the normal control eyes. Conclusion: This study suggested that MFN1 might be correlated to the development of myopia.
Collapse
Affiliation(s)
- Yun-Lin Cai
- The Second Clinical Medical College of North Sichuan Medical College, Nanchong Central Hospital, Nanchong, Sichuan, China
| | - Yun-Chun Zou
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jia-Hong Lei
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Guan-Peng Zeng
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Ying Wang
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong, Sichuan, China
| |
Collapse
|
58
|
Liao X, Lan C, Liao D, Tian J, Huang X. Exploration and detection of potential regulatory variants in refractive error GWAS. Sci Rep 2016; 6:33090. [PMID: 27604318 PMCID: PMC5015044 DOI: 10.1038/srep33090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/19/2016] [Indexed: 11/19/2022] Open
Abstract
Refractive error (RE) is a complex multifactorial disease. Genome-wide association studies (GWAS) have provided significant insight into the genetic architecture and identified plenty of robust genetic variations or single nucleotide polymorphisms (SNPs) associated with complex disease. A major current challenge is to convert those resources into causal variants and target genes. We used RegulomeDB and HaploReg to annotate regulatory information onto associated SNPs derived from the two largest RE GWAS, and additional SNPs in linkage disequilibrium (LD) with GWAS significant SNPs. Overall 868 SNPs were investigated, out of which 662 returned RegulomeDB scores of 1 to 6. It was observed that 36 out of those SNPs show strong evidence of regulatory effects with a RegulomeDB score of 1, while only four of them were GWAS significant SNPs (CD55/rs1652333, CNDP2/rs12971120, RDH5/rs3138142 and rs3138144). The results encourage us to explore those putative pathogenic variants, both GWAS significant SNPs as well as the SNPs in LD, for future discernment of functional consequence. This study offers the attractive approach for prioritizing potential functional variants by combining ENCODE data and GWAS information, and provide further insights into the pathogenesis and mechanism and ultimately therapeutics.
Collapse
Affiliation(s)
- Xuan Liao
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
| | - ChangJun Lan
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
| | - Dan Liao
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
| | - Jing Tian
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
| | - XiuQi Huang
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
- Department of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637007, Sichuan Province, China
| |
Collapse
|
59
|
Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V. G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. Stem Cell Reports 2016; 7:454-470. [PMID: 27546533 PMCID: PMC5031922 DOI: 10.1016/j.stemcr.2016.06.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 01/05/2023] Open
Abstract
Proliferating progenitor cells undergo changes in competence to give rise to post-mitotic progeny of specialized function. These cell-fate transitions typically involve dynamic regulation of gene expression by histone methyltransferase (HMT) complexes. However, the composition, roles, and regulation of these assemblies in regulating cell-fate decisions in vivo are poorly understood. Using unbiased affinity purification and mass spectrometry, we identified the uncharacterized C2H2-like zinc finger protein ZNF644 as a G9a/GLP-interacting protein and co-regulator of histone methylation. In zebrafish, functional characterization of ZNF644 orthologs, znf644a and znf644b, revealed complementary roles in regulating G9a/H3K9me2-mediated gene silencing during neurogenesis. The non-overlapping requirements for znf644a and znf644b during retinal differentiation demarcate critical aspects of retinal differentiation programs regulated by differential G9a-ZNF644 associations, such as transitioning proliferating progenitor cells toward differentiation. Collectively, our data point to ZNF644 as a critical co-regulator of G9a/H3K9me2-mediated gene silencing during neuronal differentiation.
Collapse
Affiliation(s)
- Jonathan B Olsen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Loksum Wong
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Steven Deimling
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Amanda Miles
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yue Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Medical Science Building, Toronto, ON M5S 3E1, Canada.
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada; Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada.
| |
Collapse
|
60
|
Gong B, Qu C, Huang XF, Ye ZM, Zhang DD, Shi Y, Chen R, Liu YP, Shuai P. Genetic association of COL1A1 polymorphisms with high myopia in Asian population: a Meta-analysis. Int J Ophthalmol 2016; 9:1187-93. [PMID: 27588274 DOI: 10.18240/ijo.2016.08.16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/08/2015] [Indexed: 02/05/2023] Open
Abstract
AIM To comprehensively evaluate the potential association of COL1A1 polymorphisms with high myopia by a systematic review and Meta-analysis. METHODS All association studies on COL1A1 and high myopia reported up to June 10, 2014 in PubMed, Embase, Web of Science, and the Chinese Biomedical Database were retrieved. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were analyzed for single-nucleotide polymorphisms (SNPs) using fixed- and random- effects models according to between-study heterogeneity. Publication bias analyses were conducted by Egger's test. RESULTS A total of four studies from reported papers were included in this analysis. The Meta-analyses for COL1A1 rs2075555, composed of 2304 high myopia patients and 2272 controls, failed to detect any significant association with high myopia. A total of 971 cases and 649 controls were tested for COL1A1 rs2269336. The association of COL1A1 rs2269336 with high myopia was observed in recessive model (CC vs CG+GG, P=0.03) and in heterozygous model (CG vs GG, P=0.04), but not in other models. CONCLUSION This Meta-analysis shows that COL1A1 rs2269336 (CC vs CG+GG) affects individual susceptibility to high myopia, whereas there is no association detected between SNPs rs2075555 and high myopia. Given the limited sample size, further investigations including more ethnic groups are required to validate the association.
Collapse
Affiliation(s)
- Bo Gong
- Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China
| | - Chao Qu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China; Department of Ophthalmology, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China
| | - Xiao-Fang Huang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Zi-Meng Ye
- Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China
| | - Ding-Ding Zhang
- Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China
| | - Rong Chen
- Department of Microbiology and Immunology, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yu-Ping Liu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China; Health Management Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China
| | - Ping Shuai
- Sichuan Provincial Key Laboratory for Disease Gene Study, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan Province, China; Health Management Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, Sichuan Province, China
| |
Collapse
|
61
|
Chen F, Duggal P, Klein BEK, Lee KE, Truitt B, Klein R, Iyengar SK, Klein AP. Variation in PTCHD2, CRISP3, NAP1L4, FSCB, and AP3B2 associated with spherical equivalent. Mol Vis 2016; 22:783-96. [PMID: 27440996 DOI: pmid/27440996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Ocular refraction is measured in spherical equivalent as the power of the external lens required to focus images on the retina. Myopia (nearsightedness) and hyperopia (farsightedness) are the most common refractive errors, and the leading causes of visual impairment and blindness in the world. The goal of this study is to identify rare and low-frequency variants that influence spherical equivalent. METHODS We conducted variant-level and gene-level quantitative trait association analyses for mean spherical equivalent, using data from 1,560 individuals in the Beaver Dam Eye Study. Genotyping was conducted using the Illumina exome array. We analyzed 34,976 single nucleotide variants and 11,571 autosomal genes across the genome, using single-variant tests as well as gene-based tests. RESULTS Spherical equivalent was significantly associated with five genes in gene-based analysis: PTCHD2 at 1p36.22 (p = 3.6 × 10(-7)), CRISP3 at 6p12.3 (p = 4.3 × 10(-6)), NAP1L4 at 11p15.5 (p = 3.6 × 10(-6)), FSCB at 14q21.2 (p = 1.5 × 10(-7)), and AP3B2 at 15q25.2 (p = 1.6 × 10(-7)). The variant-based tests identified evidence suggestive of association with two novel variants in linkage disequilibrium (pairwise r(2) = 0.80) in the TCTE1 gene region at 6p21.1 (rs2297336, minor allele frequency (MAF) = 14.1%, β = -0.62 p = 3.7 × 10(-6); rs324146, MAF = 16.9%, β = -0.55, p = 1.4 × 10(-5)). In addition to these novel findings, we successfully replicated a previously reported association with rs634990 near GJD2 at 15q14 (MAF = 47%, β = -0.29, p=1.8 × 10(-3)). We also found evidence of association with spherical equivalent on 2q37.1 in PRSS56 at rs1550094 (MAF = 31%, β = -0.33, p = 1.7 × 10(-3)), a region previously associated with myopia. CONCLUSIONS We identified several novel candidate genes that may play a role in the control of spherical equivalent. However, further studies are needed to replicate these findings. In addition, our results contribute to the increasing evidence that variation in the GJD2 and PRSS56 genes influence the development of refractive errors. Identifying that variation in these genes is associated with spherical equivalent may provide further insight into the etiology of myopia and consequent vision loss.
Collapse
Affiliation(s)
- Fei Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Kristine E Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Barbara Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| |
Collapse
|
62
|
Abstract
Myopia is a major cause of visual impairment worldwide. In particular, high myopia is associated with serious blinding complications, including retinal detachment, chorioretinal degeneration, and choroidal neovascularization. Myopia is multifactorial in etiology, resulting from the interaction of environmental and genetic risk factors. During the past 2 decades, a large number of gene loci and variants have been identified for myopia. There are more than 20 myopia-associated loci spanning all chromosomes. Earlier findings were obtained mainly from family linkage analyses and candidate gene studies, and more recent results are principally from genome-wide association studies and exome sequencing. Some genetic associations have been successfully validated and replicated in populations of different geographic localities and ethnicities, but some have not. Compared with Whites, Asian populations-in particular Japanese, Korean, and Chinese-have a much higher prevalence of myopia, especially high myopia. Both genetic and environmental factors contribute to such ethnic variations. This review attempts to summarize and compare the allelic frequencies of gene variants known to be associated with myopia in different ethnic groups, especially in the Asia-Pacific region.
Collapse
Affiliation(s)
- Shi Song Rong
- From the *Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong Eye Hospital, Kowloon, Hong Kong; and †Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA
| | | | | |
Collapse
|
63
|
Han B, Duong D, Sul JH, de Bakker PIW, Eskin E, Raychaudhuri S. A general framework for meta-analyzing dependent studies with overlapping subjects in association mapping. Hum Mol Genet 2016; 25:1857-66. [PMID: 26908615 PMCID: PMC4986332 DOI: 10.1093/hmg/ddw049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 01/22/2016] [Accepted: 02/15/2016] [Indexed: 11/12/2022] Open
Abstract
Meta-analysis strategies have become critical to augment power of genome-wide association studies (GWAS). To reduce genotyping or sequencing cost, many studies today utilize shared controls, and these individuals can inadvertently overlap among multiple studies. If these overlapping individuals are not taken into account in meta-analysis, they can induce spurious associations. In this article, we propose a general framework for adjusting association statistics to account for overlapping subjects within a meta-analysis. The key idea of our method is to transform the covariance structure of the data, so it can be used in downstream analyses. As a result, the strategy is very flexible and allows a wide range of meta-analysis methods, such as the random effects model, to account for overlapping subjects. Using simulations and real datasets, we demonstrate that our method has utility in meta-analyses of GWAS, as well as in a multi-tissue mouse expression quantitative trait loci (eQTL) study where our method increases the number of discovered eQTL by up to 19% compared with existing methods.
Collapse
Affiliation(s)
- Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Republic of Korea,
| | | | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, Semel Center for Informatics and Personalized Genomics, University of California, Los Angeles, CA 90095, USA
| | - Paul I W de Bakker
- Julius Center for Health Sciences and Primary Care, Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Eleazar Eskin
- Computer Science Department, Department of Human Genetics
| | - Soumya Raychaudhuri
- Division of Genetics, Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA and Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK
| |
Collapse
|
64
|
Vroom CR, Posthuma D, Li MX, Dolan CV, van der Sluis S. Multivariate Gene-Based Association Test on Family Data in MGAS. Behav Genet 2016; 46:718-725. [PMID: 27048268 DOI: 10.1007/s10519-016-9787-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/12/2016] [Indexed: 11/25/2022]
Abstract
In analyses of unrelated individuals, the program multivariate gene-based association test by extended Simes (MGAS), which facilitates multivariate gene-based association testing, was shown to have correct Type I error rate and superior statistical power compared to other multivariate gene-based approaches. Here we show, through simulation, that MGAS can also be applied to data including genetically related subjects (e.g., family data), by using p value information obtained in Plink or in generalized estimating equations (with the 'exchangeable' working correlation matrix), both of which account for the family structure on a univariate single nucleotide polymorphism-based level by applying a sandwich correction of standard errors. We show that when applied to family-data, MGAS has correct Type I error rate, and given the details of the simulation setup, adequate power. Application of MGAS to seven eye measurement phenotypes showed statistically significant association with two genes that were not discovered in previous univariate analyses of a composite score. We conclude that MGAS is a useful and convenient tool for multivariate gene-based genome-wide association analysis in both unrelated and related individuals.
Collapse
Affiliation(s)
- César-Reyer Vroom
- Department of Clinical Genetics, Section Complex Traits Genetics, VU Medical Center (VUmc), Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Danielle Posthuma
- Department of Clinical Genetics, Section Complex Traits Genetics, VU Medical Center (VUmc), Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.,Department of Complex Traits Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - Miao-Xin Li
- Department of Psychiatry, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,The Centre for Reproduction, Development and Growth, The University of Hong Kong, Pokfulam, Hong Kong.,The Centre for Genomic Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Conor V Dolan
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - Sophie van der Sluis
- Department of Clinical Genetics, Section Complex Traits Genetics, VU Medical Center (VUmc), Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| |
Collapse
|
65
|
Williams KM, Hammond CJ. GWAS in myopia: insights into disease and implications for the clinic. EXPERT REVIEW OF OPHTHALMOLOGY 2016. [DOI: 10.1586/17469899.2016.1164597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
66
|
Jimeno D, Gómez C, Calzada N, de la Villa P, Lillo C, Santos E. RASGRF2 controls nuclear migration in postnatal retinal cone photoreceptors. J Cell Sci 2016; 129:729-42. [PMID: 26743081 DOI: 10.1242/jcs.180919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/29/2015] [Indexed: 02/04/2023] Open
Abstract
Detailed immunocytochemical analyses comparing wild-type (WT), GRF1-knockout (KO), GRF2-KO and GRF1/2 double-knockout (DKO) mouse retinas uncovered the specific accumulation of misplaced, 'ectopic' cone photoreceptor nuclei in the photoreceptor segment (PS) area of retinas from GRF2-KO and GRF1/2-DKO, but not of WT or GRF1-KO mice. Localization of ectopic nuclei in the PS area of GRF2-depleted retinas occurred postnatally and peaked between postnatal day (P)11 and P15. Mechanistically, the generation of this phenotype involved disruption of the outer limiting membrane and intrusion into the PS layer by cone nuclei displaying significant perinuclear accumulation of signaling molecules known to participate in nuclear migration and cytoskeletal reorganization, such as PAR3, PAR6 and activated, phosphorylated forms of PAK, MLC2 and VASP. Electroretinographic recordings showed specific impairment of cone-mediated retinal function in GRF2-KO and GRF1/2-DKO retinas compared with WT controls. These data identify defective cone nuclear migration as a novel phenotype in mouse retinas lacking GRF2 and support a crucial role of GRF2 in control of the nuclear migration processes required for proper postnatal development and function of retinal cone photoreceptors.
Collapse
Affiliation(s)
- David Jimeno
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Carmela Gómez
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Nuria Calzada
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| | - Pedro de la Villa
- Departamento de Fisiología, Universidad Alcalá, Alcalá de Henares 28871, Spain, Spain
| | | | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC - Universidad de Salamanca), Salamanca 37007, Spain
| |
Collapse
|
67
|
Meng B, LI SM, Yang Y, Yang ZR, Sun F, Kang MT, Sun YY, Ran AR, Wang JN, Yan R, BaI YW, Wang NL, Zhan SY. The association of TGFB1 genetic polymorphisms with high myopia: a systematic review and meta-analysis. Int J Clin Exp Med 2015; 8:20355-20367. [PMID: 26884952 PMCID: PMC4723797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE The TGFB1 gene is among the most studied genes in high myopia due to its role in scleral remodeling. But reported findings of association on TGFB1 and high myopia are inconsistent. This present study is to evaluate the association of TGFB1 polymorphisms and high myopia. METHODS A comprehensive literature search was conducted on studies published up to April 5, 2015. Summary odds ratios (ORs) and 95% confidence intervals were analyzed. Heterogeneity across studies was evaluated by Cochran Q statistic test and the I(2) index. Sensitivity analyses were conducted by the approach of one-study remove to assess the influence of single study on the combined effect. RESULTS Eight studies were included in this study for meta-analysis. Rs1982073 was associated with high myopia in dominant model (OR=1.64; 95% CI=1.04~2.58; P<0.05), heterozygous model (OR=1.54; 95% CI=1.02~2.33; P<0.05), homozygous model (OR=1.90; 95% CI=1.01~3.55; P=0.05) and allelic model (OR=1.36; 95% CI=1.01~1.84; P=0.05). However, there was no statistical significance when Bonferroni correction was considered. Rs4803455 was associated with high myopia in recessive model (OR=0.40; 95% CI=0.25~0.64; P<0.01) and homozygous model (OR=0.42; 95% CI=0.26~0.68; P<0.01). Rs1800469 was associated with high myopia in allelic model (OR=0.78; 95% CI=0.64~0.96; P<0.05). And the associations can withstand Bonferroni correction in models mentioned above when referring to rs4803455 (P<0.01) and rs1800469 (P<0.05). CONCLUSIONS Meta-analysis of existing data revealed a suggestive association of TGFB1 rs1982073 and rs4803455 with high myopia.
Collapse
Affiliation(s)
- Bo Meng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science CentreBeijing 100191, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Shi-Ming LI
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Yu Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science CentreBeijing 100191, China
| | - Zhi-Rong Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science CentreBeijing 100191, China
| | - Feng Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science CentreBeijing 100191, China
| | - Meng-Tian Kang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Yun-Yun Sun
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - An-Ran Ran
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Jia-Nan Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Ran Yan
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Ya-Wen BaI
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Ning-Li Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical UniversityBeijing 100005, China
| | - Si-Yan Zhan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science CentreBeijing 100191, China
| |
Collapse
|
68
|
Chen T, Shan G, Ma J, Zhong Y. Polymorphism in the RASGRF1 gene with high myopia: A meta-analysis. Mol Vis 2015; 21:1272-80. [PMID: 26644762 PMCID: PMC4645451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/11/2015] [Indexed: 10/26/2022] Open
Abstract
PURPOSE To evaluate the association between polymorphisms of RASGRF1 rs8027411 and high myopia in Chinese and Japanese populations. METHODS All eligible studies investigating the association between the RASGRF1 gene and high myopia listed in PubMed, EMBASE, the Cochrane Library, Web of Science, and the China Biologic Medical Database were retrieved. The effects were assessed with the pooled odds ratio (OR) and 95% confidence interval (CI). Heterogeneity between studies was evaluated with the Q-statistic test. Publication bias was tested with Begg's and Egger's linear regression tests. Subgroup analysis and sensitivity analysis were performed to identify the sources of heterogeneity. RESULTS In the present meta-analysis, 2,529 individuals with high myopia and 3,127 controls from four studies were included and divided into seven groups. The results indicated that RASGRF1 rs8027411 was significantly associated with high myopia in Chinese and Japanese populations. Carriers of the rs8027411 G allele had a lower risk of high myopia compared to carriers with the T allele (G versus T, OR=0.83, 95% CI=0.77-0.89; p<0.001). Low but not significant heterogeneity was found in a recessive model. No heterogeneity was found in other genetic models. The subgroup analysis indicated that the protective effect of rs8027411 variants was more prominent in Chinese populations (G versus T, OR=0.80 in Chinese and OR=0.86 in Japanese; GG versus TT, OR=0.65 in Chinese and OR=0.77 in Japanese; GT versus TT, OR=0.76 in Chinese and OR=0.81 in Japanese; (GG+GT) versus TT, OR=0.73 in Chinese and OR=0.80 in Japanese; and GG versus (GT+TT), OR=0.77 in Chinese and OR=0.87 in Japanese). Sensitivity analysis indicated that the study results were stable in allelic, homozygote, heterozygote, and dominant models but were not stable in the recessive model. No evidence of publication bias was found. CONCLUSIONS Carriers of the rs8027411 G allele in the RASGRF1 gene may be at a lower risk of high myopia in Chinese and Japanese populations. The RASGRF1 gene may play a role in the development of high myopia, especially in Asians. Additional studies are required to validate these results.
Collapse
Affiliation(s)
- Ting Chen
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guangliang Shan
- Department of Epidemiology and Statistics, Institute of Basic Medical Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Ma
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yong Zhong
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
69
|
Tkatchenko AV, Tkatchenko TV, Guggenheim JA, Verhoeven VJM, Hysi PG, Wojciechowski R, Singh PK, Kumar A, Thinakaran G, Williams C. APLP2 Regulates Refractive Error and Myopia Development in Mice and Humans. PLoS Genet 2015; 11:e1005432. [PMID: 26313004 PMCID: PMC4551475 DOI: 10.1371/journal.pgen.1005432] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
Myopia is the most common vision disorder and the leading cause of visual impairment worldwide. However, gene variants identified to date explain less than 10% of the variance in refractive error, leaving the majority of heritability unexplained (“missing heritability”). Previously, we reported that expression of APLP2 was strongly associated with myopia in a primate model. Here, we found that low-frequency variants near the 5’-end of APLP2 were associated with refractive error in a prospective UK birth cohort (n = 3,819 children; top SNP rs188663068, p = 5.0 × 10−4) and a CREAM consortium panel (n = 45,756 adults; top SNP rs7127037, p = 6.6 × 10−3). These variants showed evidence of differential effect on childhood longitudinal refractive error trajectories depending on time spent reading (gene x time spent reading x age interaction, p = 4.0 × 10−3). Furthermore, Aplp2 knockout mice developed high degrees of hyperopia (+11.5 ± 2.2 D, p < 1.0 × 10−4) compared to both heterozygous (-0.8 ± 2.0 D, p < 1.0 × 10−4) and wild-type (+0.3 ± 2.2 D, p < 1.0 × 10−4) littermates and exhibited a dose-dependent reduction in susceptibility to environmentally induced myopia (F(2, 33) = 191.0, p < 1.0 × 10−4). This phenotype was associated with reduced contrast sensitivity (F(12, 120) = 3.6, p = 1.5 × 10−4) and changes in the electrophysiological properties of retinal amacrine cells, which expressed Aplp2. This work identifies APLP2 as one of the “missing” myopia genes, demonstrating the importance of a low-frequency gene variant in the development of human myopia. It also demonstrates an important role for APLP2 in refractive development in mice and humans, suggesting a high level of evolutionary conservation of the signaling pathways underlying refractive eye development. Gene variants identified by GWAS studies to date explain only a small fraction of myopia cases because myopia represents a complex disorder thought to be controlled by dozens or even hundreds of genes. The majority of genetic variants underlying myopia seems to be of small effect and/or low frequency, which makes them difficult to identify using classical genetic approaches, such as GWAS, alone. Here, we combined gene expression profiling in a monkey model of myopia, human GWAS, and a gene-targeted mouse model of myopia to identify one of the “missing” myopia genes, APLP2. We found that a low-frequency risk allele of APLP2 confers susceptibility to myopia only in children exposed to large amounts of daily reading, thus, providing an experimental example of the long-hypothesized gene-environment interaction between nearwork and genes underlying myopia. Functional analysis of APLP2 using an APLP2 knockout mouse model confirmed functional significance of APLP2 in refractive development and implicated a potential role of synaptic transmission at the level of glycinergic amacrine cells of the retina for the development of myopia. Furthermore, mouse studies revealed that lack of Aplp2 has a dose-dependent suppressive effect on susceptibility to form-deprivation myopia, providing a potential gene-specific target for therapeutic intervention to treat myopia.
Collapse
Affiliation(s)
- Andrei V. Tkatchenko
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University, New York, New York, United States of America
- * E-mail:
| | - Tatiana V. Tkatchenko
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
| | - Jeremy A. Guggenheim
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London School of Medicine, London, United Kingdom
| | - Robert Wojciechowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute (NIH), Baltimore, Maryland, United States of America
| | - Pawan Kumar Singh
- Department of Ophthalmology, Wayne State University, Detroit, Michigan, United States of America
| | - Ashok Kumar
- Department of Ophthalmology, Wayne State University, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan, United States of America
| | - Gopal Thinakaran
- Departments of Neurobiology, Neurology, and Pathology, University of Chicago, Chicago, Illinois, United States of America
| | | | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
70
|
Zhang Y, Wildsoet CF. RPE and Choroid Mechanisms Underlying Ocular Growth and Myopia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 134:221-40. [PMID: 26310157 DOI: 10.1016/bs.pmbts.2015.06.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myopia is the most common type of refractive errors and one of the world's leading causes of blindness. Visual manipulations in animal models have provided convincing evidence for the role of environmental factors in myopia development. These models along with in vitro studies have provided important insights into underlying mechanisms. The key locations of the retinal pigment epithelium (RPE) and choroid make them plausible conduits for relaying growth regulatory signals originating in the retina to the sclera, which ultimately determines eye size and shape. Identifying the key signal molecules and their targets may lead to the development of new myopia control treatments. This section summarizes findings implicating the RPE and choroid in myopia development. For RPE and/or choroid, changes in morphology, activity of ion channels/transporters, as well as in gene and protein expression, have been linked to altered eye growth. Both tissues thus represent potential targets for novel therapies for myopia.
Collapse
Affiliation(s)
- Yan Zhang
- School of Optometry, University of California, Berkeley, California, USA.
| | | |
Collapse
|
71
|
Zhang Q. Genetics of Refraction and Myopia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 134:269-79. [PMID: 26310160 DOI: 10.1016/bs.pmbts.2015.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Both genetic and environmental factors play roles in the development of refractive errors. Identification of genes involved in refractive errors may help in elucidating the underlying molecular mechanism related to both genetic defects and environmental pressure. Recent development of techniques for genome wide analysis provides unique opportunity in dissecting the genetic basis related to refractive errors. This chapter tries to give a brief overview on the recent progress of genetic study of refractive errors, especially myopia.
Collapse
Affiliation(s)
- Qingjiong Zhang
- State Key Lab of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, PR China.
| |
Collapse
|
72
|
Identification of myopia-associated WNT7B polymorphisms provides insights into the mechanism underlying the development of myopia. Nat Commun 2015; 6:6689. [DOI: 10.1038/ncomms7689] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 02/20/2015] [Indexed: 11/08/2022] Open
|
73
|
Chen CD, Yu ZQ, Chen XL, Zhou JQ, Zhou XT, Sun XH, Chu RY. Evaluating the association between pathological myopia and SNPs in RASGRF1. ACTC1 and GJD2 genes at chromosome 15q14 and 15q25 in a Chinese population. Ophthalmic Genet 2015; 36:1-7. [PMID: 23834555 DOI: 10.3109/13816810.2013.812737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND This study investigated the association of the 27 SNPs located in RASGRF1. GJD2, and ACTC1 genes with pathological myopia in a Chinese Han population. METHODS Myopia patients were stratified according to whether they did (n = 274) or did not (n = 131) have myopic macular degeneration (MMD). The SNPbrowser software was used to identify specific SNPs for analysis and minimal allele frequency of >20%, and a pairwise r(2) < 0.85 were genotyped using MALDI-TOF mass spectrometry. RESULTS Before controlling for false discovery rate, the frequency of the rs1867315 C/C genotype compared with healthy controls was lower in the myopia group (p = 0.006) and in myopia patients without macular degeneration (p = 0.019). The frequency of the rs670957A/A genotype was also lower in patients without MMD compared with controls (p = 0.045). For rs2070664, the frequency of the A allele was higher in the patients with MMD compared to those without MMD (p = 0.032). After controlling for a false discovery rate of 5%, there was no significant difference in genotype and allele frequencies between these groups. CONCLUSION In this study, there was no association of the analyzed SNPs located in RASGRF1. GJD2, and ACTC1 with pathological myopia, suggesting that SNPs included in our study have no or a limited role in causing pathologic myopia in this Chinese Han population.
Collapse
Affiliation(s)
- Chong-da Chen
- Key Laboratory of Myopia, Ministry of Health , Shanghai , China
| | | | | | | | | | | | | |
Collapse
|
74
|
ASSOCIATIONS OF INFLAMMATORY CYTOKINES WITH CHOROIDAL NEOVASCULARIZATION IN HIGHLY MYOPIC EYES. Retina 2015; 35:344-50. [DOI: 10.1097/iae.0000000000000311] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
75
|
Li Q, Wojciechowski R, Simpson CL, Hysi PG, Verhoeven VJM, Ikram MK, Höhn R, Vitart V, Hewitt AW, Oexle K, Mäkelä KM, MacGregor S, Pirastu M, Fan Q, Cheng CY, St Pourcain B, McMahon G, Kemp JP, Northstone K, Rahi JS, Cumberland PM, Martin NG, Sanfilippo PG, Lu Y, Wang YX, Hayward C, Polašek O, Campbell H, Bencic G, Wright AF, Wedenoja J, Zeller T, Schillert A, Mirshahi A, Lackner K, Yip SP, Yap MKH, Ried JS, Gieger C, Murgia F, Wilson JF, Fleck B, Yazar S, Vingerling JR, Hofman A, Uitterlinden A, Rivadeneira F, Amin N, Karssen L, Oostra BA, Zhou X, Teo YY, Tai ES, Vithana E, Barathi V, Zheng Y, Siantar RG, Neelam K, Shin Y, Lam J, Yonova-Doing E, Venturini C, Hosseini SM, Wong HS, Lehtimäki T, Kähönen M, Raitakari O, Timpson NJ, Evans DM, Khor CC, Aung T, Young TL, Mitchell P, Klein B, van Duijn CM, Meitinger T, Jonas JB, Baird PN, Mackey DA, Wong TY, Saw SM, Pärssinen O, Stambolian D, Hammond CJ, Klaver CCW, Williams C, Paterson AD, Bailey-Wilson JE, Guggenheim JA. Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. Hum Genet 2015; 134:131-46. [PMID: 25367360 PMCID: PMC4291519 DOI: 10.1007/s00439-014-1500-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/30/2014] [Indexed: 11/24/2022]
Abstract
To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E-8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E-07), TOX (rs7823467, P = 3.47E-07) and LINC00340 (rs12212674, P = 1.49E-06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = -0.59, P = 2.10E-04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors.
Collapse
Affiliation(s)
- Qing Li
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Robert Wojciechowski
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
| | - Claire L. Simpson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mohammad Kamran Ikram
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alex W. Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Konrad Oexle
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Kari-Matti Mäkelä
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Mario Pirastu
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - Qiao Fan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Beaté St Pourcain
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - George McMahon
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - John P. Kemp
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Kate Northstone
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Jugnoo S. Rahi
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Phillippa M. Cumberland
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Paul G. Sanfilippo
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Yi Lu
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Juho Wedenoja
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tanja Zeller
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
| | - Arne Schillert
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Dardenne Eye Hospital, Bonn, Germany
| | - Karl Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Shea Ping Yip
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Maurice K. H. Yap
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Federico Murgia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | | | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
| | - André Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lennart Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Xin Zhou
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Veluchamy Barathi
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | | | | | - Kumari Neelam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Youchan Shin
- Singapore Eye Research Institute, Singapore, Singapore
| | - Janice Lam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Ekaterina Yonova-Doing
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - S. Mohsen Hosseini
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Hoi-Suen Wong
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
| | - Chiea-Chuen Khor
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore, Singapore
| | - Terri L. Young
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
| | - Paul Mitchell
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
| | - Barbara Klein
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
| | | | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Olavi Pärssinen
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
| | - Dwight Stambolian
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
| | - Joan E. Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Jeremy A. Guggenheim
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - The CREAM Consortium
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
- Faculty of Medicine, University of Split, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
- Dardenne Eye Hospital, Bonn, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
| |
Collapse
|
76
|
Manyes L, Arribas M, Gomez C, Calzada N, Fernandez-Medarde A, Santos E. Transcriptional profiling reveals functional links between RasGrf1 and Pttg1 in pancreatic beta cells. BMC Genomics 2014; 15:1019. [PMID: 25421944 PMCID: PMC4301450 DOI: 10.1186/1471-2164-15-1019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/06/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Our prior characterization of RasGrf1 deficient mice uncovered significant defects in pancreatic islet count and size as well as beta cell development and signaling function, raising question about the mechanisms linking RasGrf1 to the generation of those "pancreatic" phenotypes. RESULTS Here, we compared the transcriptional profile of highly purified pancreatic islets from RasGrf1 KO mice to that of WT control animals using commercial oligonucleotide microarrays. RasGrf1 elimination resulted in differential gene expression of numerous components of MAPK- and Calcium-signaling pathways, suggesting a relevant contribution of this GEF to modulation of cellular signaling in the cell lineages integrating the pancreatic islets. Whereas the overall transcriptional profile of pancreatic islets was highly specific in comparison to other organs of the same KO mice, a significant specific repression of Pttg1 was a common transcriptional alteration shared with other tissues of neuroectodermal origin. This observation, together with the remarkable pancreatic phenotypic similarities between RasGrf1 KO and Pttg1 KO mice suggested the possibility of proximal functional regulatory links between RasGrf1 and Pttg1 in pancreatic cell lineages expressing these proteins.Analysis of the mPttg1 promoter region identified specific recognition sites for numerous transcription factors which were also found to be differentially expressed in RasGrf1 KO pancreatic islets and are known to be relevant for Ras-ERK signaling as well as beta cell function. Reporter luciferase assays in BT3 insulinoma cells demonstrated the ability of RasGrf1 to modulate mPttg1 promoter activity through ERK-mediated signals. Analysis of the phenotypic interplay between RasGrf1 and Pttg1 in double knockout RasGrf1/Pttg1 mice showed that combined elimination of the two loci resulted in dramatically reduced values of islet and beta cell count and glucose homeostasis function which neared those measured in single Pttg1 KO mice and were significantly lower than those observed in individual RasGrf1 KO mice. CONCLUSIONS The specific transcriptional profile and signaling behavior of RasgGrf1 KO pancreatic islets, together with the dominance of Pttg1 over RasGrf1 with regards to the generation of these phenotypes in mouse pancreas, suggest that RasGrf1 is an important upstream component of signal transduction pathways regulating Pttg1 expression and controlling beta cell development and physiological responses.
Collapse
Affiliation(s)
| | | | | | | | - Alberto Fernandez-Medarde
- Centro de Investigación del Cáncer, IBMCC (CSIC-USAL), University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain.
| | | |
Collapse
|
77
|
|
78
|
Chandra A, Mitry D, Wright A, Campbell H, Charteris DG. Genome-wide association studies: applications and insights gained in Ophthalmology. Eye (Lond) 2014; 28:1066-79. [PMID: 24971990 DOI: 10.1038/eye.2014.145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/18/2014] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) use high-throughput genotyping technologies to genotype thousands of single-nucleotide polymorphisms (SNPs) and relate them to the development of clinical and quantitative traits. Their use has been highly successful in the field of ophthalmology, and since the advent of GWAS in 2005, many genes not previously suspected of having a role in disease have been identified and the findings replicated. We conducted an extensive literature review and describe the concept, design, advantages, and limitations of GWAS and provide a detailed description of the applications and discoveries of GWAS in the field of eye disease to date. There have been many novel findings revealing previously unknown biological insights in a diverse range of common ocular conditions. GWAS have been a highly successful modality for investigating the pathogenesis of a wide variety of ophthalmic conditions. The insights gained into the pathogenesis of disease provide not only a better understanding of underlying disease mechanism but also offer a rationale for targeted treatment and preventative strategies. Expansive international collaboration and standardised phenotyping will permit the continued success of this investigative technique.
Collapse
Affiliation(s)
- A Chandra
- 1] Department of Ophthalmology, Moorfields Eye Hospital, London, UK [2] UCL Institute of Ophthalmology, London, UK
| | - D Mitry
- 1] Department of Ophthalmology, Moorfields Eye Hospital, London, UK [2] Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - A Wright
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - H Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - D G Charteris
- Department of Ophthalmology, Moorfields Eye Hospital, London, UK
| |
Collapse
|
79
|
Guo H, Jin X, Zhu T, Wang T, Tong P, Tian L, Peng Y, Sun L, Wan A, Chen J, Liu Y, Li Y, Tian Q, Xia L, Zhang L, Pan Y, Lu L, Liu Q, Shen L, Li Y, Xiong W, Li J, Tang B, Feng Y, Zhang X, Zhang Z, Pan Q, Hu Z, Xia K. SLC39A5 mutations interfering with the BMP/TGF-β pathway in non-syndromic high myopia. J Med Genet 2014; 51:518-25. [PMID: 24891338 PMCID: PMC4112430 DOI: 10.1136/jmedgenet-2014-102351] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background High myopia, with the characteristic feature of refractive error, is one of the leading causes of blindness worldwide. It has a high heritability, but only a few causative genes have been identified and the pathogenesis is still unclear. Methods We used whole genome linkage and exome sequencing to identify the causative mutation in a non-syndromic high myopia family. Direct Sanger sequencing was used to screen the candidate gene in additional sporadic cases or probands. Immunofluorescence was used to evaluate the expression pattern of the candidate gene in the whole process of eye development. Real-time quantitative PCR and immunoblot was used to investigate the functional consequence of the disease-associated mutations. Results We identified a nonsense mutation (c.141C>G:p.Y47*) in SLC39A5 co-segregating with the phenotype in a non-syndromic severe high myopia family. The same nonsense mutation (c.141C>G:p.Y47*) was detected in a sporadic case and a missense mutation (c.911T>C:p.M304T) was identified and co-segregated in another family by screening additional cases. Both disease-associated mutations were not found in 1276 control individuals. SLC39A5 was abundantly expressed in the sclera and retina across different stages of eye development. Furthermore, we found that wild-type, but not disease-associated SLC39A5 inhibited the expression of Smadl, a key phosphate protein in the downstream of the BMP/TGF-β (bone morphogenic protein/transforming growth factor-β) pathway. Conclusions Our study reveals that loss-of-function mutations of SLC39A5 are associated with the autosome dominant non-syndromic high myopia, and interference with the BMP/TGF-β pathway may be one of the molecular mechanisms for high myopia.
Collapse
Affiliation(s)
- Hui Guo
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xuemin Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tengfei Zhu
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Tianyun Wang
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Ping Tong
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Tian
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Peng
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Liangdan Sun
- Department of Dermatology, Institute of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Anran Wan
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Jingjing Chen
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Yanling Liu
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Ying Li
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Qi Tian
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lu Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lusi Zhang
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Yongcheng Pan
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lina Lu
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Qiong Liu
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lu Shen
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Yunping Li
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiada Li
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- The Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong Feng
- The Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuejun Zhang
- Department of Dermatology, Institute of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Zhuohua Zhang
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Qian Pan
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China School of Life Sciences, Central South University, Changsha, Hunan, China Key Laboratory of Medical Information Research, Changsha, Hunan, China
| |
Collapse
|
80
|
Hysi PG, Wojciechowski R, Rahi JS, Hammond CJ. Genome-wide association studies of refractive error and myopia, lessons learned, and implications for the future. Invest Ophthalmol Vis Sci 2014; 55:3344-51. [PMID: 24876304 DOI: 10.1167/iovs.14-14149] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The investigation of the genetic basis of refractive error and myopia entered a new stage with the introduction of genome-wide association studies (GWAS). Multiple GWAS on many ethnic groups have been published over the years, providing new insight into the genetic architecture and pathophysiology of refractive error. This is a review of the GWAS published to date, the main lessons learned, and future possible directions of genetic studies of myopia and refractive error.
Collapse
Affiliation(s)
- Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom Centre for Paediatric Epidemiology and Biostatistics, University College London Institute of Child Health, London, United Kingdom
| | | | - Jugnoo S Rahi
- Centre for Paediatric Epidemiology and Biostatistics, University College London Institute of Child Health, London, United Kingdom
| | - Chris J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| |
Collapse
|
81
|
Physiopathologie de la myopie, entre hérédité et environnement. J Fr Ophtalmol 2014; 37:407-14. [DOI: 10.1016/j.jfo.2014.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 02/07/2023]
|
82
|
Barman A, Assmann A, Richter S, Soch J, Schütze H, Wüstenberg T, Deibele A, Klein M, Richter A, Behnisch G, Düzel E, Zenker M, Seidenbecher CI, Schott BH. Genetic variation of the RASGRF1 regulatory region affects human hippocampus-dependent memory. Front Hum Neurosci 2014; 8:260. [PMID: 24808846 PMCID: PMC4010733 DOI: 10.3389/fnhum.2014.00260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/08/2014] [Indexed: 11/30/2022] Open
Abstract
The guanine nucleotide exchange factor RASGRF1 is an important regulator of intracellular signaling and neural plasticity in the brain. RASGRF1-deficient mice exhibit a complex phenotype with learning deficits and ocular abnormalities. Also in humans, a genome-wide association study has identified the single nucleotide polymorphism (SNP) rs8027411 in the putative transcription regulatory region of RASGRF1 as a risk variant of myopia. Here we aimed to assess whether, in line with the RASGRF1 knockout mouse phenotype, rs8027411 might also be associated with human memory function. We performed computer-based neuropsychological learning experiments in two independent cohorts of young, healthy participants. Tests included the Verbal Learning and Memory Test (VLMT) and the logical memory section of the Wechsler Memory Scale (WMS). Two sub-cohorts additionally participated in functional magnetic resonance imaging (fMRI) studies of hippocampus function. 119 participants performed a novelty encoding task that had previously been shown to engage the hippocampus, and 63 subjects participated in a reward-related memory encoding study. RASGRF1 rs8027411 genotype was indeed associated with memory performance in an allele dosage-dependent manner, with carriers of the T allele (i.e., the myopia risk allele) showing better memory performance in the early encoding phase of the VLMT and in the recall phase of the WMS logical memory section. In fMRI, T allele carriers exhibited increased hippocampal activation during presentation of novel images and during encoding of pictures associated with monetary reward. Taken together, our results provide evidence for a role of the RASGRF1 gene locus in hippocampus-dependent memory and, along with the previous association with myopia, point toward pleitropic effects of RASGRF1 genetic variations on complex neural function in humans.
Collapse
Affiliation(s)
- Adriana Barman
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Anne Assmann
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Otto von Guericke University Magdeburg, Germany
| | - Sylvia Richter
- Department of Clinical Psychology, University of Salzburg Salzburg, Austria
| | - Joram Soch
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Otto von Guericke University Magdeburg, Germany ; Bernstein Center for Computational Neuroscience, Humboldt University Berlin, Germany
| | - Hartmut Schütze
- Institute of Cognitive Neurology and Dementia Research, Otto von Guericke University Magdeburg, Germany
| | - Torsten Wüstenberg
- Department of Psychiatry, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Anna Deibele
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Otto von Guericke University Magdeburg, Germany
| | - Marieke Klein
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Department of Genetics, Radboud University Nijmegen Medical Center Nijmegen, Netherlands
| | - Anni Richter
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Gusalija Behnisch
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany
| | - Emrah Düzel
- Institute of Cognitive Neurology and Dementia Research, Otto von Guericke University Magdeburg, Germany ; Helmholtz Center for Neurodegenerative Diseases Magdeburg, Germany ; Center for Behavioral Brain Sciences Magdeburg, Germany
| | - Martin Zenker
- Department of Human Genetics, Otto von Guericke University Magdeburg, Germany
| | - Constanze I Seidenbecher
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Center for Behavioral Brain Sciences Magdeburg, Germany
| | - Björn H Schott
- Department of Behavioral Neurology and Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Germany ; Department of Psychiatry, Charité Universitätsmedizin Berlin Berlin, Germany ; Center for Behavioral Brain Sciences Magdeburg, Germany ; Department of Neurology, Otto von Guericke University Magdeburg, Germany
| |
Collapse
|
83
|
Qiang Y, Li W, Wang Q, He K, Li Z, Chen J, Song Z, Qu J, Zhou X, Qin S, Shen J, Wen Z, Ji J, Shi Y. Association study of 15q14 and 15q25 with high myopia in the Han Chinese population. BMC Genet 2014; 15:51. [PMID: 24767175 PMCID: PMC4014749 DOI: 10.1186/1471-2156-15-51] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 04/01/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Refractive errors and high myopia are the most common ocular disorders, and both of them are leading causes of blindness in the world. Recently, genetic association studies in European and Japanese population identified that common genetic variations located in 15q14 and 15q25 were associated with high myopia. To validate whether the same variations conferred risk to high myopia in the Han Chinese population, we genotyped 1,461 individuals (940 controls and 521 cases samples) recruited of Han Chinese origin. RESULT We found rs8027411 in 15q25 (P = 0.012 after correction, OR = 0.78) was significantly associated with high myopia but rs634990 in 15q14 (P = 0.54 after correction), OR = 0.88) was not. CONCLUSIONS Our findings supported that 15q25 is a susceptibility locus for high myopia, and gene RASGRF1 was possible to play a role in the pathology of high myopia.
Collapse
Affiliation(s)
- Yu Qiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Wenjin Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Qingzhong Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Kuanjun He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
- Schizophrenia Program, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, P.R China
| | - Zhijian Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Jia Qu
- Wenzhou Medical College, Wenzhou 325003, P.R China
| | | | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Jiawei Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Zujia Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Jue Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, P.R China
- Shanghai Changning Mental Health Center, 299 Xiehe Road, Shanghai 200042, P.R China
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai 200042, P.R China
| |
Collapse
|
84
|
The NEIGHBOR consortium primary open-angle glaucoma genome-wide association study: rationale, study design, and clinical variables. J Glaucoma 2014; 22:517-25. [PMID: 22828004 DOI: 10.1097/ijg.0b013e31824d4fd8] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Primary open-angle glaucoma (POAG) is a common disease with complex inheritance. The identification of genes predisposing to POAG is an important step toward the development of novel gene-based methods of diagnosis and treatment. Genome-wide association studies (GWAS) have successfully identified genes contributing to complex traits such as POAG however, such studies frequently require very large sample sizes, and thus, collaborations and consortia have been of critical importance for the GWAS approach. In this report we describe the formation of the NEIGHBOR consortium, the harmonized case control definitions used for a POAG GWAS, the clinical features of the cases and controls, and the rationale for the GWAS study design.
Collapse
|
85
|
Low copy number of the salivary amylase gene predisposes to obesity. Nat Genet 2014; 46:492-7. [PMID: 24686848 PMCID: PMC6485469 DOI: 10.1038/ng.2939] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts. Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue. We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects. Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 × 10(-14)) and serum enzyme levels (P < 2.20 × 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 × 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 × 10(-10)). The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution. Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies.
Collapse
|
86
|
Liu J, Zhang HX. Polymorphism in the 11q24.1 genomic region is associated with myopia: a comprehensive genetic study in Chinese and Japanese populations. Mol Vis 2014; 20:352-8. [PMID: 24672220 PMCID: PMC3962689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 03/19/2014] [Indexed: 10/31/2022] Open
Abstract
PURPOSE To evaluate the association of polymorphisms in the 11q24.1 genomic region and the CTNND2 gene with myopia. METHODS We conducted a comprehensive meta-analysis included 6,954 cases and 9,346 controls. Odds ratios (ORs) were calculated using Carlin's method. Publication bias was assessed using Egger et al.'s approach. Sensitivity, heterogeneity, and trim and fill analyses were also conducted. RESULTS For the 11q24.1 genomic region, the rs11218544 polymorphism showed significant association with myopia [OR and 95% confidence interval (CI): 1.167 (1.032-1.319), p=0.013], while rs577948 showed no association with the disease [OR and 95%CI: 0.988 (0.727-1.342), p=0.936]. For the CTNND2 gene, neither rs6885224 nor rs12716080 was significantly associated with myopia {rs6885224: [OR and 95%CI: 1.051 (0.795-1.391), p=0.725], rs12716080: [OR and 95%CI: 1.173 (0.990-1.390), p=0.065]}. CONCLUSIONS Our study indicated that the 11q24.1 genomic region, and particularly the rs11218544 polymorphism, has a genetic association with the development of myopia.
Collapse
Affiliation(s)
- Jie Liu
- Shanghai Institute of Orthopaedics and Traumatology, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hong-xin Zhang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Shanghai Institute of Hematology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China
| |
Collapse
|
87
|
Hysi PG, Mahroo OA, Cumberland P, Wojciechowski R, Williams KM, Young TL, Mackey DA, Rahi JS, Hammond CJ. Common mechanisms underlying refractive error identified in functional analysis of gene lists from genome-wide association study results in 2 European British cohorts. JAMA Ophthalmol 2014; 132:50-6. [PMID: 24264139 DOI: 10.1001/jamaophthalmol.2013.6022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
IMPORTANCE To date, relatively few genes responsible for a fraction of heritability have been identified by means of large genetic association studies of refractive error. OBJECTIVE To explore the genetic mechanisms that lead to refractive error in the general population. DESIGN, SETTING, AND PARTICIPANTS Genome-wide association studies were carried out in 2 British population-based independent cohorts (N = 5928 participants) to identify genes moderately associated with refractive error. MAIN OUTCOMES AND MEASURES Enrichment analyses were used to identify sets of genes overrepresented in both cohorts. Enriched groups of genes were compared between both participating cohorts as a further measure against random noise. RESULTS Groups of genes enriched at highly significant statistical levels were remarkably consistent in both cohorts. In particular, these results indicated that plasma membrane (P = 7.64 × 10⁻³⁰), cell-cell adhesion (P = 2.42 × 10⁻¹⁸), synaptic transmission (P = 2.70 × 10⁻¹⁴), calcium ion binding (P = 3.55 × 10⁻¹⁵), and cation channel activity (P = 2.77 × 10⁻¹⁴) were significantly overrepresented in relation to refractive error. CONCLUSIONS AND RELEVANCE These findings provide evidence that development of refractive error in the general population is related to the intensity of photosignal transduced from the retina, which may have implications for future interventions to minimize this disorder. Pathways connected to the procession of the nerve impulse are major mechanisms involved in the development of refractive error in populations of European origin.
Collapse
Affiliation(s)
- Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, England
| | - Omar A Mahroo
- Department of Ophthalmology, King's College London, London, England3Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, England
| | - Phillippa Cumberland
- Centre for Paediatric Epidemiology and Biostatistics, Institute of Child Health, University College London, London, England
| | | | - Katie M Williams
- Department of Ophthalmology, King's College London, London, England
| | - Terri L Young
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina
| | - David A Mackey
- Lions Eye Institute, University of Western Australia, Centre for Ophthalmology and Visual Science, Perth, Australia
| | - Jugnoo S Rahi
- Centre for Paediatric Epidemiology and Biostatistics, Institute of Child Health, University College London, London, England
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, England2Department of Ophthalmology, King's College London, London, England
| |
Collapse
|
88
|
Kuo JZ, Wong TY, Rotter JI. Challenges in elucidating the genetics of diabetic retinopathy. JAMA Ophthalmol 2014; 132:96-107. [PMID: 24201651 DOI: 10.1001/jamaophthalmol.2013.5024] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
IMPORTANCE In the past decade, significant progress in genomic medicine and technologic developments has revolutionized our approach to common complex disorders in many areas of medicine, including ophthalmology. A disorder that still needs major genetic progress is diabetic retinopathy (DR), one of the leading causes of blindness in adults. OBJECTIVE To perform a literature review, present the current findings, and highlight some key challenges in DR genetics. DESIGN, SETTING, AND PARTICIPANTS We performed a thorough literature review of the genetic factors for DR, including heritability scores, twin studies, family studies, candidate gene studies, linkage studies, and genome-wide association studies (GWASs). MAIN OUTCOME MEASURES Environmental and genetic factors for DR. RESULTS Although there is clear demonstration of a genetic contribution in the development and progression of DR, the identification of susceptibility loci through candidate gene approaches, linkage studies, and GWASs is still in its infancy. The greatest obstacles remain a lack of power because of small sample size of available studies and a lack of phenotype standardization. CONCLUSIONS AND RELEVANCE The field of DR genetics is still in its infancy and is a challenge because of the complexity of the disease. This review outlines some strategies and lessons for future investigation to improve our understanding of this complex genetic disorder.
Collapse
Affiliation(s)
- Jane Z Kuo
- Medical Genetics Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California2Department of Ophthalmology, University of California San Diego, La Jolla3Department of Ophthalmology, Chang Gung Memorial Hospital and
| | - Tien Y Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore5Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jerome I Rotter
- Medical Genetics Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California6Institute for Translational Genomics and Population Sciences, Los Angeles Bio Medical Research Institute, Harbor-UCLA Medical Center, To
| |
Collapse
|
89
|
|
90
|
Sherwin JC, Mackey DA. Update on the epidemiology and genetics of myopic refractive error. EXPERT REVIEW OF OPHTHALMOLOGY 2014. [DOI: 10.1586/eop.12.81] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
91
|
Yoshida M, Meguro A, Okada E, Nomura N, Mizuki N. Association study of fibroblast growth factor 10 (FGF10) polymorphisms with susceptibility to extreme myopia in a Japanese population. Mol Vis 2013; 19:2321-9. [PMID: 24265547 PMCID: PMC3834595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/15/2013] [Indexed: 10/29/2022] Open
Abstract
PURPOSE The fibroblast growth factor 10 (FGF10) gene polymorphism rs339501 was previously reported to be associated with high myopia in a Chinese population. In the present study, we investigated whether FGF10 polymorphisms are associated with extreme myopia in a Japanese population as well. METHODS A total of 433 Japanese patients with extreme myopia (≤ -10.00 diopters) and 542 Japanese healthy controls (+1.50 to -1.50 diopters) were recruited. We genotyped seven tagging single-nucleotide polymorphisms (SNPs), including rs339501, in FGF10. We also performed an imputation analysis to evaluate the potential association of ungenotyped FGF10 SNPs, and 34 SNPs were imputed. RESULTS It was found that rs339501 and rs12517396 exhibited the strongest association with extreme myopia (p=3.9 × 10⁻⁴, corrected p [Pc]=0.0030). A significant association was also observed for rs10462070 (p=6.5 × 10⁻⁴, Pc=0.0059). These three SNPs were in strong linkage disequilibrium (D' ≥0.99, r² ≥0.96). However, the frequency of the A allele of rs339501 was increased in cases compared to controls, which differs from the increased frequency of the G allele in cases in the previous Chinese population. CONCLUSIONS Three FGF10 SNPs in complete linkage disequilibrium--rs339501, rs12517396, and rs10462070--were associated with extreme myopia in the Japanese population, and the risk allele of rs339501 differed from the previous Chinese population. Therefore, these three SNPs may not be an important risk factor for susceptibility to extreme myopia. Further studies are needed to elucidate the possible contribution of the FGF10 region in the development of extreme myopia.
Collapse
Affiliation(s)
- Masao Yoshida
- Department of Public Health, Kyorin University School of Medicine, Tokyo, Japan
| | - Akira Meguro
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | | | - Naoko Nomura
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Nobuhisa Mizuki
- Department of Ophthalmology and Visual Science, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| |
Collapse
|
92
|
Regional replication of association with refractive error on 15q14 and 15q25 in the Age-Related Eye Disease Study cohort. Mol Vis 2013; 19:2173-86. [PMID: 24227913 PMCID: PMC3826323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 10/30/2013] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Refractive error is a complex trait with multiple genetic and environmental risk factors, and is the most common cause of preventable blindness worldwide. The common nature of the trait suggests the presence of many genetic factors that individually may have modest effects. To achieve an adequate sample size to detect these common variants, large, international collaborations have formed. These consortia typically use meta-analysis to combine multiple studies from many different populations. This approach is robust to differences between populations; however, it does not compensate for the different haplotypes in each genetic background evidenced by different alleles in linkage disequilibrium with the causative variant. We used the Age-Related Eye Disease Study (AREDS) cohort to replicate published significant associations at two loci on chromosome 15 from two genome-wide association studies (GWASs). The single nucleotide polymorphisms (SNPs) that exhibited association on chromosome 15 in the original studies did not show evidence of association with refractive error in the AREDS cohort. This paper seeks to determine whether the non-replication in this AREDS sample may be due to the limited number of SNPs chosen for replication. METHODS We selected all SNPs genotyped on the Illumina Omni2.5v1_B array or custom TaqMan assays or imputed from the GWAS data, in the region surrounding the SNPs from the Consortium for Refractive Error and Myopia study. We analyzed the SNPs for association with refractive error using standard regression methods in PLINK. The effective number of tests was calculated using the Genetic Type I Error Calculator. RESULTS Although use of the same SNPs used in the Consortium for Refractive Error and Myopia study did not show any evidence of association with refractive error in this AREDS sample, other SNPs within the candidate regions demonstrated an association with refractive error. Significant evidence of association was found using the hyperopia categorical trait, with the most significant SNPs rs1357179 on 15q14 (p=1.69×10⁻³) and rs7164400 on 15q25 (p=8.39×10⁻⁴), which passed the replication thresholds. CONCLUSIONS This study adds to the growing body of evidence that attempting to replicate the most significant SNPs found in one population may not be significant in another population due to differences in the linkage disequilibrium structure and/or allele frequency. This suggests that replication studies should include less significant SNPs in an associated region rather than only a few selected SNPs chosen by a significance threshold.
Collapse
|
93
|
Makrythanasis P, Antonarakis SE. Pathogenic variants in non-protein-coding sequences. Clin Genet 2013; 84:422-428. [DOI: 10.1111/cge.12272] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- P Makrythanasis
- Department of Genetic Medicine and Development; University of Geneva Medical School; Geneva Switzerland
| | - SE Antonarakis
- Department of Genetic Medicine and Development; University of Geneva Medical School; Geneva Switzerland
- Service of Genetic Medicine; University Hospitals of Geneva; Geneva Switzerland
| |
Collapse
|
94
|
Activated Ras as a Therapeutic Target: Constraints on Directly Targeting Ras Isoforms and Wild-Type versus Mutated Proteins. ISRN ONCOLOGY 2013; 2013:536529. [PMID: 24294527 PMCID: PMC3833460 DOI: 10.1155/2013/536529] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 10/04/2013] [Indexed: 12/12/2022]
Abstract
The ability to selectively and directly target activated Ras would provide immense utility for treatment of the numerous cancers that are driven by oncogenic Ras mutations. Patients with disorders driven by overactivated wild-type Ras proteins, such as type 1 neurofibromatosis, might also benefit from progress made in that context. Activated Ras is an extremely challenging direct drug target due to the inherent difficulties in disrupting the protein:protein interactions that underlie its activation and function. Major investments have been made to target Ras through indirect routes. Inhibition of farnesyl transferase to block Ras maturation has failed in large clinical trials. Likely reasons for this disappointing outcome include the significant and underappreciated differences in the isoforms of Ras. It is still plausible that inhibition of farnesyl transferase will prove effective for disease that is driven by activated H-Ras. The principal current focus of drugs entering clinic trial is inhibition of pathways downstream of activated Ras, for example, trametinib, a first-in-class MEK inhibitor. The complexity of signaling that is driven by activated Ras indicates that effective inhibition of oncogenic transduction through this approach will be difficult, with resistance being likely to emerge through switch to parallel pathways. Durable disease responses will probably require combinatorial block of several downstream targets.
Collapse
|
95
|
Lubke GH, Laurin C, Walters R, Eriksson N, Hysi P, Spector TD, Montgomery GW, Martin NG, Medland SE, Boomsma DI. Gradient Boosting as a SNP Filter: an Evaluation Using Simulated and Hair Morphology Data. JOURNAL OF DATA MINING IN GENOMICS & PROTEOMICS 2013; 4:10.4172/2153-0602.1000143. [PMID: 24404405 PMCID: PMC3882018 DOI: 10.4172/2153-0602.1000143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Typically, genome-wide association studies consist of regressing the phenotype on each SNP separately using an additive genetic model. Although statistical models for recessive, dominant, SNP-SNP, or SNP-environment interactions exist, the testing burden makes an evaluation of all possible effects impractical for genome-wide data. We advocate a two-step approach where the first step consists of a filter that is sensitive to different types of SNP main and interactions effects. The aim is to substantially reduce the number of SNPs such that more specific modeling becomes feasible in a second step. We provide an evaluation of a statistical learning method called "gradient boosting machine" (GBM) that can be used as a filter. GBM does not require an a priori specification of a genetic model, and permits inclusion of large numbers of covariates. GBM can therefore be used to explore multiple GxE interactions, which would not be feasible within the parametric framework used in GWAS. We show in a simulation that GBM performs well even under conditions favorable to the standard additive regression model commonly used in GWAS, and is sensitive to the detection of interaction effects even if one of the interacting variables has a zero main effect. The latter would not be detected in GWAS. Our evaluation is accompanied by an analysis of empirical data concerning hair morphology. We estimate the phenotypic variance explained by increasing numbers of highest ranked SNPs, and show that it is sufficient to select 10K-20K SNPs in the first step of a two-step approach.
Collapse
Affiliation(s)
- GH Lubke
- Department of Psychology, University of Notre Dame, Notre Dame, IN, USA
- Department of Biological Psychology, VU University Amsterdam, Amsterdam Netherlands
| | - C Laurin
- Department of Psychology, University of Notre Dame, Notre Dame, IN, USA
| | - R Walters
- Department of Psychology, University of Notre Dame, Notre Dame, IN, USA
| | | | - P Hysi
- Twin Research and Genetic Epidemiology, Genetic Epidemiologist, King's College London, London, England
| | - TD Spector
- Twin Research and Genetic Epidemiology, Genetic Epidemiologist, King's College London, London, England
| | - GW Montgomery
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - NG Martin
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - SE Medland
- Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - DI Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam Netherlands
| |
Collapse
|
96
|
Yoshida M, Meguro A, Yoshino A, Nomura N, Okada E, Mizuki N. Association study of IGF1 polymorphisms with susceptibility to high myopia in a Japanese population. Clin Ophthalmol 2013; 7:2057-62. [PMID: 24204106 PMCID: PMC3804590 DOI: 10.2147/opth.s52726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Polymorphisms in the insulin-like growth factor 1 (IGF1) gene were previously associated with high or extreme myopia in Caucasian and Chinese populations. In the present study, we investigated whether IGF1 polymorphisms are associated with high myopia in a Japanese population. METHODS A total of 446 Japanese patients with high myopia (≤-9.00 diopters) and 481 Japanese healthy controls (+1.50 diopters to -1.50 diopters) were recruited. We genotyped seven tagging single-nucleotide polymorphisms (SNPs) in IGF1 and assessed allelic and haplotypic diversity in cases and controls. RESULTS There were no statistically significant differences in the allele frequencies of IGF1 SNPs and genotypes between cases and controls (P>0.05). However, the A allele of rs5742629 and the G allele of rs12423791 were associated with a moderately increased risk of high myopia (odds ratio [OR] =1.20 and OR =1.21, respectively) with borderline statistical significance (P=0.0502, corrected P (Pc) =0.21 and P=0.064, Pc=0.29, respectively). The haplotype consisting of the A allele of rs5742629 and the G allele of rs12423791 was marginally associated with the risk of high myopia (P=0.041; OR =1.21); this association was not significant after correction (Pc=0.19). CONCLUSION We found that the IGF1 SNPs are not significantly associated with high myopia in our Japanese population. Our results are in contrast to a previous study in which extreme myopia cases had significantly higher frequencies of the G allele of rs5742629 and the C allele of rs12423791 than controls. Therefore, the IGF1 SNPs may not be important factors for susceptibility to high myopia in all populations. Further genetic studies are needed to elucidate the possible contributions of the IGF1 region to the development of high myopia.
Collapse
Affiliation(s)
- Masao Yoshida
- Department of Public Health, Kyorin University School of Medicine, Mitaka, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
97
|
Nag A, Hammond CJ. Twin studies in inherited eye disease. Clin Exp Ophthalmol 2013; 42:84-93. [PMID: 24118999 DOI: 10.1111/ceo.12233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/17/2013] [Indexed: 01/15/2023]
Abstract
Eye diseases represent a significant source of health impairment in humans. Twin studies offer an excellent model to dissect the genetic basis of human diseases. In this review, we discuss the potential advantages of using twin-based studies in investigating the genetics of eye diseases--from heritability estimation to identifying underlying genetic and epigenetic changes. We also discuss some of the notable findings of twin studies exploring the genetics of eye diseases. Finally, we suggest other novel approaches that can be utilized to tap the potential of twin studies to provide a more complete understanding of genetic factors underlying ocular diseases.
Collapse
Affiliation(s)
- Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK
| | | |
Collapse
|
98
|
Cooke Bailey JN, Sobrin L, Pericak-Vance MA, Haines JL, Hammond CJ, Wiggs JL. Advances in the genomics of common eye diseases. Hum Mol Genet 2013; 22:R59-65. [PMID: 23962718 DOI: 10.1093/hmg/ddt396] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWAS) and other genomic technologies have accelerated the discovery of genes and genomic regions contributing to common human ocular disorders with complex inheritance. Age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma and myopia account for the majority of visual impairment worldwide. Over 19 genes and/or genomic regions have been associated with AMD. Current investigations are assessing the clinical utility of risk score panels and therapies targeting disease-specific pathways. DR is the leading cause of blindness in the United States and globally is a major cause of vision loss. Genomic investigations have identified molecular pathways associated with DR in animal models which could suggest novel therapeutic targets. Three types of glaucoma, primary-open-angle glaucoma (POAG), angle-closure glaucoma and exfoliation syndrome (XFS) glaucoma, are common age-related conditions. Five genomic regions have been associated with POAG, three with angle-closure glaucoma and one with XFS. Myopia causes substantial ocular morbidity throughout the world. Recent large GWAS have identified >20 associated loci for this condition. In this report, we present a comprehensive overview of the genes and genomic regions contributing to disease susceptibility for these common blinding ocular disorders and discuss the next steps toward translation to effective gene-based screening tests and novel therapies targeting the molecular events contributing to disease.
Collapse
|
99
|
Khor CC, Miyake M, Chen LJ, Shi Y, Barathi VA, Qiao F, Nakata I, Yamashiro K, Zhou X, Tam POS, Cheng CY, Tai ES, Vithana EN, Aung T, Teo YY, Wong TY, Moriyama M, Ohno-Matsui K, Mochizuki M, Matsuda F, Yong RYY, Yap EPH, Yang Z, Pang CP, Saw SM, Yoshimura N. Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia. Hum Mol Genet 2013; 22:5288-94. [PMID: 23933737 DOI: 10.1093/hmg/ddt385] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Severe myopia (defined as spherical equivalent < -6.0 D) is a predominant problem in Asian countries, resulting in substantial morbidity. We performed a meta-analysis of four genome-wide association studies (GWAS), all of East Asian descent totaling 1603 cases and 3427 controls. Two single nucleotide polymorphisms (SNPs) (rs13382811 from ZFHX1B [encoding for ZEB2] and rs6469937 from SNTB1) showed highly suggestive evidence of association with disease (P < 1 × 10(-7)) and were brought forward for replication analysis in a further 1241 severe myopia cases and 3559 controls from a further three independent sample collections. Significant evidence of replication was observed, and both SNP markers surpassed the formal threshold for genome-wide significance upon meta-analysis of both discovery and replication stages (P = 5.79 × 10(-10), per-allele odds ratio (OR) = 1.26 for rs13382811 and P = 2.01 × 10(-9), per-allele OR = 0.79 for rs6469937). The observation at SNTB1 is confirmatory of a very recent GWAS on severe myopia. Both genes were expressed in the human retina, sclera, as well as the retinal pigmented epithelium. In an experimental mouse model for myopia, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for Zfhx1b and Sntb1. These new data advance our understanding of the molecular pathogenesis of severe myopia.
Collapse
Affiliation(s)
- Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
100
|
Aldahmesh M, Khan A, Alkuraya H, Adly N, Anazi S, Al-Saleh A, Mohamed J, Hijazi H, Prabakaran S, Tacke M, Al-Khrashi A, Hashem M, Reinheckel T, Assiri A, Alkuraya F. Mutations in LRPAP1 are associated with severe myopia in humans. Am J Hum Genet 2013; 93:313-20. [PMID: 23830514 DOI: 10.1016/j.ajhg.2013.06.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022] Open
Abstract
Myopia is an extremely common eye disorder but the pathogenesis of its isolated form, which accounts for the overwhelming majority of cases, remains poorly understood. There is strong evidence for genetic predisposition to myopia, but determining myopia genetic risk factors has been difficult to achieve. We have identified Mendelian forms of myopia in four consanguineous families and implemented exome/autozygome analysis to identify homozygous truncating variants in LRPAP1 and CTSH as the likely causal mutations. LRPAP1 encodes a chaperone of LRP1, which is known to influence TGF-β activity. Interestingly, we observed marked deficiency of LRP1 and upregulation of TGF-β in cells from affected individuals, the latter being consistent with available data on the role of TGF-β in the remodeling of the sclera in myopia and the high frequency of myopia in individuals with Marfan syndrome who characteristically have upregulation of TGF-β signaling. CTSH, on the other hand, encodes a protease and we show that deficiency of the murine ortholog results in markedly abnormal globes consistent with the observed human phenotype. Our data highlight a role for LRPAP1 and CTSH in myopia genetics and demonstrate the power of Mendelian forms in illuminating new molecular mechanisms that may be relevant to common phenotypes.
Collapse
|