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Kondkar AA, Azad TA, Sultan T, Osman EA, Almobarak FA, Al-Obeidan SA. Association of rs12997 variant in the ACVR1 gene: a member of bone morphogenic protein signaling pathway with primary open-angle glaucoma in a Saudi cohort. J Investig Med 2021; 69:402-407. [PMID: 33443061 DOI: 10.1136/jim-2020-001596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 12/18/2022]
Abstract
We investigated the association between variants rs12997 in activin A receptor type I (ACVR1) and rs1043784 in BMP6 located in the 3' untranslated region, and primary open-angle glaucoma (POAG). The retrospective case-control study used TaqMan real-time PCR assay to genotype 400 subjects, including 150 patients with POAG and 250 controls. The minor 'G' allele of rs12997 in ACVR1 showed significant association with POAG (p=0.027, OR=1.39, 95% CI=1.03 to 1.87). Likewise, rs12997 genotypes showed moderate association with POAG in recessive (p=0.048, OR=1.80, 95% CI=1.01 to 3.20) and log-additive models (p=0.030, OR=1.39, 95% CI=1.03 to 1.87), but did not survive Bonferroni correction. Rs1043784 in BMP6 showed no associations. Furthermore, rs12997 G/G genotype significantly (p=0.033) increased the risk of POAG (twofolds) independent of age, sex and rs1043784 genotypes in regression analysis. However, clinical variables such as intraocular pressure and cup/disc ratio showed no association with both the polymorphisms. To conclude, the study shows a modest association between rs12997 in the ACVR1 gene, a member of the bone morphogenic protein signaling pathway and POAG. However, the results need further replication in large population-based cohorts and different ethnicities to validate its role as an important genetic biomarker.
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Affiliation(s)
- Altaf A Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia .,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Taif A Azad
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Osman
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal A Almobarak
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Kim YW, Lee YH, Kim JS, Lee J, Kim YJ, Cheong HS, Kim SH, Park KH, Kim DM, Choi HJ, Jeoung JW. Genetic analysis of primary open-angle glaucoma-related risk alleles in a Korean population: the GLAU-GENDISK study. Br J Ophthalmol 2020; 105:1307-1312. [PMID: 32933932 DOI: 10.1136/bjophthalmol-2020-316089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/21/2020] [Accepted: 08/22/2020] [Indexed: 11/04/2022]
Abstract
AIM To validate six previously known primary open-angle glaucoma (POAG)-related loci in a Korean population. METHODS Representative POAG-related single-nucleotide polymorphisms (SNPs) from six loci (cyclin-dependent kinase 4 inhibitor B antisense RNA 1 (CDKN2B)-AS1, sineoculis homeobox homolog 1/sineoculis homeobox homolog 6(SIX1/SIX6), atonal BHLH transcription factor 7 (ATOH7), cell division cycle 7-transforming growth factor beta receptor 3, CAV1, transmembrane and coiled-coil domain family 1 (TMCO1) were selected and genotyped from discovery (POAG=309, heathy=5400) and replication cohorts (POAG=310, healthy=5612 and POAG=221, healthy=6244, respectively). Data were analysed using logistic regression to calculate the OR for POAG risk associated with SNP. RESULTS From the discovery cohort, rs1900004 in ATOH7 (OR=1.29, p=0.0024); rs1063192 (OR=0.69, p=0.0006), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.63, p=0.0006) in CDKN2B-AS1, and rs10483727 in SIX1/SIX6 (OR=0.68, p=7.9E-05) were nominally associated with the risk of POAG. The replication cohorts revealed nominal associations with rs2157719 (OR=0.72, p=0.0135), rs1063192 (OR=0.63, p=0.0007) and rs7865618 (OR=0.52, p=0.0004) in CDKN2B-AS1. A mega-analysis from the entire Korean population revealed significance with rs1063192 (OR=0.77, p=6.0E-05), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.58, p=1.9E-06) in CDKN2B-AS1 and with rs10483727 in SIX1/SIX6 (OR=0.79, p=9.4E-05), with the same direction of effect between the discovery association and the replication sample. CONCLUSIONS Variants near CDKN2B-AS1 and SIX1/SIX6 may require further investigation to obtain more genetic information on POAG development in a Korean population.
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Affiliation(s)
- Yong Woo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Yun Hwan Lee
- Department of Public Health Sciences, Seoul National University, Seoul, Korea
| | - Jin-Soo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Jinho Lee
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon, Korea
| | - Yu Jeong Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ki Ho Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Dong Myung Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea .,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
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The Genetic and Endoplasmic Reticulum-Mediated Molecular Mechanisms of Primary Open-Angle Glaucoma. Int J Mol Sci 2020; 21:ijms21114171. [PMID: 32545285 PMCID: PMC7312987 DOI: 10.3390/ijms21114171] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Glaucoma is a heterogenous, chronic, progressive group of eye diseases, which results in irreversible loss of vision. There are several types of glaucoma, whereas the primary open-angle glaucoma (POAG) constitutes the most common type of glaucoma, accounting for three-quarters of all glaucoma cases. The pathological mechanisms leading to POAG pathogenesis are multifactorial and still poorly understood, but it is commonly known that significantly elevated intraocular pressure (IOP) plays a crucial role in POAG pathogenesis. Besides, genetic predisposition and aggregation of abrogated proteins within the endoplasmic reticulum (ER) lumen and subsequent activation of the protein kinase RNA-like endoplasmic reticulum kinase (PERK)-dependent unfolded protein response (UPR) signaling pathway may also constitute important factors for POAG pathogenesis at the molecular level. Glaucoma is commonly known as a ‘silent thief of sight’, as it remains asymptomatic until later stages, and thus its diagnosis is frequently delayed. Thereby, detailed knowledge about the glaucoma pathophysiology is necessary to develop both biochemical and genetic tests to improve its early diagnosis as well as develop a novel, ground-breaking treatment strategy, as currently used medical therapies against glaucoma are limited and may evoke numerous adverse side-effects in patients.
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Kondkar AA, Azad TA, Sultan T, Al-Mobarak FA, Kalantan H, Al-Obeidan SA. Polymorphisms rs693421 and rs2499601 at locus 1q43 and their haplotypes are not associated with primary open-angle glaucoma: a case-control study. BMC Res Notes 2019; 12:453. [PMID: 31337432 PMCID: PMC6651941 DOI: 10.1186/s13104-019-4491-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/17/2019] [Indexed: 11/30/2022] Open
Abstract
Objective The genetic spectrum of primary open-angle glaucoma (POAG) in middle-eastern Saudi’s is still elusive. To this end, we investigated an association between rs693421, rs2499601 and their haplotypes at chromosome 1q43 locus with POAG and its related clinical phenotypes. Genotyping was performed with TaqMan® assays. Haplotypes and their interaction analysis were carried out by SHEsis and SNPStats online tools. Results The minor “T” allele frequency of rs693421 was 0.48 in controls and 0.52 in cases (odds ratio (OR) = 1.15, 95% confidence interval (CI) 0.85–1.54, p = 0.368). Similarly, for rs2499601, the minor “C” allele frequency was 0.49 in controls as compared to 0.53 in cases (OR = 1.19, 95% CI 0.89–1.60, p = 0.236). Besides, genotype distribution for both these polymorphisms was also not significant in additive, dominant and recessive models. rs693421 and rs2499601, showed significant linkage disequilibrium (D’ statistics = 0.69, p < 0.001) but haplotype association was non-significant (p = 0.698). The significance did not vary after adjustment to age and sex. No significant genotype association was observed with intraocular pressure, cup/disc ratio and number of anti-glaucoma medication in POAG group. Furthermore, age, sex and genotypes did not contribute any significant risk of POAG in regression analysis. We report no association between rs693421, rs2499601 and their haplotypes with POAG and related phenotypes. Electronic supplementary material The online version of this article (10.1186/s13104-019-4491-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Altaf A Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia. .,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
| | - Taif A Azad
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Faisal A Al-Mobarak
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hatem Kalantan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Saleh A Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Lack of Association between Variant rs7916697 in ATOH7 and Primary Open Angle Glaucoma in a Saudi Cohort. GENETICS RESEARCH INTERNATIONAL 2018; 2018:2148056. [PMID: 30519491 PMCID: PMC6241241 DOI: 10.1155/2018/2148056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
A case-control genetic association study was performed to investigate whether variant rs7916697 in atonal bHLH transcription factor 7 (ATOH7), which has been previously reported to be associated with optic disc parameters and primary open angle glaucoma (POAG) in different ethnic groups, is a risk factor for POAG or any of its clinical phenotypes in a Saudi cohort. Genotyping of rs7916697 (G>A) variant was performed in 186 unrelated POAG cases and 171 unrelated nonglaucomatous controls of Saudi origin using real-time Taq-Man® assay. Genotypic and allelic association with POAG and its related clinical indices were evaluated. Demographic and systemic disease status did not differ significantly between POAG cases and controls. Association analysis between POAG cases and controls showed no significant genotype effect under additive (p=0.707), dominant (p=0.458), and recessive (p=0.554) models. Besides, the minor ‘A' allele frequency was 0.39 in POAG cases and 0.36 in controls with no significant distribution (p=0.406). In addition, there was no significant difference between genotypes and clinical phenotypes such as intraocular pressure and cup/disc ratio within the POAG group, or any age and sex adjusted genotype effect on the disease outcome in regression analysis. Variant rs7916697 in ATOH7 is not associated with POAG or its clinical indices such as IOP and cup/disc ratio in a Saudi cohort.
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Azad TA, Edward NB, Kondkar AA, Kalantan H, Altuwaijri S, Sultan T, Al-Mobarak FA, Al-Obeidan SA, Abu-Amero KK. Polymorphism rs547984 on human chromosome 1q43 is not associated with primary open angle glaucoma in a Saudi cohort. J Negat Results Biomed 2017. [PMID: 28648143 PMCID: PMC5483842 DOI: 10.1186/s12952-017-0077-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background To investigate the association between polymorphism rs547984, located in close proximity to the Zona Pellucida Glycoprotein 4 (ZP4) gene on human chromosome 1q43 and primary open angle glaucoma (POAG). Method Polymorphism rs547984 was genotyped using Taq-Man® assay in 185 subjects comprising of 90 unrelated POAG cases and 95 controls of Saudi origin. Results Association analysis between cases and controls revealed no significant genotype distribution under additive (p = 0.356), dominant (p = 0.517) and recessive (p = 0.309) models. Besides, the allele frequency distribution was also found to be non-significant (p = 0.70). The minor “A” allele frequency was found to be 0.49 and 0.50 among POAG cases and controls, respectively. In addition, specific clinical indices used to assess severity of glaucoma such as intraocular pressure (IOP), cup/disc ratio and number of anti-glaucoma medication also did not show any significant genotype distribution in POAG cases. Conclusion Polymorphism rs547984 is neither associated with any clinical indices important for POAG such as IOP and cup/disc ratio nor is a risk factor for POAG in the Saudi cohort.
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Affiliation(s)
- Taif A Azad
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | | | - Altaf A Kondkar
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | - Hatem Kalantan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | - Saleh Altuwaijri
- SAAD Research & Development Center, Clinical Research Lab., SAAD Specialist Hospital, P.O. Box 30353, Al Khobar, 31952, Saudi Arabia.,Qassim University, Buraydah, Saudi Arabia
| | - Tahira Sultan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | - Faisal A Al-Mobarak
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | - Saleh A Al-Obeidan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, 11411, Saudi Arabia. .,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA. .,Ophthalmic Genetics Laboratory, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.
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