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Lo Faro V, Bhattacharya A, Zhou W, Zhou D, Wang Y, Läll K, Kanai M, Lopera-Maya E, Straub P, Pawar P, Tao R, Zhong X, Namba S, Sanna S, Nolte IM, Okada Y, Ingold N, MacGregor S, Snieder H, Surakka I, Shortt J, Gignoux C, Rafaels N, Crooks K, Verma A, Verma SS, Guare L, Rader DJ, Willer C, Martin AR, Brantley MA, Gamazon ER, Jansonius NM, Joos K, Cox NJ, Hirbo J. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation. Cell Rep Med 2024; 5:101430. [PMID: 38382466 PMCID: PMC10897632 DOI: 10.1016/j.xcrm.2024.101430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/28/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness globally, shows disparity in prevalence and manifestations across ancestries. We perform meta-analysis across 15 biobanks (of the Global Biobank Meta-analysis Initiative) (n = 1,487,441: cases = 26,848) and merge with previous multi-ancestry studies, with the combined dataset representing the largest and most diverse POAG study to date (n = 1,478,037: cases = 46,325) and identify 17 novel significant loci, 5 of which were ancestry specific. Gene-enrichment and transcriptome-wide association analyses implicate vascular and cancer genes, a fifth of which are primary ciliary related. We perform an extensive statistical analysis of SIX6 and CDKN2B-AS1 loci in human GTEx data and across large electronic health records showing interaction between SIX6 gene and causal variants in the chr9p21.3 locus, with expression effect on CDKN2A/B. Our results suggest that some POAG risk variants may be ancestry specific, sex specific, or both, and support the contribution of genes involved in programmed cell death in POAG pathogenesis.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dan Zhou
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Esteban Lopera-Maya
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands
| | - Peter Straub
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Priyanka Pawar
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Serena Sanna
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands; Institute for Genetics and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Nathan Ingold
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ida Surakka
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anurag Verma
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shefali S Verma
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Guare
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Cristen Willer
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milam A Brantley
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nomdo M Jansonius
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands
| | - Karen Joos
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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Zhu Y, Tazearslan C, Rosenfeld MG, Fiser A, Suh Y. Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16 INK4a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541339. [PMID: 37292862 PMCID: PMC10245730 DOI: 10.1101/2023.05.18.541339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications. The chromosome 9p21.3 locus is among the most replicated glaucoma risk loci discovered by GWAS. Nonetheless, the absence of protein-coding genes in the locus makes interpreting the disease association challenging, leaving the causal variant and molecular mechanism elusive. In this study, we report the identification of a functional glaucoma risk variant, rs6475604. By employing computational and experimental methods, we demonstrated that rs6475604 resides in a repressive regulatory element. Risk allele of rs6475604 disrupts the binding of YY1, a transcription factor known to repress the expression of a neighboring gene in 9p21.3, p16INK4A, which plays a crucial role in cellular senescence and aging. These findings suggest that the glaucoma disease variant contributes to accelerated senescence, providing a molecular link between glaucoma risk and an essential cellular mechanism for human aging.
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Affiliation(s)
- Yizhou Zhu
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032, USA
| | - Cagdas Tazearslan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY10461, USA
| | - Michael G. Rosenfeld
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093
| | - Andras Fiser
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY10032, USA
- Department of Genetics and Development, Columbia University, New York, NY10032, USA
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Huang G, Liang D, Luo L, Lan C, Luo C, Xu H, Lai J. Significance of the lncRNAs MALAT1 and ANRIL in occurrence and development of glaucoma. J Clin Lab Anal 2022; 36:e24215. [PMID: 35028972 PMCID: PMC8842314 DOI: 10.1002/jcla.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Background Primary open‐angle glaucoma (POAG) is the commonest form of glaucoma which is estimated to cause bilaterally blind within 11.1 million people by 2020. Therefore, the primary objectives of this study were to investigate the clinical significance of single‐nucleotide polymorphisms (SNPs) in the lncRNAs MALAT1 and ANRIL in a Chinese Han POAG cohort. Methods Three hundred and forty‐six glaucoma patients and 263 healthy controls were recruited, and totally 14 SNPs in MALAT1 and ANRIL were genotyped between the two populations. Results The MALAT1 SNPs rs619586 (A>G), rs3200401 (C>T), and rs664589 (C>G) were associated with POAG risk, and the ANRIL SNPs rs2383207 (A>G), rs564398 (A>G), rs2157719 (A>G), rs7865618 (G>A), and rs4977574 (A>G) were associated with POAG (p < 0.05). The MALAT1 haplotypes ACG and ATC, comprised rs619586, rs3200401, and rs664589, increased POAG risk, and the ANRIL haplotype AAGAA, made up of rs2383207, rs7865618, rs4977574, rs564398, and rs2157719, show a significantly increased risk of POAG. In addition, rs619586 (A>G) of MALAT1 and rs564398/rs2157719 of ANRIL were associated with a smaller vertical cup‐to‐disc ratio, while rs619586 of MALAT1 and rs2383207/rs4977574 of ANRIL were associated with higher intraocular pressure in the POAG population. Conclusion Single‐nucleotide polymorphisms and haplotypes in ANRIL and MALAT1 were associated with POAG onset in our study population, which provide more possibilities to POAG diagnosis and treatment.
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Affiliation(s)
- Guoqiang Huang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Dong Liang
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Lidan Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chenghong Lan
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Chengfeng Luo
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Hongwang Xu
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
| | - Jiangfeng Lai
- Department of Ophthalmology, Meizhou People's Hospital, Meizhou City, China
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Park DH, Park SW, Sung MS. Choroidal Thickness in Advanced Glaucoma Patients. JOURNAL OF THE KOREAN OPHTHALMOLOGICAL SOCIETY 2021. [DOI: 10.3341/jkos.2021.62.12.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Purpose: We investigated choroidal thickness according to the classification of glaucoma and related factors in patients with advanced glaucoma.Methods: The present study included 133 eyes of 133 advanced glaucoma patients with a mean deviation of <-12 dB. Patients were classified into primary open angle glaucoma (POAG) and normal-tension glaucoma (NTG) groups. Factors related to the subfoveal and peripapillary choroidal thickness were analyzed using linear regression analysis.Results: The mean peripapillary choroid thickness was 99.20 ± 46.85 µm in the NTG group, which was significantly thinner than in the POAG group (121.85 ± 45.39 µm, p = 0.006). Additionally, in the sectoral comparison, the NTG group had thinner choroids than the POAG group in all areas (p < 0.05 for all). In the linear regression analysis, glaucoma class (p = 0.007), age (p = 0.005), and intraocular pressure (IOP) (p = 0.024) significantly affected the peripapillary choroid thickness. Moreover, age (p = 0.029) and macular thickness (p = 0.002) were significantly associated with subfoveal choroid thickness.Conclusions: In advanced glaucoma, low baseline IOP, NTG, and old age were significantly associated with a thin peripapillary choroid, suggesting an association between thin peripapillary choroid and the etiology of NTG. Further studies are needed to clarify the significance of a thin choroid in the pathogenesis of glaucoma.
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Liu S, Chen S, Niu T. Genetic association between CDKN2B-AS1 polymorphisms and the susceptibility of primary open-angle glaucoma (POAG): a meta-analysis from 21,775 subjects. Ir J Med Sci 2021; 191:2385-2392. [PMID: 34648117 PMCID: PMC9492586 DOI: 10.1007/s11845-021-02794-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Background Primary open-angle glaucoma (POAG) is affected by both genetics and environmental factors. CDKN2B-AS1 polymorphisms have been reported to be involved in the pathogenesis of POAG. However, the results of the genetic associations between the CDKN2B-AS1 polymorphisms and POAG risk were inconclusive. Aims This study aimed to evaluate the correlation of CDKN2B-AS1 polymorphisms and POAG susceptibility using a meta-analysis. Methods Meta-analysis was performed by searching PubMed, Web of science, the Cochrane database of system reviews, CNKI, and Embase databases. The relationship of CDKN2B-AS1 rs4977756, rs10120688, rs2157719, and rs7049105 polymorphisms and POAG risk was evaluated by the odds ratios (ORs) and 95% confidence intervals (CIs). Results Eleven studies with 8290 cases and 13,485 controls were included in the present meta-analysis. The alleles of rs4977756 and rs10120688 significantly increased the risk of POAG (rs4977756: OR = 1.20, 95%CI = 1.03–1.39, p = 0.02; rs10120688: OR = 1.36, 95%CI = 1.29–1.44, p < 0.00001). As for ethnicity, rs4977756 polymorphism significantly increased POAG risk in Caucasians (OR = 1.33, 95%CI = 1.12–1.57, p = 0.0009), but not in Asians. In addition, the rs2157719 allele was significantly associated with POAG risk in Asians (OR = 0.66, 95%CI = 0.55–0.80, p < 0.0001), but not in Caucasians (p > 0.05). Conclusions The CDKN2B-AS1 rs4977756 might increase the POAG risk in Caucasian population, and rs2157719 might decrease the POAG risk in Asian population, while rs10120688 might increase the risk of POAG.
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Affiliation(s)
- Shanshan Liu
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China
| | - Siwen Chen
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China
| | - Tongtong Niu
- Department of Ophthalmology, The Fourth People's Hospital of Shenyang, Huanggu District, 20 Huanghe South Street, Shenyang, 11031, China.
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Jin HN, Kang YS, Sung MS, Park SW. Characteristics of Visual Field Defects in Korean Advanced Glaucoma. JOURNAL OF THE KOREAN OPHTHALMOLOGICAL SOCIETY 2021. [DOI: 10.3341/jkos.2021.62.8.1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Purpose: We investigated the clinical characteristics of visual field (VF) defects in Korean advanced glaucoma patients.Methods: The present study included 109 eyes of 109 advanced glaucoma patients whose mean deviation (MD) is under -12 dB. The subjects were classified into primary open angle glaucoma (POAG) and normal tension glaucoma (NTG) group. Average numeric decibel in each VF points were visualized with color topographic image and dot graph image using python 3.5. VF was divided into four quadrants or two half fields, and the differences in the degree of VF defects in each locations were assessed with raw decibel data. Additionally, mean sensitivity of central 12 points were compared between the two groups.Results: Generally the features of VF defects were severely depressed VF sensitivity at the superonasal quadrant and relatively preserved central area and inferotemporal quadrant in both of the glaucoma groups. But we found the extent of deflection for VF defect in the NTG eyes was higher than that of the POAG eyes (p < 0.05). The POAG eyes tended to show more diffuse and evenly distributed VF defect, whereas NTG eyes tended to have more severely depressed VF at the superonasal quadrant and relatively preserved VF at the inferotemporal quadrant. There was no significant difference in the degree of central VF defects between the two groups.Conclusions: The characteristics of VF defect in Korean advanced glaucoma revealed different features based on the glaucoma diagnosis. The POAG eyes tended to show diffuse VF defects, whereas NTG eyes tended to have more severely depressed VF sensitivity at the superonasal quadrant and relatively preserved VF at the inferotemporal quadrant.
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Eliseeva N, Ponomarenko I, Reshetnikov E, Dvornyk V, Churnosov M. The haplotype of the CDKN2B-AS1 gene is associated with primary open-angle glaucoma and pseudoexfoliation glaucoma in the Caucasian population of Central Russia. Ophthalmic Genet 2021; 42:698-705. [PMID: 34387529 DOI: 10.1080/13816810.2021.1955275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE To replicate the finding of the association of five CDKN2B-AS1 gene polymorphisms (rs7865618, rs1063192, rs944800, rs2157719, and rs4977756) with primary open-angle glaucoma (POAG) and to analyze them for possible association with pseudoexfoliation glaucoma (PXFG) in a Caucasian population of Central Russia. METHODS A total of 932 participants of Russian ethnicity (self-reported), including 328 patients with PXFG, 208 patients with POAG (high-tension glaucoma), and 396 controls, were enrolled in the study. The SNPs were analyzed for possible associations using logistic regression. RESULTS Several haplotypes based on the studied SNPs were associated with POAG (three haplotypes) and PXFG (six haplotypes). Haplotype AAAGG of loci rs1063192-rs7865618-rs2157719-rs944800-rs4977756 conferred the highest risk for both POAG (OR = 3.99, рperm = 0.001) and PXFG (OR = 2.84, рperm = 0.001). CONCLUSIONS The CDKN2B-AS1 gene was associated with an increased risk of both POAG and PXFG in Caucasians of Central Russia. The gene may be related to the development of various types of glaucoma.
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Affiliation(s)
- Natalya Eliseeva
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Irina Ponomarenko
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Evgeny Reshetnikov
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Volodymyr Dvornyk
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
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Thakur N, Pandey RK, Mannan R, Pruthi A, Mehrotra S. Association of TGFB -509C>T promoter polymorphism with primary angle closure glaucoma in a North Indian Punjabi cohort. BMC Ophthalmol 2021; 21:165. [PMID: 33832461 PMCID: PMC8028242 DOI: 10.1186/s12886-021-01924-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/22/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Transforming growth factor beta (TGFB) is an important candidate gene implicated in glaucoma pathogenesis because it affects retinal ganglionic cell survival. The present study assessed the genetic association of -509C > T variant in the TGFB promoter region with primary open angle glaucoma (POAG) and primary angle closure glaucoma (PACG) in a North Indian Punjabi population. METHOD A total of 867 subjects (307 POAG, 133 PACG cases and 427 controls) were recruited from the targeted population. Genotyping was done by PCR-RFLP method and the data was analyzed using PLINK software (v1.07). Logistic regression under different genetic models was applied and genotype phenotype correlation was assessed by one-way ANOVA. RESULT A statistically significant difference in the frequency of heterozygotes among PACG cases (53.16%) and controls (30.07%) (p = 0.0002) was observed. Genetic model analysis revealed that mutant "TT" genotype conferred 2-fold risk towards PACG development under recessive model (p = 0.0019) while dominant model and co-dominant model provided 0.62 and 0.37 fold protection against PACG (p = 0.025 and p = 0.0001, respectively). Data segregation based on sex revealed a strong protective effect of heterozygous 'CT' genotype against progression of PACG among females (p = 0.002, OR = 0.37, 95% CI = 0.19-0.70), but conferred 2.14-fold risk among female POAG subjects (p = 0.013). CONCLUSION The study revealed a strong genetic association of -509C > T variant in TGFB with PACG in females. There is a need to replicate the results in a larger PACG cohort in other populations and further assess the contribution of sex specific factors in modifying genetic susceptibility to PACG.
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Affiliation(s)
- Nanamika Thakur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | | | - Rashim Mannan
- All India Institute of Medical Sciences, New Delhi, India
| | - Archna Pruthi
- All India Institute of Medical Sciences, New Delhi, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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Thakur N, Kupani M, Mannan R, Pruthi A, Mehrotra S. Genetic association between CDKN2B/CDKN2B-AS1 gene polymorphisms with primary glaucoma in a North Indian cohort: an original study and an updated meta-analysis. BMC Med Genomics 2021; 14:1. [PMID: 33397358 PMCID: PMC7780652 DOI: 10.1186/s12920-020-00855-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/10/2020] [Indexed: 01/07/2023] Open
Abstract
Background Variants in CDKN2B/CDKN2B-AS1 have been reported to modulate glaucoma risk in several GWAS across different populations. CDKN2B/CDKN2A encodes tumor suppressor proteins p16INK4A/p15INK4B which influences cell proliferation/senescence in RGCs, the degeneration of which is a risk factor for glaucoma. CDKN2B-AS1 codes a long non-coding RNA in antisense direction and is involved in influencing nearby CDKN2A/CDKN2B via regulatory mechanisms. Methods Current study investigated four SNPs (rs2157719, rs3217992, rs4977756, rs1063192) of aforementioned genes in a case–control study in a North Indian cohort. Genotyping was done with Taqman chemistry. In addition, an updated meta-analysis was performed. Results Two SNPs, rs3217992 and rs2157719 were found to be significantly associated with the disease. The frequency of ‘T’ allele of rs3217992 was significantly lower in cases (POAG/PACG) [p = 0.045; OR = 0.80(CI = 0.65–0.99) and p = 0.024; OR = 0.73(CI = 0.55–0.96)], respectively than in controls. Genetic model analysis revealed that TT + CT genotype confers 0.73-fold protection against POAG [p = 0.047; OR = 0.73(CI = 0.54–0.99)] and trend assumed additive model gives 0.53 times higher protection against PACG progression. However the association of rs3217992 with POAG and PACG did not remain significant after Bonferroni correction. For rs2157719, the ‘C’ allele was found to be less prevalent among cases (POAG/PACG) with respect to controls. Cochran Armitage trend test assuming additive model revealed 0.77 and 0.64-fold protection against POAG and PACG respectively. Bonferroni correction (pcorr = 0.003) was applied and the association of rs2157719 remained significant in PACG cases but not among POAG cases (p = 0.024). The ‘CC’ genotype also confers protection against primary glaucoma (POAG/PACG) among males and female subjects. The frequency rs1063192 and rs4977756 did not vary significantly among subjects, however the haplotype ‘CATA’ was found to be associated with increased glaucoma risk. An updated meta-analysis conducted on pooled studies on POAG cases and controls revealed significant association between rs1063192, rs2157719, rs4977756 and POAG except rs3217992. Conclusion The study concludes significant association between INK4 variants and primary glaucoma in the targeted North Indian Punjabi cohort. We believe that deep-sequencing of INK4 locus may help in identifying novel variants modifying susceptibility to glaucoma. Functional studies can further delineate the role of CDKN2B and CDKN2B-AS1 in primary glaucoma for therapeutic intervention.
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Affiliation(s)
- Nanamika Thakur
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Manu Kupani
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Rashim Mannan
- All India Institute of Medical Sciences, New Delhi, India
| | - Archna Pruthi
- All India Institute of Medical Sciences, New Delhi, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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Molecular Genetics of Glaucoma: Subtype and Ethnicity Considerations. Genes (Basel) 2020; 12:genes12010055. [PMID: 33396423 PMCID: PMC7823611 DOI: 10.3390/genes12010055] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022] Open
Abstract
Glaucoma, the world’s leading cause of irreversible blindness, is a complex disease, with differential presentation as well as ethnic and geographic disparities. The multifactorial nature of glaucoma complicates the study of genetics and genetic involvement in the disease process. This review synthesizes the current literature on glaucoma and genetics, as stratified by glaucoma subtype and ethnicity. Primary open-angle glaucoma (POAG) is the most common cause of glaucoma worldwide, with the only treatable risk factor (RF) being the reduction of intraocular pressure (IOP). Genes associated with elevated IOP or POAG risk include: ABCA1, AFAP1, ARHGEF12, ATXN2, CAV1, CDKN2B-AS1, FOXC1, GAS7, GMDS, SIX1/SIX6, TMCO1, and TXNRD2. However, there are variations in RF and genetic factors based on ethnic and geographic differences; it is clear that unified molecular pathways accounting for POAG pathogenesis remain uncertain, although inflammation and senescence likely play an important role. There are similar ethnic and geographic complexities in primary angle closure glaucoma (PACG), but several genes have been associated with this disorder, including MMP9, HGF, HSP70, MFRP, and eNOS. In exfoliation glaucoma (XFG), genes implicated include LOXL1, CACNA1A, POMP, TMEM136, AGPAT1, RBMS3, and SEMA6A. Despite tremendous progress, major gaps remain in resolving the genetic architecture for the various glaucoma subtypes across ancestries. Large scale carefully designed studies are required to advance understanding of genetic loci as RF in glaucoma pathophysiology and to improve diagnosis and treatment options.
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11
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Li XS, Yan CY, Fan YJ, Yang JL, Zhao SX. NUCB2 polymorphisms are associated with an increased risk for type 2 diabetes in the Chinese population. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:290. [PMID: 32355734 PMCID: PMC7186676 DOI: 10.21037/atm.2020.03.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Background The nucleobindin 2 (NUCB2) gene encodes the NUCB2 protein, which plays a critical role in glucose metabolism and diabetes. This study explored the correlation between NUCB2 genetic variants and type 2 diabetes mellitus (T2DM). The study further examined the different NUCB2 variants that confer risk to T2DM in Chinese Han populations. Methods This study evaluated the anthropometric and glycemic profiles of 578 T2DM patients and 1,609 healthy controls. Subsequently, we genotyped five single nucleotide polymorphisms (SNPs) (rs10832756, rs1330, rs10766383, rs10832757, and rs11024251) in all the study participants using a Sequenom Mass ARRAY SNP genotyping platform. Results The distribution of polymorphisms was significantly different between the T2DM patients and healthy controls. Our logistic regression analysis results showed that the five NUCB2 SNPs are significantly correlated with the risk for T2DM, especially rs11024251(P=2.97×10−6). Interestingly, analysis of male and female sub-populations separately showed that only two of the SNPs (rs10832757 and rs11024251) have significant correlation to T2DM in males [P=0.0244, odds ratio (OR) 1.28 and P=0.0062, OR 1.35, respectively). In females however, we identified four significant SNPs (rs1330, rs10766383, rs10832757, and rs11024251; P<0.05, OR 1.31–1.42). Furthermore, we found that rs1330 is associated with body mass index of female subpopulation only (P=0.0174, β =0.0060). Conclusions NUCB2 polymorphisms could have a pivotal role in the presence of T2DM. Sex-specific SNPs of NUCB2 could account for the differences in clinical features of T2DM between male and female subpopulations. Nevertheless, our results should be replicated using larger sample sizes, and experimental investigations are needed to elucidate the molecular mechanisms of the associations observed in this study.
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Affiliation(s)
- Xue-Song Li
- Department of Endocrinology and Metabolism, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Chen-Yan Yan
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai 200011, China
| | - Yu-Juan Fan
- Department of Endocrinology and Metabolism, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Jia-Lin Yang
- Department of Endocrinology and Metabolism, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Shuang-Xia Zhao
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai 200011, China
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12
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Yan CY, Ma YR, Sun F, Zhang RJ, Fang Y, Zhang QY, Wu FY, Zhao SX, Song HD. Candidate gene associations reveal sex-specific Graves' disease risk alleles among Chinese Han populations. Mol Genet Genomic Med 2020; 8:e1249. [PMID: 32342657 PMCID: PMC7336758 DOI: 10.1002/mgg3.1249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND With several susceptibility single nucleotide polymorphisms identified by case-control association studies, Graves' disease is one of the most common forms of autoimmune thyroid disease. In this study, we aimed to determine whether any observed differences in genetic associations are influenced by sex in Chinese Han populations. METHODS A total of 8,835 patients with Graves' disease and 9,936 sex-matched healthy controls were enrolled in the study. Confirmed by a two-staged association analysis, sex-specific analyses among 20 Graves' disease susceptibility loci were conducted. RESULTS A significant sex-gene interaction was detected primarily at rs5912838 on Xq21.1 between the GPR174 and ITM2A genes, whereby male Graves' disease patients possessed a significantly higher frequency of risk alleles than their female counterparts. Interestingly, compared to women, male patients with Graves' disease had a higher cumulative genetic risk and higher persistent thyroid stimulating hormone receptor antibody-positive rate after receiving antithyroid drug therapy for at least 1 year. CONCLUSION The findings of this study suggest the existence of one potential sex-specific Graves' disease variant on Xq21.1. This could increase our understanding of the pivotal mechanism behind Graves' disease and ultimately aid in identifying possible therapeutic targets.
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Affiliation(s)
- Chen-Yan Yan
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Ru Ma
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Sun
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui-Jia Zhang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Fang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian-Yue Zhang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng-Yao Wu
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuang-Xia Zhao
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huai-Dong Song
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Chen M, Yu X, Xu J, Ma J, Chen X, Chen B, Gu Y, Wang K. Association of Gene Polymorphisms With Primary Open Angle Glaucoma: A Systematic Review and Meta-Analysis. ACTA ACUST UNITED AC 2019; 60:1105-1121. [PMID: 30901387 DOI: 10.1167/iovs.18-25922] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Min Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Xiaoning Yu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Jia Xu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Jian Ma
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Xinyi Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Binbin Chen
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Yuxiang Gu
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
| | - Kaijun Wang
- Eye Center, the 2nd Affiliated Hospital, Medical College of Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, China
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14
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Collins DW, Gudiseva HV, Chavali VRM, Trachtman B, Ramakrishnan M, Merritt WT, Pistilli M, Rossi RA, Blachon S, Sankar PS, Miller-Ellis E, Lehman A, Addis V, O'Brien JM. The MT-CO1 V83I Polymorphism is a Risk Factor for Primary Open-Angle Glaucoma in African American Men. Invest Ophthalmol Vis Sci 2018; 59:1751-1759. [PMID: 29610859 PMCID: PMC5886029 DOI: 10.1167/iovs.17-23277] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/23/2018] [Indexed: 01/05/2023] Open
Abstract
Purpose We investigate the function of the V83I polymorphism (m.6150G>A, rs879053914) in the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene and its role in African American (AA) primary open-angle glaucoma (POAG). Methods This study used Sanger sequencing (1339 cases, 850 controls), phenotypic characterization of Primary Open-Angle African American Glaucoma Genetics study (POAAGG) cases, a masked chart review of CO1 missense cases (V83I plus M117T, n = 29) versus wild type cases (n = 29), a yeast 2-hybrid (Y2H) cDNA library screen, and quantification of protein-protein interactions by Y2H and ELISA. Results The association of V83I with POAG in AA was highly significant for men (odds ratio [OR] 6.5; 95% confidence interval [CI] 2.0-21.3, P = 0.0001), but not for women (OR 1.1; 95% CI, 0.62-2.00, P = 0.78). POAG cases having CO1 double missense mutation (V83I + M117T, L1c2 haplogroup) had a higher cup-to-disc ratio (0.77 vs. 0.71, P = 0.04) and significantly worse visual function (average pattern standard deviation, 6.5 vs. 4.3, P = 0.009; average mean deviation -10.4 vs. -4.5, P = 0.006) when compared to matched wild type cases (L1b haplogroup). Interaction of the V83I region of CO1 with amyloid beta peptide (Aβ) was confirmed by ELISA assay, and this interaction was abrogated by V83I. A Y2H screen of an adult human brain cDNA library with the V83 region of CO1 as bait retrieved the UBQLN1 gene. Conclusions The V83I polymorphism was associated strongly with POAG in AA men and disrupts Aβ-binding to CO1. This region also interacts with a neuroprotective protein, UBQLN1.
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Affiliation(s)
- David W. Collins
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Harini V. Gudiseva
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Venkata R. M. Chavali
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Benjamin Trachtman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Meera Ramakrishnan
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - William T. Merritt
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Maxwell Pistilli
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Rebecca A. Rossi
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | | | - Prithvi S. Sankar
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Eydie Miller-Ellis
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Amanda Lehman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Victoria Addis
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joan M. O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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15
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Sakurada Y, Mabuchi F. Genetic Risk Factors for Glaucoma and Exfoliation Syndrome Identified by Genome-wide Association Studies. Curr Neuropharmacol 2018; 16:933-941. [PMID: 28721823 PMCID: PMC6120117 DOI: 10.2174/1570159x15666170718142406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 06/25/2017] [Accepted: 07/12/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Glaucoma is a neurodegenerative disease characterized by the progressive loss of retinal ganglion cells and optic nerve axons. According to its anatomical features, glaucoma is mainly subdivided into primary open-angle glaucoma (POAG) and primary angle-closure glaucoma (PACG). Exfoliation syndrome (XFS) and glaucoma (XFG) are characterized by the accumulation of extracellular materials in ocular tissues, particularly the lens surface and pupillary border. In addition to the two major forms of glaucoma, XFG is the most common cause of secondary open-angle glaucoma. Recent genome-wide association studies(GWASs) revealed genetic loci associated with each glaucoma subtype. METHODS Review of literatures regarding GWASs for POAG, PACG and XFS. RESULTS Several genetic loci were found to be independently associated with POAG, PACG, and XFS by large-scale GWASs. CONCLUSIONS Genetic studies may not only provide a better understanding of the pathophysiological mechanisms underlying the diseases, but also facilitate the development of new drugs or treatments.
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Affiliation(s)
- Yoichi Sakurada
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, 409-3898, Japan
| | - Fumihiko Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Shimokato 1110, Chuo, Yamanashi, 409-3898, Japan
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16
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Burdon KP, Awadalla MS, Mitchell P, Wang JJ, White A, Keane MC, Souzeau E, Graham SL, Goldberg I, Healey PR, Landers J, Mills RAD, Best S, Hewitt AW, Sharma S, Craig JE. DNA methylation at the 9p21 glaucoma susceptibility locus is associated with normal-tension glaucoma. Ophthalmic Genet 2017; 39:221-227. [PMID: 29265947 DOI: 10.1080/13816810.2017.1413659] [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: 02/08/2023]
Abstract
PURPOSE Recent genome-wide association studies reported strong association of genetic variation at the CDKN2B/CDKN2B-AS1 locus on 9p21 with normal-tension glaucoma (NTG) in multiple populations. The mechanism by which this locus causes disease remains to be elucidated. We investigated the association of DNA methylation of CpG islands at this locus with NTG. METHODS We conducted a retrospective case-control study of 178 NTG cases and 202 unaffected controls from Australia. CDKN2B and CDKN2B-AS1 promoter methylation was measured quantitatively using the MassCleave assay, and assessed for association with the disease, and the genotype of the associated risk variants using IBM SPSS statistics 22.0 CpG sites at which methylation status was associated with NTG were validated using pyrosequencing. RESULTS We identified one CpG site (F1:13-14) in the CDKN2B promoter which showed significant association with NTG (p = 0.001). The association was highly significant in female cases (p = 0.006) but not in male cases (p = 0.054). The association was validated using an independent method confirming the likely association of DNA methylation with NTG in females (p = 0.015), but not in males (p = 0.497). In addition, methylation at CpG sites in CDKN2B was also associated with genotype at rs1063192, which is known to confer risk for NTG. CONCLUSION This study reveals an association of methylation status in the CDKN2B promoter with NTG, particularly in females. This suggests that the observed genetic association with the disease at this locus could be in part due to epigenetic mechanisms, and is likely to be independent of the association of nonsynonymous coding variation within the gene.
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Affiliation(s)
- Kathryn P Burdon
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia.,b Menzies Institute for Medical Research , University of Tasmania , Sydney , Australia
| | - Mona S Awadalla
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Paul Mitchell
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Jie Jin Wang
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Andrew White
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Miriam C Keane
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Emmanuelle Souzeau
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Stuart L Graham
- d Department of Clinical Medicine, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , New South Wales , Australia
| | - Ivan Goldberg
- e Eye Associates, Glaucoma Unit , Sydney Eye Hospital , Australia
| | - Paul R Healey
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia.,e Eye Associates, Glaucoma Unit , Sydney Eye Hospital , Australia.,f Discipline of Ophthalmology , The University of Sydney , Australia
| | - John Landers
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Richard A D Mills
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Stephen Best
- g Auckland Eye , Auckland , New Zealand.,h Auckland District Health Board , Greenlane Clinical Centre , Auckland , New Zealand.,i Discipline of Ophthalmology , University of Auckland , Auckland , New Zealand
| | - Alex W Hewitt
- b Menzies Institute for Medical Research , University of Tasmania , Sydney , Australia.,j Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Ophthalmology, Department of Surgery , The University of Melbourne , Melbourne, Australia
| | - Shiwani Sharma
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Jamie E Craig
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
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17
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Ocular and Systemic Risk Factors of Different Morphologies of Scotoma in Patients with Normal-Tension Glaucoma. J Ophthalmol 2017; 2017:1480746. [PMID: 28815087 PMCID: PMC5549477 DOI: 10.1155/2017/1480746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
THE AIM The aim of this study was to assess general and ocular profiles of patients with single-localisation changes in visual field. MATERIAL AND METHODS The study group consisted of 215 Caucasian patients with normal-tension glaucoma with scotoma on single localisation or with preperimetric glaucoma. During regular follow-up visits, ophthalmic examination was carried out and medical history was recorded. The results of the visual field were allocated as paracentral scotomas, arcuate scotomas, peripheral defects, or hemispheric defects. Statistical analysis was conducted with Statistica 12, and p < 0.05 was considered statistically significant. RESULTS Risk factors such as notch, disc hemorrhage, general hypertension, migraine, and diabetes were strongly associated with specific visual field defects. Paracentral defect was significantly more frequent for women (p = 0.05) and patients with disc hemorrhage (p < 0.001). Arcuate scotoma occurred frequently in patients without disc hemorrhage (p = 0.046) or migraines (p = 0.048) but was observed in coexistence with general hypertension (p < 0.001). The hemispheric defect corresponded with notch (p = 0.0036) and migraine (p = 0.081). Initial IOP was highest in patients with arcuate scotoma and lowest in patients with preperimetric glaucoma (p = 0.0120). CONCLUSIONS The specific morphology of scotoma in patients with normal-tension glaucoma is connected with definite general and ocular risk factors.
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Yoshikawa M, Yamashiro K, Nakanishi H, Miyata M, Miyake M, Hosoda Y, Tabara Y, Matsuda F, Yoshimura N. Association of SIX1/SIX6 locus polymorphisms with regional circumpapillary retinal nerve fibre layer thickness: The Nagahama study. Sci Rep 2017; 7:4393. [PMID: 28663559 PMCID: PMC5491508 DOI: 10.1038/s41598-017-02299-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/07/2017] [Indexed: 12/23/2022] Open
Abstract
SIX1 and SIX6 are glaucoma susceptibility genes. Previous reports indicate that the single nucleotide polymorphism (SNP) rs33912345 in SIX6 is associated with inferior circumpapillary retinal nerve fibre layer (cpRNFL) thickness (cpRNFLT). Although the region of visual field defect in glaucoma patients is directly related to cpRNFL thinning, a detailed sector analysis has not been performed in genetic association studies. In the present study, we evaluated 26 tagging SNPs in the SIX1/SIX6 locus ±50 kb region in a population of 2,306 Japanese subjects with 4- and 32-sector cpRNFLT analysis. While no SNPs showed a significant association with cpRNFLT in the 4-sectored analysis, the finer 32-sector assessment clearly showed a significant association between rs33912345 in the SIX1/SIX6 locus with inferior cpRNFL thinning at 292.5-303.8° (β = -4.55, P = 3.0 × 10-5). Furthermore, the fine-sectored cpRNFLT analysis indicated that SIX1/SIX6 polymorphisms would affect cpRNFL thinning at 281.3-303.8°, which corresponds to parafoveal scotoma in a visual field test of glaucoma patients.
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Affiliation(s)
- Munemitsu Yoshikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan. .,Department of Ophthalmology, Otsu Red Cross Hospital, 1-1-35 Nagara, Otsu, 520-8511, Japan.
| | - Hideo Nakanishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Manabu Miyata
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Yoshikatsu Hosoda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
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19
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Hu Z, He C. CDKN2B gene rs1063192 polymorphism decreases the risk of glaucoma. Oncotarget 2017; 8:21167-21176. [PMID: 28416752 PMCID: PMC5400574 DOI: 10.18632/oncotarget.15504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/08/2017] [Indexed: 01/07/2023] Open
Abstract
The aim of this meta-analysis was to evaluate the association between cyclin-dependent kinase Inhibitor-2B (CDKN2B) gene rs1063192 polymorphism and glaucoma risk. We searched the databases of PubMed, and Embase. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using fixed-effect or random-effect models. A total of 14 case-control studies involving 11,316 cases and 24,055 controls were included. Meta-analysis showed that CDKN2B gene rs1063192 polymorphism was associated with a decreased risk of glaucoma. Stratification analysis of ethnicity indicated that rs1063192 polymorphism decreased the risk of glaucoma among Caucasians and Asians. Stratification analysis by type of glaucoma revealed that rs1063192 polymorphism conferred a protective factor of primary open-angle glaucoma (POAG) and non-POAG. Stratification by source of controls uncovered an association between rs1063192 polymorphism and glaucoma in groups of population-based controls. In conclusion, this meta-analysis indicates that CDKN2B gene rs1063192 polymorphism is significantly associated with a decreased risk of glaucoma.
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Affiliation(s)
- Zhenxian Hu
- Department of Ophthalmology, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang, China
| | - Chenliang He
- Department of Ophthalmology, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang, China
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20
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Liu Y, Allingham RR. Major review: Molecular genetics of primary open-angle glaucoma. Exp Eye Res 2017; 160:62-84. [PMID: 28499933 DOI: 10.1016/j.exer.2017.05.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/07/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common type, is a complex inherited disorder that is characterized by progressive retinal ganglion cell death, optic nerve head excavation, and visual field loss. The discovery of a large, and growing, number of genetic and chromosomal loci has been shown to contribute to POAG risk, which carry implications for disease pathogenesis. Differential gene expression analyses in glaucoma-affected tissues as well as animal models of POAG are enhancing our mechanistic understanding in this common, blinding disorder. In this review we summarize recent developments in POAG genetics and molecular genetics research.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States; James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States; Duke - National University of Singapore (Duke-NUS), Singapore.
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