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Ohno-Oishi M, Meiai Z, Sato K, Kanno S, Kawano C, Ishikawa M, Nakazawa T. SH-SY5Y human neuronal cells with mutations of the CDKN2B-AS1 gene are vulnerable under cultured conditions. Biochem Biophys Rep 2024; 38:101723. [PMID: 38737728 PMCID: PMC11088231 DOI: 10.1016/j.bbrep.2024.101723] [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] [Received: 09/14/2023] [Revised: 03/19/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Glaucoma is a common cause of blindness worldwide. Genetic effects are believed to contribute to the onset and progress of glaucoma, but the underlying pathological mechanisms are not fully understood. Here, we set out to introduce mutations into the CDKN2B-AS1 gene, which is known as being the closely associated with glaucoma, in a human neuronal cell line in vitro. We introduced gene mutations with CRISPR/Cas9 into exons and introns into the CDKN2B-AS1 gene. Both mutations strongly promoted neuronal cell death in normal culture conditions. RNA sequencing and pathway analysis revealed that the transcriptional factor Fos is a target molecule regulating CDKN2B-AS1 overexpression. We demonstrated that gene mutation of CDKN2B-AS1 is directly associated with neuronal cell vulnerability in vitro. Additionally, Fos, which is a downstream signaling molecule of CDKN2B-AS1, may be a potential source of new therapeutic targets for neuronal degeneration in diseases such as glaucoma.
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Affiliation(s)
- Michiko Ohno-Oishi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Zou Meiai
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiya Kanno
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chihiro Kawano
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Ishikawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
- Collaborative Program for Ophthalmic Drug Discovery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
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2
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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] [Grants] [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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3
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Verma SS, Gudiseva HV, Chavali VRM, Salowe RJ, Bradford Y, Guare L, Lucas A, Collins DW, Vrathasha V, Nair RM, Rathi S, Zhao B, He J, Lee R, Zenebe-Gete S, Bowman AS, McHugh CP, Zody MC, Pistilli M, Khachatryan N, Daniel E, Murphy W, Henderer J, Kinzy TG, Iyengar SK, Peachey NS, Taylor KD, Guo X, Chen YDI, Zangwill L, Girkin C, Ayyagari R, Liebmann J, Chuka-Okosa CM, Williams SE, Akafo S, Budenz DL, Olawoye OO, Ramsay M, Ashaye A, Akpa OM, Aung T, Wiggs JL, Ross AG, Cui QN, Addis V, Lehman A, Miller-Ellis E, Sankar PS, Williams SM, Ying GS, Cooke Bailey J, Rotter JI, Weinreb R, Khor CC, Hauser MA, Ritchie MD, O'Brien JM. A multi-cohort genome-wide association study in African ancestry individuals reveals risk loci for primary open-angle glaucoma. Cell 2024; 187:464-480.e10. [PMID: 38242088 DOI: 10.1016/j.cell.2023.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/24/2023] [Accepted: 12/04/2023] [Indexed: 01/21/2024]
Abstract
Primary open-angle glaucoma (POAG), the leading cause of irreversible blindness worldwide, disproportionately affects individuals of African ancestry. We conducted a genome-wide association study (GWAS) for POAG in 11,275 individuals of African ancestry (6,003 cases; 5,272 controls). We detected 46 risk loci associated with POAG at genome-wide significance. Replication and post-GWAS analyses, including functionally informed fine-mapping, multiple trait co-localization, and in silico validation, implicated two previously undescribed variants (rs1666698 mapping to DBF4P2; rs34957764 mapping to ROCK1P1) and one previously associated variant (rs11824032 mapping to ARHGEF12) as likely causal. For individuals of African ancestry, a polygenic risk score (PRS) for POAG from our mega-analysis (African ancestry individuals) outperformed a PRS from summary statistics of a much larger GWAS derived from European ancestry individuals. This study quantifies the genetic architecture similarities and differences between African and non-African ancestry populations for this blinding disease.
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Affiliation(s)
- Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Harini V Gudiseva
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Venkata R M Chavali
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca J Salowe
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Guare
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David W Collins
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vrathasha Vrathasha
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rohini M Nair
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sonika Rathi
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bingxin Zhao
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie He
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roy Lee
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Selam Zenebe-Gete
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anita S Bowman
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Maxwell Pistilli
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Naira Khachatryan
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ebenezer Daniel
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jeffrey Henderer
- Department of Ophthalmology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Tyler G Kinzy
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | - Neal S Peachey
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA; Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Linda Zangwill
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Girkin
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Radha Ayyagari
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey Liebmann
- Department of Ophthalmology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | | | - Susan E Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Akafo
- Unit of Ophthalmology, Department of Surgery, University of Ghana Medical School, Accra, Ghana
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adeyinka Ashaye
- Department of Ophthalmology, University of Ibadan, Ibadan, Nigeria
| | - Onoja M Akpa
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tin Aung
- Singapore Eye Research Institute, Singapore, Singapore
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ahmara G Ross
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qi N Cui
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Victoria Addis
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Lehman
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eydie Miller-Ellis
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prithvi S Sankar
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gui-Shuang Ying
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica Cooke Bailey
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA; Department of Pharmacology and Toxicology, Center for Health Disparities, Brody School of Medicine. East Carolina University, Greenville, NC, 27834, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Robert Weinreb
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan M O'Brien
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. joan.o'
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Tirendi S, Domenicotti C, Bassi AM, Vernazza S. Genetics and Glaucoma: the state of the art. Front Med (Lausanne) 2023; 10:1289952. [PMID: 38152303 PMCID: PMC10751926 DOI: 10.3389/fmed.2023.1289952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Glaucoma is the second leading cause of irreversible blindness worldwide. Although genetic background contributes differently to rare early-onset glaucoma (before age 40) or common adult-onset glaucoma, it is now considered an important factor in all major forms of the disease. Genetic and genomic studies, including GWAS, are contributing to identifying novel loci associated with glaucoma or to endophenotypes across ancestries to enrich the knowledge about glaucoma genetic susceptibility. Moreover, new high-throughput functional genomics contributes to defining the relevance of genetic results in the biological pathways and processes involved in glaucoma pathogenesis. Such studies are expected to advance significantly our understanding of glaucoma's genetic basis and provide new druggable targets to treat glaucoma. This review gives an overview of the role of genetics in the pathogenesis or risk of glaucoma.
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Affiliation(s)
- Sara Tirendi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Cinzia Domenicotti
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Anna Maria Bassi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
| | - Stefania Vernazza
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Genoa, Italy
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5
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Grassi L, Salazar Vega D, De Gainza A, Bouris E, Morales E, Caprioli J. Phenotypic expressions of the optic disc in primary open-angle glaucoma. Eye (Lond) 2023; 37:3839-3846. [PMID: 37355755 PMCID: PMC10698030 DOI: 10.1038/s41433-023-02627-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Which phenotypes are we able to recognize in the optic nerve of patients with primary open angle glaucoma? METHODS Retrospective interventional case series. 885 eyes from 885 patients at an outpatient tertiary care centre who met specified criteria for POAG were included. Disc photographs were classified by three glaucoma specialists into the following phenotypes according to their predominant characteristics: (1) concentric rim thinning, (2) focal rim thinning, (3) acquired pit of the optic nerve (APON), (4) tilted, (5) extensive peripapillary atrophy (PPA), and (6) broad rim thinning. Demographic, medical, and ocular data were collected. Kruskal-Wallis was used as a non-parametric test and pairwise comparison was performed by using Wilcoxon rank sum test corrected. RESULTS Phenotypic distribution was as follows: 398(45%) focal thinning, 153(18%) concentric thinning, 153(17%) broad thinning, 109(12%) tilted, 47(5%) extensive PPA and 25(3%) APON. Phenotypic traits of interest included a higher proportion of female patients with the focal thinning phenotype (p = 0.015); myopia (p = 0.000), Asian race (OR: 8.8, p = 0.000), and younger age (p = 0.000) were associated with the tilted phenotype; the concentric thinning patients had thicker RNFL (p = 0.000), higher MD (p = 0.008) and lower PSD (p = 0.043) than broad thinning, despite no difference in disc sizes (p = 0.849). The focal thinning group had a localized VF pattern with high PSD compared to concentric thinning (p = 0.005). CONCLUSION We report six phenotypic classifications of POAG patients with demographic and ocular differences between phenotypes. Future refinement of phenotypes should allow enhanced identification of genetic associations and improved individualization of patient care.
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Affiliation(s)
- Lourdes Grassi
- Glaucoma Division, Jules Stein Eye Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Diana Salazar Vega
- Department of Ophthalmology, Vision Consultants and Surgeons, Falls Church, VA, USA
| | | | - Ella Bouris
- Glaucoma Division, Jules Stein Eye Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Esteban Morales
- Glaucoma Division, Jules Stein Eye Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Joseph Caprioli
- Glaucoma Division, Jules Stein Eye Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA.
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6
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Kuang G, Salowe R, O'Brien J. Paving the way while playing catch up: mitochondrial genetics in African ancestry primary open-angle glaucoma. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1267119. [PMID: 38983031 PMCID: PMC11182247 DOI: 10.3389/fopht.2023.1267119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 07/11/2024]
Abstract
Glaucoma, the leading cause of irreversible blindness worldwide, disproportionately affects individuals of African descent. Specifically, previous research has indicated that primary open-angle glaucoma (POAG), the most common form of disease, is more prevalent, severe, early-onset, and rapidly-progressive in populations of African ancestry. Recent studies have identified genetic variations that may contribute to the greater burden of disease in this population. In particular, mitochondrial genetics has emerged as a profoundly influential factor in multiple neurodegenerative diseases, including POAG. Several hypotheses explaining the underlying mechanisms of mitochondrial genetic contribution to disease progression have been proposed, including nuclear-mitochondrial gene mismatch. Exploring the fundamentals of mitochondrial genetics and disease pathways within the understudied African ancestry population can lead to groundbreaking advancements in the research and clinical understanding of POAG. This article discusses the currently known involvements of mitochondrial genetic factors in POAG, recent directions of study, and potential future prospects in mitochondrial genetic studies in individuals of African descent.
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Affiliation(s)
- Grace Kuang
- Penn Medicine Center for Genetics in Complex Disease, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Rebecca Salowe
- Penn Medicine Center for Genetics in Complex Disease, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Joan O'Brien
- Penn Medicine Center for Genetics in Complex Disease, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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7
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Walters RG, Millwood IY, Lin K, Schmidt Valle D, McDonnell P, Hacker A, Avery D, Edris A, Fry H, Cai N, Kretzschmar WW, Ansari MA, Lyons PA, Collins R, Donnelly P, Hill M, Peto R, Shen H, Jin X, Nie C, Xu X, Guo Y, Yu C, Lv J, Clarke RJ, Li L, Chen Z. Genotyping and population characteristics of the China Kadoorie Biobank. CELL GENOMICS 2023; 3:100361. [PMID: 37601966 PMCID: PMC10435379 DOI: 10.1016/j.xgen.2023.100361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 02/09/2023] [Accepted: 06/24/2023] [Indexed: 08/22/2023]
Abstract
The China Kadoorie Biobank (CKB) is a population-based prospective cohort of >512,000 adults recruited from 2004 to 2008 from 10 geographically diverse regions across China. Detailed data from questionnaires and physical measurements were collected at baseline, with additional measurements at three resurveys involving ∼5% of surviving participants. Analyses of genome-wide genotyping, for >100,000 participants using custom-designed Axiom arrays, reveal extensive relatedness, recent consanguinity, and signatures reflecting large-scale population movements from recent Chinese history. Systematic genome-wide association studies of incident disease, captured through electronic linkage to death and disease registries and to the national health insurance system, replicate established disease loci and identify 14 novel disease associations. Together with studies of candidate drug targets and disease risk factors and contributions to international genetics consortia, these demonstrate the breadth, depth, and quality of the CKB data. Ongoing high-throughput omics assays of collected biosamples and planned whole-genome sequencing will further enhance the scientific value of this biobank.
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Affiliation(s)
- Robin G. Walters
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Iona Y. Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dan Schmidt Valle
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Pandora McDonnell
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Alex Hacker
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Daniel Avery
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Ahmed Edris
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Hannah Fry
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Na Cai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - M. Azim Ansari
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Paul A. Lyons
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Michael Hill
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Richard Peto
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Hongbing Shen
- Department of Epidemiology, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211116, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Guo
- Fuwai Hospital, Chinese Academy of Medical Sciences, Beijing 100037, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Robert J. Clarke
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
| | - China Kadoorie Biobank Collaborative Group
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
- MRC Population Health Research Unit, University of Oxford, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Epidemiology, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211116, China
- BGI-Shenzhen, Shenzhen 518083, China
- Fuwai Hospital, Chinese Academy of Medical Sciences, Beijing 100037, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing 100191, China
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8
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Tomasoni M, Beyeler MJ, Vela SO, Mounier N, Porcu E, Corre T, Krefl D, Button AL, Abouzeid H, Lazaros K, Bochud M, Schlingemann R, Bergin C, Bergmann S. Genome-Wide Association Studies of Retinal Vessel Tortuosity Identify Numerous Novel Loci Revealing Genes and Pathways Associated with Ocular and Cardiometabolic Diseases. OPHTHALMOLOGY SCIENCE 2023; 3:100288. [PMID: 37131961 PMCID: PMC10149284 DOI: 10.1016/j.xops.2023.100288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
Purpose To identify novel susceptibility loci for retinal vascular tortuosity, to better understand the molecular mechanisms modulating this trait, and reveal causal relationships with diseases and their risk factors. Design Genome-wide Association Studies (GWAS) of vascular tortuosity of retinal arteries and veins followed by replication meta-analysis and Mendelian randomization (MR). Participants We analyzed 116 639 fundus images of suitable quality from 63 662 participants from 3 cohorts, namely the UK Biobank (n = 62 751), the Swiss Kidney Project on Genes in Hypertension (n = 397), and OphtalmoLaus (n = 512). Methods Using a fully automated retina image processing pipeline to annotate vessels and a deep learning algorithm to determine the vessel type, we computed the median arterial, venous and combined vessel tortuosity measured by the distance factor (the length of a vessel segment over its chord length), as well as by 6 alternative measures that integrate over vessel curvature. We then performed the largest GWAS of these traits to date and assessed gene set enrichment using the novel high-precision statistical method PascalX. Main Outcome Measure We evaluated the genetic association of retinal tortuosity, measured by the distance factor. Results Higher retinal tortuosity was significantly associated with higher incidence of angina, myocardial infarction, stroke, deep vein thrombosis, and hypertension. We identified 175 significantly associated genetic loci in the UK Biobank; 173 of these were novel and 4 replicated in our second, much smaller, metacohort. We estimated heritability at ∼25% using linkage disequilibrium score regression. Vessel type specific GWAS revealed 116 loci for arteries and 63 for veins. Genes with significant association signals included COL4A2, ACTN4, LGALS4, LGALS7, LGALS7B, TNS1, MAP4K1, EIF3K, CAPN12, ECH1, and SYNPO2. These tortuosity genes were overexpressed in arteries and heart muscle and linked to pathways related to the structural properties of the vasculature. We demonstrated that retinal tortuosity loci served pleiotropic functions as cardiometabolic disease variants and risk factors. Concordantly, MR revealed causal effects between tortuosity, body mass index, and low-density lipoprotein. Conclusions Several alleles associated with retinal vessel tortuosity suggest a common genetic architecture of this trait with ocular diseases (glaucoma, myopia), cardiovascular diseases, and metabolic syndrome. Our results shed new light on the genetics of vascular diseases and their pathomechanisms and highlight how GWASs and heritability can be used to improve phenotype extraction from high-dimensional data, such as images. Financial Disclosures The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Mattia Tomasoni
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | - Michael Johannes Beyeler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sofia Ortin Vela
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ninon Mounier
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Eleonora Porcu
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Tanguy Corre
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Daniel Krefl
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexander Luke Button
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hana Abouzeid
- Division of Ophthalmology, Geneva University Hospitals, Geneva, Switzerland
- Clinical Eye Research Center Memorial Adolphe de Rothschild, Geneva, Switzerland
| | | | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Reinier Schlingemann
- Jules-Gonin Eye Hospital, Lausanne, Switzerland
- Department of Ophthalmology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Correspondence: Sven Bergmann, PhD, University of Lausanne, Genopode, Lausanne 1016, Switzerland.
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Lee YC, Lee MY, Shin HY. Lack of association between SIX1/SIX6 locus polymorphisms and pseudoexfoliation syndrome in a population from the Republic of Korea. Medicine (Baltimore) 2022; 101:e31542. [PMID: 36596020 PMCID: PMC9803459 DOI: 10.1097/md.0000000000031542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Previous studies have reported the association of the SIX1/SIX6 locus with open-angle glaucoma in various ethnic populations. However, the relevance of the SIX1/SIX6 locus to pseudoexfoliation syndrome (XFS) appears uncertain at present. Thus, we investigated the relationship between polymorphisms in the SIX1/SIX6 locus and XFS in a Korean XFS cohort. A total of 246 participants comprising 167 unrelated Korean patients with XFS and 79 ethnically matched control subjects were recruited. Four polymorphisms of the SIX1/SIX6 locus (rs33912345, rs12436579, rs2179970, and rs10483727) were genotyped using a TaqMan® allelic discrimination assay. Genotypic and allelic associations were analyzed using logistic regression. The minor allele frequency (MAF) of rs33912345 was found to be 0.287 and 0.247 in the XFS cases and controls, respectively, and the MAF of rs12436579 was found to be 0.383 and 0.361 in the XFS cases and control subjects, respectively. The MAF of rs2179970 was found to be 0.090 and 0.095 in the XFS cases and control subjects, respectively, and the MAF of rs10483727 was found to be 0.293 and 0.253 in the XFS cases and control subjects, respectively. Genetic association analysis of 4 SIX1/SIX6 locus single nucleotide polymorphisms (SNPs) revealed no significant difference in genotype distribution between the XFS cases and control subjects in the allelic, dominant, or recessive models (all, P > .05). The current study suggested that SIX1/SIX6 locus polymorphisms (rs33912345, rs12436579, rs2179970, and rs10483727) may not be associated with a genetic susceptibility to XFS in a Korean cohort.
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Affiliation(s)
- Young Chun Lee
- Department of Ophthalmology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Mee Yon Lee
- Department of Ophthalmology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hye-Young Shin
- Department of Ophthalmology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- * Correspondence: Hye-Young Shin, Department of Ophthalmology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea, 271 Cheonbo-ro, Uijeongbu-si, Gyeonggi-do, Seoul, Republic of Korea (e-mail: )
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10
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Terao R, Ahmed T, Suzumura A, Terasaki H. Oxidative Stress-Induced Cellular Senescence in Aging Retina and Age-Related Macular Degeneration. Antioxidants (Basel) 2022; 11:2189. [PMID: 36358561 PMCID: PMC9686487 DOI: 10.3390/antiox11112189] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 07/30/2023] Open
Abstract
Aging leads to a gradual decline of function in multiple organs. Cataract, glaucoma, diabetic retinopathy, and age-related macular degeneration (AMD) are age-related ocular diseases. Because their pathogenesis is unclear, it is challenging to combat age-related diseases. Cellular senescence is a cellular response characterized by cell cycle arrest. Cellular senescence is an important contributor to aging and age-related diseases through the alteration of cellular function and the secretion of senescence-associated secretory phenotypes. As a driver of stress-induced premature senescence, oxidative stress triggers cellular senescence and age-related diseases by inducing senescence markers via reactive oxygen species and mitochondrial dysfunction. In this review, we focused on the mechanism of oxidative stress-induced senescence in retinal cells and its role in the pathogenesis of AMD.
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Affiliation(s)
- Ryo Terao
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Tazbir Ahmed
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Ayana Suzumura
- Department of Ophthalmology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan
| | - Hiroko Terasaki
- Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8601, Japan
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11
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Zhou Q, Yang J, Vats D, Roberts GO, Rosenthal JS. Dimension‐free mixing for high‐dimensional Bayesian variable selection. J R Stat Soc Series B Stat Methodol 2022. [DOI: 10.1111/rssb.12546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Quan Zhou
- Department of Statistics Texas A&M University College Station Texas USA
| | - Jun Yang
- Department of Statistics University of Oxford Oxford UK
| | - Dootika Vats
- Department of Mathematics and Statistics Indian Institute of Technology Kanpur Kanpur India
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12
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Coronary artery disease and cancer: a significant resemblance. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:187. [PMID: 36071253 DOI: 10.1007/s12032-022-01789-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/01/2022] [Indexed: 10/14/2022]
Abstract
Cancer and coronary artery disease (CAD) are two of the most common causes of death, and they frequently coexist, especially as the world's population ages. CAD can develop prior to or following cancer diagnosis, as well as a side effect of cancer treatment. CAD develops as complex interactions of lifestyle and hereditary variables, just like the development of the most complex and non-communicable diseases. Cancer is caused by both external/acquired factors (tobacco, food, physical activity, alcohol consumption, epigenetic alterations) and internal/inherited factors (genetic mutations, hormones, and immunological diseases). The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (Cas9) system has recently emerged as a strong tool for gene therapy for both cancer as well as CAD treatment due to its great accuracy and efficiency. A deeper understanding of the complex link between CAD and cancer should lead to better prevention, faster detection, and safer treatment strategies.
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Association of Polymorphisms at the SIX1/SIX6 Locus with Normal Tension Glaucoma in a Population from the Republic of Korea. J Glaucoma 2022; 31:763-766. [PMID: 35658088 DOI: 10.1097/ijg.0000000000002060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/20/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Several previous studies have reported that the relevance of the SIX1/SIX6 locus to open angle glaucoma (OAG) in various ethnic populations. However, definitions of OAG patients were different among those studies. The relevance of the SIX1/SIX6 locus to normal tension glaucoma (NTG) in a Korean population remains uncertain. Therefore, the purpose of this study was to investigate the relationship of the SIX1/SIX6 locus with NTG in a Korean cohort. METHOD Patients with NTG and ethnically-matched healthy controls were recruited from eye clinics in Korea (210 cases and 117 controls). Four polymorphisms (rs33912345, rs12436579, rs2179970, and rs10483727) of the SIX1/SIX6 locus were genotyped for 327 subjects using a TaqMan SNP genotyping assay. RESULTS The rs33912345 polymorphism was significantly correlated with NTG in the recessive model (OR: 0.265; 95%CI: 0.078-0.898, P=0.033), but not in the allelic and dominant models (both P>0.05). The SNP rs10483727 was significantly associated with NTG in the allelic model (OR: 0.674; 95% CI: 0.464-0.979, P=0.038) and the recessive model (OR: 0.187; 95%vCI: 0.058-0.602, P=0.005). Genetic association analysis of SNP rs12436579 and rs2179970 revealed no significant difference in genotype distribution between NTG cases and controls in allelic, dominant, or recessive model (all P>0.05). CONCLUSION The current study found that SIX1-SIX6 locus rs10483727 and rs33912345 polymorphisms were significantly associated with NTG risk in Korean population.
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14
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Asian Race and Primary Open-Angle Glaucoma: Where Do We Stand? J Clin Med 2022; 11:jcm11092486. [PMID: 35566612 PMCID: PMC9099679 DOI: 10.3390/jcm11092486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 01/27/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by irreversible retinal ganglion cell damage and visual field loss. The global POAG prevalence is estimated to be 3.05%, and near term is expected to significantly rise, especially within aging Asian populations. Primary angle-closure glaucoma disproportionately affects Asians, with up to four times greater prevalence of normal-tension glaucoma reported compared with high-tension glaucoma. Estimates for overall POAG prevalence in Asian populations vary, with Chinese and Indian populations representing the majority of future cases. Structural characteristics associated with glaucoma progression including the optic nerve head, retina, and cornea are distinct in Asians, serving as intermediates between African and European descent populations. Patterns in IOP suggest some similarities between races, with a significant inverse relationship between age and IOP only in Asian populations. Genetic differences have been suggested to play a role in these differences, however, a clear genetic pattern is yet to be established. POAG pathogenesis differs between Asians and other ethnicities, and it may differ within the broad classification of the Asian race. Greater awareness and further research are needed to improve treatment plans and outcomes for the increasingly high prevalence of normal tension glaucoma within aging Asian populations.
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Lo Faro V, Nolte IM, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Mitochondrial Genome Study Identifies Association Between Primary Open-Angle Glaucoma and Variants in MT-CYB, MT-ND4 Genes and Haplogroups. Front Genet 2021; 12:781189. [PMID: 34976016 PMCID: PMC8719162 DOI: 10.3389/fgene.2021.781189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Background and purpose: Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by death of retinal ganglion cells and atrophy of the optic nerve head. The susceptibility of the optic nerve to damage has been shown to be mediated by mitochondrial dysfunction. In this study, we aimed to determine a possible association between mitochondrial SNPs or haplogroups and POAG. Methods: Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) were genotyped using the Illumina Infinium Global Screening Array-24 (GSA) 700K array set. Genetic analyses were performed in a POAG case-control study involving the cohorts, Groningen Longitudinal Glaucoma Study-Lifelines Cohort Study and Amsterdam Glaucoma Study, including 721 patients and 1951 controls in total. We excluded samples not passing quality control for nuclear genotypes and samples with low call rate for mitochondrial variation. The mitochondrial variants were analyzed both as SNPs and haplogroups. These were determined with the bioinformatics software HaploGrep, and logistic regression analysis was used for the association, as well as for SNPs. Results: Meta-analysis of the results from both cohorts revealed a significant association between POAG and the allele A of rs2853496 [odds ratio (OR) = 0.64; p = 0.006] within the MT-ND4 gene, and for the T allele of rs35788393 (OR = 0.75; p = 0.041) located in the MT-CYB gene. In the mitochondrial haplogroup analysis, the most significant p-value was reached by haplogroup K (p = 1.2 × 10−05), which increases the risk of POAG with an OR of 5.8 (95% CI 2.7–13.1). Conclusion: We identified an association between POAG and polymorphisms in the mitochondrial genes MT-ND4 (rs2853496) and MT-CYB (rs35788393), and with haplogroup K. The present study provides further evidence that mitochondrial genome variations are implicated in POAG. Further genetic and functional studies are required to substantiate the association between mitochondrial gene polymorphisms and POAG and to define the pathophysiological mechanisms of mitochondrial dysfunction in glaucoma.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jacoline B. Ten Brink
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, Netherlands
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, Netherlands
- *Correspondence: Arthur A. Bergen,
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Shah MH, Kumaran M, Chermakani P, Kader MA, Ramakrishnan R, Krishnadas SR, Devarajan B, Sundaresan P. Whole-exome sequencing identifies multiple pathogenic variants in a large South Indian family with primary open-angle glaucoma. Indian J Ophthalmol 2021; 69:2461-2468. [PMID: 34427245 PMCID: PMC8544095 DOI: 10.4103/ijo.ijo_3301_20] [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] [Indexed: 11/22/2022] Open
Abstract
Purpose: To identify the pathogenic variants associated with primary open-angle glaucoma (POAG) using whole-exome sequencing (WES) data of a large South Indian family. Methods: We recruited a large five-generation South Indian family (n = 84) with a positive family history of POAG (n = 19). All study participants had a comprehensive ocular evaluation. We performed WES for 16 samples (nine POAG and seven unaffected controls) since Sanger sequencing of the POAG candidate genes (MYOC, OPTN, and TBK1) showed no genetic variation. We used an in-house pipeline for prioritizing the pathogenic variants based on their segregation among the POAG individual. Results: We identified one novel and five low-frequency pathogenic variants with consistent co-segregation in all affected individuals. The variant c.G3719A in RPGR-interacting domain of RPGRIP1 that segregated heterozygously with the six POAG cases is distinct from variants causing photoreceptor dystrophies, reported affecting the RPGR protein complex signaling in primary cilia. The cilia in trabecular meshwork (TM) cells has been reported to mediate the intraocular pressure (IOP) sensation. Furthermore, we identified a novel c.A1295G variant in Rho guanine nucleotide exchange factors Gene 40 (ARHGEF40) and a likely pathogenic variant in the RPGR gene, suggesting that they may alter the RhoA activity essential for IOP regulation. Conclusion: Our study supports that low-frequency pathogenic variants in multiple genes and pathways probably affect Primary Open Angle Glaucoma’s pathogenesis in the large South Indian family. Furthermore, it requires larger case-controls to perform family-based association tests and to strengthen our analysis.
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Affiliation(s)
- Mohd Hussain Shah
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Manojkumar Kumaran
- Department of Bioinformatics, Aravind Medical Research Foundation, Madurai; School of Chemical and Biotechnology, SASTRA (Deemed to be University), Thanjavur, India
| | - Prakash Chermakani
- Department of Genetics, Aravind Medical Research Foundation; Department of Molecular Biology, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - R Ramakrishnan
- Glaucoma Clinic, Aravind Eye Hospital, Tirunelveli, India
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Eliseeva NV, Ponomarenko IV, Churnosov MI. [Analysis of the functional role of polymorphism in the CDKN2B-AS1 gene GWAS-significant for primary open-angle glaucoma (an in-silico study)]. Vestn Oftalmol 2021; 137:43-50. [PMID: 34410056 DOI: 10.17116/oftalma202113704143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Primary open-angle glaucoma (POAG) is the most common form of glaucoma in which genetic factors play a significant role. According to genome-wide studies (GWAS), the CDKN2B-AS1 gene is associated with POAG. PURPOSE To study in silico the functional significance of the CDKN2B-AS1 gene polymorphism GWAS-significant for primary open-angle glaucoma. MATERIAL AND METHODS The in-silico analysis was based on data from the GWAS catalog, five polymorphic loci of the CDKN2B-AS1 gene (rs1063192, rs7865618, rs2157719, rs944800, rs4977756) associated with POAG were selected. The study evaluated the regulatory potential, the relationship with the expression and alternative splicing of genes of the CDKN2B-AS1 gene polymorphism using modern databases for functional genomics - HaploReg and GTExportal. RESULTS An important functional significance of the polymorphic loci rs1063192, rs7865618, rs2157719, rs944800, rs4977756 of the CDKN2B-AS1 gene was revealed. These loci are located in the region of histones marking enhancers and in the region of hypersensitivity to DNAse-1, can be found in more than ten different organs and tissues, in the regions of regulatory DNA motifs to five transcription factors (AIRE, GATA, Tgif1, Pou2f2, and Zfp187), and are associated with expression of three genes (CDKN2B-AS1, CDKN2B, CDKN2A) and alternative splicing of transcripts of two genes (CDKN2B-AS1 and RP11-149I2.4) in cell cultures, organs and tissues with pathogenic significance for glaucoma development. CONCLUSION Polymorphism of the CDKN2B-AS1 gene (rs1063192, rs7865618, rs2157719, rs944800, rs4977756) has significant regulatory potential and is associated with the expression and alternative splicing of genes, which possibly underlies its association with primary open-angle glaucoma.
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Affiliation(s)
- N V Eliseeva
- Belgorod State National Research University, Belgorod, Russia
| | - I V Ponomarenko
- Belgorod State National Research University, Belgorod, Russia
| | - M I Churnosov
- Belgorod State National Research University, Belgorod, Russia
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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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20
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Lo Faro V, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma. BMC Genomics 2021; 22:590. [PMID: 34348663 PMCID: PMC8336345 DOI: 10.1186/s12864-021-07846-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs. RESULTS We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways. CONCLUSIONS Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A Bergen
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Department of Ophthalmology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands. .,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands.
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21
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A Comparison of Genomic Advances in Exfoliation Syndrome and Primary Open-Angle Glaucoma. CURRENT OPHTHALMOLOGY REPORTS 2021. [DOI: 10.1007/s40135-021-00270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Eliseeva NV, Ponomarenko IV, Churnosov MI. CDKN2B-AS1 gene polymorphism is associated with primary open-angle glaucoma in women of the Central Black Earth Region, Russia. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2021. [DOI: 10.24075/brsmu.2021.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Primary open-angle glaucoma (POAG) is a complex disorder. Genetic factors play a vital part in POAG. The prevalence of POAG is gender-specific: the disorder is more often diagnosed in women. Results of the genome-wide association studies (GWAS) strongly support the association of CDKN2B-AS1 gene polymorphism with POAG. The aim was to perform the replicative study of CDKN2B-AS1 gene polymorphic loci association with POAG in women of the Central Black Earth Region, Russia. Five CDKN2B-AS1 gene single nucleotide polymorphisms (SNP), rs1063192, rs7865618, rs2157719, rs944800, and rs4977756, were genotyped in 290 female patients with POAG and 220 female controls. The differences in the haplotype block structure between the POAG patients (no haplotype blocks) and the controls (haplotype block consisting of three SNPs, rs1063192, rs7865618 and rs2157719, was detected) for the set of studied CDKN2B-AS1 SNPs were revealed using the Solid Spine algorithm (D’ > 0.8). CDKN2B-AS1 gene haplotype GGG rs1063192–rs7865618–rs2157719 is associated with POAG in women. This haplotype is considered a protective factor of the disorder (OR = 0.66; p = 0.006, рperm = 0.037).
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Affiliation(s)
- NV Eliseeva
- Belgorod State National Research University, Belgorod, Russia
| | - IV Ponomarenko
- Belgorod State National Research University, Belgorod, Russia
| | - MI Churnosov
- Belgorod State National Research University, Belgorod, Russia
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23
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Chai X, Low KY, Tham YC, Chee ML, Thakur S, Zhang L, Tan NY, Khor CC, Aung T, Wong TY, Cheng CY. Association of Glaucoma Risk Genes with Retinal Nerve Fiber Layer in a Multi-ethnic Asian Population: The Singapore Epidemiology of Eye Diseases Study. Invest Ophthalmol Vis Sci 2021; 61:37. [PMID: 32821913 PMCID: PMC7445359 DOI: 10.1167/iovs.61.10.37] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Purpose Genome-wide association studies have identified several genes associated with glaucoma. However, their roles in the pathogenesis of glaucoma remain unclear, particularly their effects on retinal nerve fiber layer (RNFL) thickness. The aim of this study was to investigate the associations between the identified glaucoma risk genes and RNFL thickness. Methods A total of 3843 participants (7,020 healthy eyes) were enrolled from the Singapore Epidemiology of Eye Diseases (SEED) study, a population-based study composing of three major ethnic groups—Malay, Indian, and Chinese—in Singapore. Ocular examinations were performed, and spectral-domain optical coherence tomography (SD-OCT) was used to measure circumpapillary RNFL thickness. We selected 35 independent glaucoma-associated genetic loci for analysis. An linear regression model was conducted to determine the association of these variants with circumpapillary RNFL, assuming an additive genetic model. We conducted association analysis in each of the three ethnic groups, followed by a meta-analysis of them. Results The mean age of the included participants was 59.4 ± 8.9 years, and the mean RFNL thickesss is 92.3 ± 11.2 µm. In the meta-analyses, of the 35 glacuoma loci, we found that only SIX6 was significantly associated with reduction in global RNFL thickness (rs33912345; β = −1.116 um per risk allele, P = 1.64E-05), and the effect size was larger in the inferior RNFL quadrant (β = −2.015 µm, P = 2.9E-6), and superior RNFL quadrant (β = −1.646 µm, P = 6.54E-5). The SIX6 association were consistently observed across all three ethnic groups. Other than RNFL, we also found several genetic varaints associated with vertical cuo-to-disc ratio (ATOH7, CDKN2B-AS1, and TGFBR3-CDC7), rim area (SIX6 and CDKN2B-AS1), and disc area (SIX6, ATOH7, and TGFBR3-CDC7). The association of SIX6 rs33912345 with NRFL thickness remained similar after further adjusting for disc area and 3 other disc parameter associated SNPs (ATOH7, CDKN2B-AS1, and TGFBR3-CDC7). Conclusions Of the 35 glaucoma identified risk loci, only SIX6 is significantly and independently associated with thinner RNFL. Our study further supports the involvement of SIX6 with RNFL thickness and pathogensis of glaucoma.
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Affiliation(s)
- Xiaoran Chai
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
| | - Kok Yao Low
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Miao Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Sahil Thakur
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Liang Zhang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Nicholas Y Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Chiea Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
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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] [MESH Headings] [Grants] [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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Abstract
The article reviews literature on developmental stages of genome-wide association studies (GWAS) of primary open-angle glaucoma (POAG). This problem is currently developing and one of the most complex in ophthalmology. The article considers main GWAS of POAG and established GWAS-significant polymorphisms associated with the disease. The topic of genome-wide studies of primary open-angle glaucoma will be of certain interest to ophthalmologists, materials on GWAS-significant loci can be used both in the selection of polymorphisms in replicative studies of POAG in various populations of Russia, and to expand ideas about the molecular genetic mechanisms of the development of the disease.
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Affiliation(s)
- N V Eliseeva
- Belgorod State National Research University, Belgorod, Russia
| | - M I Churnosov
- Belgorod State National Research University, Belgorod, Russia
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27
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Rathi S, Danford I, Gudiseva HV, Verkuil L, Pistilli M, Vishwakarma S, Kaur I, Dave TV, O’Brien JM, Chavali VRM. Molecular Genetics and Functional Analysis Implicate CDKN2BAS1-CDKN2B Involvement in POAG Pathogenesis. Cells 2020; 9:cells9091934. [PMID: 32825664 PMCID: PMC7564117 DOI: 10.3390/cells9091934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
The genes in the 9p21 locus (CDKN2B-AS1 & CDKN2B) are widely associated with Primary open-angle glaucoma (POAG). However, the functional importance of this locus in POAG pathogenesis is still unexplored. This study investigated the role of CDKN2BAS1-CDKN2B axis in POAG. We observed significant association of CDKN2B-AS1 SNP rs4977756 with POAG and its endophenotypic traits (vertical cup-disc ratio (p = 0.033) and central corneal thickness (p = 0.008)) by screening African American POAG cases (n = 1567) and controls (n = 1600). A luciferase reporter assay in Human embryonic kidney 293T (HEK293T) cells revealed that the region surrounding rs4977756 likely serves as a transcriptional repressor. siRNA-mediated knockdown of CDKN2B-AS1 in HEK293T cells and trabecular meshwork (TM) cells resulted in significantly increased expression of CDKN2B, which was also observed in human POAG ocular tissues. Pathway focused qRT-PCR gene expression analysis showed increased cellular senescence, TGFβ signaling and ECM deposition in TM cells after CDKN2B-AS1 suppression. In conclusion, we report that CDKN2B-AS1 may act as a regulator, and it could function by modulating the expression of CDKN2B. In addition, increase in CDKN2B levels due to CDKN2B-AS1 suppression may result in the senescence of trabecular meshwork cells leading to POAG pathogenesis.
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Affiliation(s)
- Sonika Rathi
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
| | - Ian Danford
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
- Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Harini V. Gudiseva
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
| | - Lana Verkuil
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
| | - Maxwell Pistilli
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
| | - Sushma Vishwakarma
- Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana 500034, India; (S.V.); (I.K.)
| | - Inderjeet Kaur
- Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana 500034, India; (S.V.); (I.K.)
| | - Tarjani Vivek Dave
- Ophthalmic Plastic Surgery Service, Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana 500034, India;
| | - Joan M. O’Brien
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
- Correspondence: Joan.O’ (J.M.O.); (V.R.M.C.)
| | - Venkata R. M. Chavali
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA 19104, USA; (S.R.); (I.D.); (H.V.G.); (L.V.); (M.P.)
- Correspondence: Joan.O’ (J.M.O.); (V.R.M.C.)
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28
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Dataset of allele, genotype and haplotype frequencies of five polymorphisms CDKN2B-AS1 gene in Russian patients with primary open-angle glaucoma. Data Brief 2020; 31:105722. [PMID: 32509935 PMCID: PMC7265048 DOI: 10.1016/j.dib.2020.105722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/20/2022] Open
Abstract
Data on the allele, genotype and haplotype frequencies of the five single nucleotide polymorphisms (SNPs) such as rs1063192, rs7865618, rs2157719, rs944800 and rs4977756 of the CDKN2B-AS gene in Russian patients with primary open-angle glaucoma (POAG) are provided. These SNPs are found to be associated with the risk of POAG by genome-wide association studies (GWAS). The frequencies of alleles, genotypes and haplotypes of CDKN2B-AS gene were present separately for entire group of patients, females and males, and may be used as reference data of Russian population.
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Moschos MM, Dettoraki M, Karekla A, Lamprinakis I, Damaskos C, Gouliopoulos N, Tibilis M, Gazouli M. Polymorphism analysis of miR182 and CDKN2B genes in Greek patients with primary open angle glaucoma. PLoS One 2020; 15:e0233692. [PMID: 32492046 PMCID: PMC7269255 DOI: 10.1371/journal.pone.0233692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/10/2020] [Indexed: 12/28/2022] Open
Abstract
Glaucoma is a progressive optic neuropathy resulting from retinal ganglion cells death; it represents one of the leading causes of irreversible blindness worldwide. Although, primary open angle glaucoma (POAG) is the most common type of the disease, the pathogenesis of POAG and the genetic factors contributing to disease development remain poorly understood. The aim of this study was to investigate whether the polymorphisms rs76481776 in miR182 gene and rs3217992 in cyclin-dependent kinase inhibitor-2B (CDKN2B) gene are risk factors for POAG in a series of patients of Greek origin. A case-control study was conducted including 120 patients with POAG and 113 unaffected healthy controls of Greek origin, surveyed for polymorphisms with potential correlation to POAG. DNA from each individual was tested for the miR182 rs76481776 and CDKN2B rs3217992 polymorphisms. Regarding the miR182 rs76481776 polymorphism, the T allele occurred with significantly higher frequency in POAG patients compared to controls (OR: 2.62, 95% CI: 1.56-4.39; p = 0.0002). The CDKN2B rs3217992 A allele frequency was found significantly increased in POAG patients compared to healthy individuals (OR: 1.72, 95% CI: 1.18-2.49; p = 0.005). Therefore, both rs76481776 polymorphism in miR182 gene and rs3217992 polymorphism in CDKN2B gene seem to be associated with the development of POAG in a Greek population. The carriers of the T allele of rs76481776 in miR182 and the carriers of the A allele of rs3217992 in CDKN2B have an increased risk of developing POAG.
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Affiliation(s)
- Marilita M. Moschos
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- * E-mail:
| | - Maria Dettoraki
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Aggela Karekla
- Department of Ophthalmology, “Evangelismos” General Hospital, Athens, Greece
| | - Ioannis Lamprinakis
- Department of Ophthalmology, “Evangelismos” General Hospital, Athens, Greece
| | - Christos Damaskos
- Second Department of Propedeutic Surgery, “Laiko” General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Gouliopoulos
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Marios Tibilis
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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30
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Kim YW, Kim YJ, Cheong HS, Shiga Y, Hashimoto K, Song YJ, Kim SH, Choi HJ, Nishiguchi KM, Kawai Y, Nagasaki M, Nakazawa T, Park KH, Kim DM, Jeoung JW. Exploring the Novel Susceptibility Gene Variants for Primary Open-Angle Glaucoma in East Asian Cohorts: The GLAU-GENDISK Study. Sci Rep 2020; 10:221. [PMID: 31937794 PMCID: PMC6959350 DOI: 10.1038/s41598-019-57066-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Primary open-angle glaucoma (POAG) can develop even within normal ranges of intraocular pressure, and this type of glaucoma (so-called ‘normal-tension glaucoma [NTG]’) is highly prevalent in East Asia including Korea and Japan. We conducted exome chip analysis to identify low-frequency and rare variants associated with POAG from the primary cohort (309 POAG patients and 5,400 control, all Koreans). For replication, Korean (310 POAG patients and 5,612 controls) and Japanese (565 POAG patients and 1,104 controls) cohorts were further investigated by targeted genotyping. SNP rs116121322 in LRRC27 showed nominally significant association with POAG in the discovery cohort (OR = 29.85, P = 2E–06). This SNP was validated in the Korean replication cohort but only in the NTG subgroups (OR = 9.86, P = 0.007). Japanese replication cohort did not show significant association with POAG (P .00.44). However, the meta-analysis in the entire cohort revealed significant association of rs116121322 with POAG (ORcombined = 10.28, Pcombined = 1.4E–07). The LRRC27 protein expression was confirmed from human trabecular meshwork cells. For gene-based testing, METTL20 showed a significant association in POAG (Pcombined = 0.002) and in the subgroup of NTG (Pcombined = 0.02), whereas ZNF677 were significantly associated with only in the subgroup of high-tension glaucoma (Pcombined = 1.5E–06). Our findings may provide further genetic backgrounds into the pathogenesis of POAG, especially for the patients who have lower baseline intraocular pressures.
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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
| | - 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
| | - Yukihiro Shiga
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yong Ju Song
- Department of Ophthalmology, Chosun University College of Medicine, Gwangju, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Hospital, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Koji M Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.,Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan.,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - 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
| | - 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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31
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A Common Glaucoma-risk Variant of SIX6 Alters Retinal Nerve Fiber Layer and Optic Disc Measures in a European Population: The EPIC-Norfolk Eye Study. J Glaucoma 2019; 27:743-749. [PMID: 30005032 DOI: 10.1097/ijg.0000000000001026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE A common missense variant in the SIX6 gene (rs33912345) is strongly associated with primary open-angle glaucoma (POAG). We aimed to examine the association of rs33912345 with optic disc and retinal nerve fiber layer (RNFL) measures in a European population. METHODS We examined participants of the population-based EPIC-Norfolk Eye Study. Participants underwent confocal laser scanning tomography (Heidelberg Retina Tomograph II, HRT) to estimate optic disc rim area and vertical cup-disc ratio (VCDR). Scanning laser polarimetry (GDxVCC) was used to estimate average RNFL thickness. The mean of right and left eye values was considered for each participant. Genotyping was performed using the Affymetrix UK Biobank Axiom Array. Multivariable linear regression with the optic nerve head parameter as outcome variable and dosage of rs33912345 genotype as primary explanatory variable was used, adjusted for age, sex, disc area, axial length, and intraocular pressure. We further repeated analyses stratified into age tertiles. RESULTS In total, 5433 participants with HRT data and 3699 participants with GDxVCC data were included. Each "C" allele of rs33912345 was associated with a smaller rim area (-0.030 mm [95% CI -0.040, -0.020]; P=5.4×10), a larger VCDR (0.025 [95% CI 0.017, 0.033]; P=3.3×10) and a thinner RNFL (-0.39 μm [95% CI -0.62, -0.15]; P=0.001). The RNFL association was strongest in the oldest age tertile, whereas rim area and VCDR associations were strongest in the youngest and oldest age tertiles. CONCLUSIONS The protein-coding SIX6 variant rs33912345, previously associated with POAG, has a functional effect on glaucoma-associated optic nerve head traits in Europeans.
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32
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Choquet H, Wiggs JL, Khawaja AP. Clinical implications of recent advances in primary open-angle glaucoma genetics. Eye (Lond) 2019; 34:29-39. [PMID: 31645673 DOI: 10.1038/s41433-019-0632-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
Over the last decade, genetic studies, including genome-wide association studies (GWAS), have accelerated the discovery of genes and genomic regions contributing to primary open-angle glaucoma (POAG), a leading cause of irreversible vision loss. Here, we review the findings of genetic studies of POAG published in English prior to September 2019. In total, 74 genomic regions have been associated at a genome-wide level of significance with POAG susceptibility. Recent POAG GWAS provide not only insight into global and ethnic-specific genetic risk factors for POAG susceptibility across populations of diverse ancestry, but also important functional insights underlying biological mechanisms of glaucoma pathogenesis. In this review, we also summarize the genetic overlap between POAG, glaucoma endophenotypes, such as intraocular pressure and vertical cup-disc ratio (VCDR), and other eye disorders. We also discuss approaches recently developed to increase power for POAG locus discovery and to predict POAG risk. Finally, we discuss the recent development of POAG gene-based therapies and future strategies to treat glaucoma effectively. Understanding the genetic architecture of POAG is essential for an earlier diagnosis of this common eye disorder, predictive testing of at-risk patients, and design of gene-based targeted medical therapies none of which are currently available.
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Affiliation(s)
- Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, 94612, USA.
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
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33
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Alkhatib R, Abudhaim N, Al-Eitan L, Abdo N, Alqudah A, Aman H. Genetic Analysis Of ABCA1 Gene Of Primary Glaucoma In Jordanian Arab Population. APPLICATION OF CLINICAL GENETICS 2019; 12:181-189. [PMID: 31632126 PMCID: PMC6783111 DOI: 10.2147/tacg.s213818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/11/2019] [Indexed: 01/30/2023]
Abstract
Background Glaucoma is a neurodegenerative disease that leads to progressive loss of retinal ganglion cells, causing irreversible visual field defects. At the present time, glaucoma is clinically defined but the exact etiology is unknown. The aim of this study is to genotype rs2472493 and rs2487032 SNIPs within ABCA1 gene in 52 Jordanian Arab patients with primary glaucoma and 96 control subjects, and also to investigate the genetic association of these SNPs with primary glaucoma. Methods DNA was extracted from both patients and controls according to a well-established procedure. Then, DNA was amplified by PCR using specific primers for this gene. Analysis of polymorphisms was carried out by using DNA sequencing genotyping method. Results The results showed that the two SNPs (rs2472493 and rs2487032) located upstream of ABCA1 gene have no significant associations with primary glaucoma disorder (P > 0.05). Conclusion This study is the first of its kind to reveal no genetic association between ABCA1 gene and primary glaucoma disorder in Jordanian population of Arab descent.
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Affiliation(s)
- Rami Alkhatib
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Nada Abudhaim
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Laith Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Nour Abdo
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Asem Alqudah
- Department of Ophthalmology, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Hatem Aman
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
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34
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Lu SY, He ZZ, Xu JX, Yang C, Chen LJ, Gong B. Association of Polymorphisms at the SIX1-SIX6 Locus With Primary Open-Angle Glaucoma. ACTA ACUST UNITED AC 2019; 60:2914-2924. [PMID: 31284308 DOI: 10.1167/iovs.18-26489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zong Ze He
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jia Xin Xu
- School of Clinic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Chen Yang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
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35
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Xu J, Luo H, Yu M, Yang C, Shu Y, Gong B, Lin Y, Wang J. Association of polymorphism rs11656696 in GAS7 with primary open-Angle Glaucoma in a Chinese Population. Ophthalmic Genet 2019; 40:237-241. [PMID: 31269845 DOI: 10.1080/13816810.2019.1627465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: It has been shown that genetic factors play an important role in the pathogenesis of primary open-angle glaucoma (POAG). This study was conducted to investigate the association between the polymorphism rs11656696 located in the growth arrest-specific 7 gene (GAS7) and POAG. Methods: A cohort of 799 unrelated POAG patients and 799 unrelated control subjects was enrolled in this case-control association study. The polymorphism rs11656696 was genotyped using the SNaPshot method. The genotype and allele frequencies were evaluated using the χ2 tests. Results: The allele frequency distribution of rs11656696 in the GAS7 gene showed that there was significant difference between POAG cases and controls (P= .006448, OR = 0.82, 95%CI = (0.72-0.95). The minor "A" allele frequency of this polymorphism was 0.477 in the POAG cases, whereas it was 0.526 in controls, suggesting a protective effect for POAG. Significant associations were detected under the homozygous model (p = .006425, OR = 0.68, 95%CI = 0.51-0.90) and recessive model (p = .0003432, OR = 0.66, 95%CI = 0.52-0.84), indicating that subjects carrying rs11656696 AA genotype were less likely to suffer from POAG than those carrying AC/CC genotypes. Conclusion: This case-control association study showed that polymorphism rs11656696 in GAS7 is related to POAG and might be a protective factor against POAG.
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Affiliation(s)
- Jiaxin Xu
- a School of Clinic Medicine , Southwest Medical University , Luzhou , Sichuan , China
| | - Huanchao Luo
- b Department of Clinical Laboratory , Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Man Yu
- c Department of Ophthalmology , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Chen Yang
- d Department of Laboratory Medicine , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Yi Shu
- d Department of Laboratory Medicine , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Bo Gong
- d Department of Laboratory Medicine , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Yin Lin
- a School of Clinic Medicine , Southwest Medical University , Luzhou , Sichuan , China.,d Department of Laboratory Medicine , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
| | - Jin Wang
- d Department of Laboratory Medicine , Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China , Chengdu , Sichuan , China
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36
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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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37
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Taylor KD, Guo X, Zangwill LM, Liebmann JM, Girkin CA, Feldman RM, Dubiner H, Hai Y, Samuels BC, Panarelli JF, Mitchell JP, Al-Aswad LA, Park SC, Tello C, Cotliar J, Bansal R, Sidoti PA, Cioffi GA, Blumberg D, Ritch R, Bell NP, Blieden LS, Davis G, Medeiros FA, Das SK, Divers J, Langefeld CD, Palmer ND, Freedman BI, Bowden DW, Ng MCY, Ida Chen YD, Ayyagari R, Rotter JI, Weinreb RN. Genetic Architecture of Primary Open-Angle Glaucoma in Individuals of African Descent: The African Descent and Glaucoma Evaluation Study III. Ophthalmology 2019; 126:38-48. [PMID: 30352225 PMCID: PMC6309605 DOI: 10.1016/j.ophtha.2018.10.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/04/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE To find genetic contributions to glaucoma in African Americans. DESIGN Cross-sectional, case-control study. PARTICIPANTS One thousand eight hundred seventy-five primary open-angle glaucoma (POAG) patients and 1709 controls, self-identified as being of African descent (AD), from the African Descent and Glaucoma Evaluation Study (ADAGES) III and Wake Forest School of Medicine. METHODS MegaChip genotypes were imputed to Thousand Genomes data. Association of single nucleotide polymorphisms (SNPs) with POAG and advanced POAG was tested by linear mixed model correcting for relatedness and population stratification. Genetic risk scores were tested by receiver operator characteristic curves (ROC-AUCs). MAIN OUTCOME MEASURES Primary open-angle glaucoma defined by visual field loss without other nonocular conditions (n = 1875). Advanced POAG was defined by age-based mean deviation of visual field (n = 946). RESULTS Eighteen million two hundred eighty-one thousand nine hundred twenty SNPs met imputation quality of r2 > 0.7 and minor allele frequency > 0.005. Association of a novel locus, EN04, was observed for advanced POAG (rs185815146 β, 0.36; standard error, 0.065; P < 3×10-8). For POAG, an AD signal was observed at the 9p21 European descent (ED) POAG signal (rs79721419; P < 6.5×10-5) independent of the previously observed 9p21 ED signal (rs2383204; P < 2.3×10-5) by conditional analyses. An association with POAG in FNDC3B (rs111698934; P < 3.9×10-5) was observed, not in linkage disequilibrium (LD) with the previously reported ED SNP. Additional previously identified loci associated with POAG in persons of AD were: 8q22, AFAP1, and TMC01. An AUC of 0.62 was observed with an unweighted genetic risk score comprising 11 SNPs in candidate genes. Two additional risk scores were studied by using a penalized matrix decomposition with cross-validation; risk scores of 50 and 400 SNPs were identified with ROC of AUC = 0.74 and AUC = 0.94, respectively. CONCLUSIONS A novel association with advanced POAG in the EN04 locus was identified putatively in persons of AD. In addition to this finding, this genome-wide association study in POAG patients of AD contributes to POAG genetics by identification of novel signals in prior loci (9p21), as well as advancing the fine mapping of regions because of shorter average LD (FNDC3B). Although not useful without confirmation and clinical trials, the use of genetic risk scores demonstrated that considerable AD-specific genetic information remains in these data.
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Affiliation(s)
- Kent D Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Linda M Zangwill
- Department of Ophthalmology, Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, La Jolla, California
| | - Jeffrey M Liebmann
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Christopher A Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert M Feldman
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | | | - Yang Hai
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Brian C Samuels
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Joseph F Panarelli
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - John P Mitchell
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Lama A Al-Aswad
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Sung Chul Park
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Celso Tello
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Jeremy Cotliar
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Rajendra Bansal
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Paul A Sidoti
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - George A Cioffi
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Dana Blumberg
- Bernard and Shirlee Brown Glaucoma Research Laboratory, Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Nicholas P Bell
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Lauren S Blieden
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Garvin Davis
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Felipe A Medeiros
- Department of Ophthalmology, Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, La Jolla, California
| | - Swapan K Das
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jasmin Divers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Nicholette D Palmer
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina; Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Barry I Freedman
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina; Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina; Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Radha Ayyagari
- Department of Ophthalmology, Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, La Jolla, California
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, La Jolla, California.
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Association of the SIX6 locus with primary open angle glaucoma in southern Chinese and Japanese. Exp Eye Res 2018; 180:129-136. [PMID: 30586556 DOI: 10.1016/j.exer.2018.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/15/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
The purpose of the study was to evaluate the association profiles of the SIX6 locus with primary open-angle glaucoma (POAG) in southern Chinese and Japanese. In this study, we tested single marker and haplotype-based associations of 11 tagging single nucleotide polymorphisms (SNPs) covering the SIX6 locus with POAG in a Hong Kong Chinese cohort (N = 1402). A novel SNP (i.e., rs12436579) and two SNPs (i.e., rs33912345 and rs10483727) from previous genome-wide association studies were further tested in a Chinese cohort from Shantou (N = 888) and a Japanese cohort from Osaka (N = 463). Results from the three cohorts were meta-analysed using a random-effect model. We found rs12436579, which has not been previously reported, was associated with POAG in Hong Kong and Shantou Chinese (Pcombined = 4.3 × 10-5, OR = 0.72, I2 = 0). Additionally, we replicated the association of one known SNP, rs33912345 (Pcombined = 0.0061, OR = 0.69, I2 = 45%), with POAG in the Chinese cohorts but not in the Japanese cohort (P > 0.6). Another known SNP, rs10483727, was nominally associated with POAG in the two Chinese cohorts (Pcombined = 0.017, OR = 0.70, I2 = 53%). All these three SNPs were significantly associated with POAG when the three cohorts were combined in meta-analysis (Pcombined<0.005). Furthermore, two haplotypes, C-C (Pcombined = 1.13 × 10-5, OR = 1.41, I2 = 0) and A-A (Pcombined = 0.045, OR = 0.68, I2 = 70%), defined by rs33912345-rs12436579 were associated with POAG in Chinese but not in Japanese. In conclusion, this study confirmed the association between two GWAS SNPs in SIX6 (rs33912345 and rs10483727) and POAG. Also, a SNP, rs12436579, not associated with POAG before, was found to be associated with POAG in Chinese. Further studies are warranted to elucidate the role of this novel SNP in POAG.
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Restrepo NA, Laper SM, Farber-Eger E, Crawford DC. Local genetic ancestry in CDKN2B-AS1 is associated with primary open-angle glaucoma in an African American cohort extracted from de-identified electronic health records. BMC Med Genomics 2018; 11:70. [PMID: 30255811 PMCID: PMC6157155 DOI: 10.1186/s12920-018-0392-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Glaucoma is a leading cause of blindness in developed countries. Primary open-angle glaucoma (POAG), the most prevalent clinical subtype of glaucoma in the United States, affects African Americans at a higher rate compared with European Americans. Risk factors identified for POAG include increased age and family history, which coupled with heritability estimates, suggest this complex condition is associated with genetic and environmental factors. To date, several genome-wide studies have identified loci significantly associated with POAG risk, but most of these studies were performed in populations of European-descent. METHODS To identify population-specific and trans-population genetic associations for POAG, we genotyped 11,521 African Americans using the Illumina Metabochip as part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessing BioVU, the Vanderbilt University Medical Center's biorepository linked to de-identified electronic health records. Among this study population, we identified 138 cases of POAG and 1376 controls and performed Metabochip-wide tests of association. We also estimated local genetic ancestry at CDKN2B-AS1, a POAG-associated locus established in European-descent populations. RESULTS Overall, we did not identify significant single SNP-POAG associations after adjusting for multiple testing. We did, however, detect a significant association between POAG risk and local African genetic ancestry at CDKN2B-AS1, where on average cases were of 90% African descent compared with controls at 58% (p = 2 × 10- 6). CONCLUSIONS These data suggest that CDKN2B-AS1 is an important locus for POAG risk among African Americans, warranting further investigation to identify the variants underlying this association.
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Affiliation(s)
- Nicole A Restrepo
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA
| | | | - Eric Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA.
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A multiethnic genome-wide association study of primary open-angle glaucoma identifies novel risk loci. Nat Commun 2018; 9:2278. [PMID: 29891935 PMCID: PMC5995837 DOI: 10.1038/s41467-018-04555-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/23/2018] [Indexed: 01/18/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is a leading cause of irreversible vision loss, yet much of the genetic risk remains unaccounted for, especially in African-Americans who have a higher risk for developing POAG. We conduct a multiethnic genome-wide association study (GWAS) of POAG in the GERA cohort, with replication in the UK Biobank (UKB), and vice versa, GWAS in UKB with replication in GERA. We identify 24 loci (P < 5.0 × 10-8), including 14 novel, of which 9 replicate (near FMNL2, PDE7B, TMTC2, IKZF2, CADM2, DGKG, ANKH, EXOC2, and LMX1B). Functional studies support intraocular pressure-related influences of FMNL2 and LMX1B, with certain Lmx1b mutations causing high IOP and glaucoma resembling POAG in mice. The newly identified loci increase the proportion of variance explained in each GERA race/ethnicity group, with the largest gain in African-Americans (0.5-3.1%). A meta-analysis combining GERA and UKB identifies 24 additional loci. Our study provides important insights into glaucoma pathogenesis.
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Shiga Y, Akiyama M, Nishiguchi KM, Sato K, Shimozawa N, Takahashi A, Momozawa Y, Hirata M, Matsuda K, Yamaji T, Iwasaki M, Tsugane S, Oze I, Mikami H, Naito M, Wakai K, Yoshikawa M, Miyake M, Yamashiro K, Kashiwagi K, Iwata T, Mabuchi F, Takamoto M, Ozaki M, Kawase K, Aihara M, Araie M, Yamamoto T, Kiuchi Y, Nakamura M, Ikeda Y, Sonoda KH, Ishibashi T, Nitta K, Iwase A, Shirato S, Oka Y, Satoh M, Sasaki M, Fuse N, Suzuki Y, Cheng CY, Khor CC, Baskaran M, Perera S, Aung T, Vithana EN, Cooke Bailey JN, Kang JH, Pasquale LR, Haines JL, Wiggs JL, Burdon KP, Gharahkhani P, Hewitt AW, Mackey DA, MacGregor S, Craig JE, Allingham RR, Hauser M, Ashaye A, Budenz DL, Akafo S, Williams SEI, Kamatani Y, Nakazawa T, Kubo M. Genome-wide association study identifies seven novel susceptibility loci for primary open-angle glaucoma. Hum Mol Genet 2018; 27:1486-1496. [PMID: 29452408 PMCID: PMC6251544 DOI: 10.1093/hmg/ddy053] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/12/2022] Open
Abstract
Primary open-angle glaucoma (POAG) is the leading cause of irreversible blindness worldwide for which 15 disease-associated loci had been discovered. Among them, only 5 loci have been associated with POAG in Asians. We carried out a genome-wide association study and a replication study that included a total of 7378 POAG cases and 36 385 controls from a Japanese population. After combining the genome-wide association study and the two replication sets, we identified 11 POAG-associated loci, including 4 known (CDKN2B-AS1, ABCA1, SIX6 and AFAP1) and 7 novel loci (FNDC3B, ANKRD55-MAP3K1, LMX1B, LHPP, HMGA2, MEIS2 and LOXL1) at a genome-wide significance level (P < 5.0×10-8), bringing the total number of POAG-susceptibility loci to 22. The 7 novel variants were subsequently evaluated in a multiethnic population comprising non-Japanese East Asians (1008 cases, 591 controls), Europeans (5008 cases, 35 472 controls) and Africans (2341 cases, 2037 controls). The candidate genes located within the new loci were related to ocular development (LMX1B, HMGA2 and MAP3K1) and glaucoma-related phenotypes (FNDC3B, LMX1B and LOXL1). Pathway analysis suggested epidermal growth factor receptor signaling might be involved in POAG pathogenesis. Genetic correlation analysis revealed the relationships between POAG and systemic diseases, including type 2 diabetes and cardiovascular diseases. These results improve our understanding of the genetic factors that affect the risk of developing POAG and provide new insight into the genetic architecture of POAG in Asians.
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Affiliation(s)
- Yukihiro Shiga
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Nobuhiro Shimozawa
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Makoto Hirata
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koichi Matsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Munemitsu Yoshikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Ophthalmology, Otsu Red-Cross Hospital, Otsu, Japan
| | | | - Kenji Kashiwagi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, Tokyo Medical Center, National Hospital Organization, Tokyo, Japan
| | - Fumihiko Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | | | - Mineo Ozaki
- Ozaki Eye Hospital, Hyuga, Miyazaki, Japan
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazuhide Kawase
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Makoto Aihara
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan
| | - Makoto Araie
- Kanto Central Hospital of the Mutual Aid Association of Public School Teachers, Tokyo, Japan
| | - Tetsuya Yamamoto
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshiaki Kiuchi
- Department of Ophthalmology and Visual Sciences, Hiroshima University, Hiroshima, Japan
| | - Makoto Nakamura
- Division of Ophthalmology, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Nitta
- Fukuiken Saiseikai Hospital, Fukui, Japan
| | | | | | | | - Mamoru Satoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Miyagi, Japan
| | - Yoichi Suzuki
- Department of Education and Training, Tohoku Medical Megabank Organization, Miyagi, Japan
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Mani Baskaran
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Shamira Perera
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Melbourne, VIC, Australia
- Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, VIC, Australia
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | | | | | - Adeyinka Ashaye
- Department of Ophthalmology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina at Chapel Hill, USA
| | - Stephan Akafo
- University of Ghana School of Medicine and Dentistry, Ghana
| | - Susan E I Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, South Africa
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Cissé Y, Bai L, Meng T. LncRNAs in genetic basis of glaucoma. BMJ Open Ophthalmol 2018; 3:e000131. [PMID: 29963644 PMCID: PMC6020790 DOI: 10.1136/bmjophth-2017-000131] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/19/2018] [Accepted: 03/02/2018] [Indexed: 12/31/2022] Open
Abstract
Glaucoma is an umbrella term used to designate a heterogeneous group of ocular disorders characterised by progressive excavation of the optic disc, optic atrophy and gradual loss of the visual field caused by the slow death of retinal ganglion cells and their axons. Glaucoma can potentially lead to blindness if left untreated. It usually starts from the periphery and progresses gradually toward the centre of the visual field. Vision loss caused by glaucoma is irreversible and causes a heavy burden on affected families and society, therefore the importance of early diagnosis and prevention should be emphasised. Genetic factors appear to play a role in glaucoma pathogenesis; it has been shown that individuals with a positive family history are at a greater risk because they are more likely predisposed be affected. Notable advances have been recorded in the past decade concerning the genetic and environmental factors likely to contribute or cause glaucoma with the discovery of multiple glaucoma-associated genes and genetic loci. Thorough investigations by a handful of studies on the function of long non-coding RNAs discovered that, although lacking protein-coding potential, lncRNAs can still participate in the regulation of gene expression at various levels, thus their possible implication in different disease aetiologies. In this review, we focus on the lncRNAs characteristics and its regulation, and summarise these results from separate, independent, glaucoma-related studies in addition to discussing possible pathways by which lncRNAs might contribute to glaucoma.
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Affiliation(s)
- Yacouba Cissé
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lang Bai
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Meng
- Department of Ophthalmology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Wang Z, Zhang Q, Zhang W, Lin JR, Cai Y, Mitra J, Zhang ZD. HEDD: Human Enhancer Disease Database. Nucleic Acids Res 2018; 46:D113-D120. [PMID: 29077884 PMCID: PMC5753236 DOI: 10.1093/nar/gkx988] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections. In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases. HEDD currently provides comprehensive genomic information for ∼2.8 million human enhancers identified by ENCODE, FANTOM5 and RoadMap with disease association scores based on enhancer-gene and gene-disease connections. It also provides Web-based analytical tools to visualize enhancer networks and score enhancers given a set of selected genes in a specific gene network. HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php.
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Affiliation(s)
- Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wen Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ying Cai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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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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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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Shiga Y, Nishiguchi KM, Kawai Y, Kojima K, Sato K, Fujita K, Takahashi M, Omodaka K, Araie M, Kashiwagi K, Aihara M, Iwata T, Mabuchi F, Takamoto M, Ozaki M, Kawase K, Fuse N, Yamamoto M, Yasuda J, Nagasaki M, Nakazawa T. Genetic analysis of Japanese primary open-angle glaucoma patients and clinical characterization of risk alleles near CDKN2B-AS1, SIX6 and GAS7. PLoS One 2017; 12:e0186678. [PMID: 29261660 PMCID: PMC5737967 DOI: 10.1371/journal.pone.0186678] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022] Open
Abstract
PURPOSE To test the genetic association between Japanese patients with primary open-angle glaucoma (POAG) and the previously reported POAG susceptibility loci and to perform genotype-phenotype analysis. METHODS Genetic associations for 27 SNPs from 16 loci previously linked to POAG were assessed using genome-wide SNP data of the primary cohort (565 Japanese POAG patients and 1,104 controls). Reproducibility of the assessment was tested in 607 POAG cases and 455 controls (second cohort) with a targeted genotyping approach. For POAG-associated variants, a genotype-phenotype correlation study (additive, dominant, recessive model) was performed using the objective clinical data derived from 598 eyes of 598 POAG patients. RESULTS Among 27 SNPs from 16 loci previously linked to POAG, genotypes for total of 20 SNPs in 13 loci were available for targeted association study. Among 8 SNPs in 3 loci that showed at least nominal association (P < 5.00E-02) in the primary cohort, a representative SNP for each loci (rs2157719 for CDKN2B-AS1, rs33912345 for SIX6, and rs9913911 for GAS7) were selected. For these SNPs the association was found significant in both the second cohort analysis and meta-analysis. The genotype-phenotype analysis revealed significant correlations between CDKN2B-AS1 (rs2157719) and decreased intraocular pressure (β = -6.89 mmHg, P = 1.70E-04; dominant model) after multiple corrections. In addition, nominal correlation was observed between CDKN2B-AS1 (rs2157719) and optic nerve head blood flow (β = -0.54 and -0.67 arbitrary units (AU), P = 2.00E-02 and 1.39E-02), between SIX6 (rs33912345) and decreased total peripapillary retinal nerve fiber layer thickness (β = -2.16 and -2.82 μm, P = 4.68E-02 and 2.40E-02, additive and recessive model, respectively) and increased optic nerve head blood flow (β = 0.44 AU, P = 2.20E-02; additive model) and between GAS7 (rs9913911) and increased cup volume (β = 0.03 mm3, P = 4.60E-02) and mean cup depth (β = 0.03 mm3, P = 4.11E-02; additive model) and decreased pattern standard deviation (β = -0.87 dB, P = 2.44E-02; dominant model). CONCLUSION The association between SNPs near GAS7 and POAG was found in Japanese patients for the first time. Clinical characterization of the risk variants is an important step toward understanding the pathology of the disease and optimizing treatment of patients with POAG.
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Affiliation(s)
- Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Koji M. Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yosuke Kawai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Miyagi, Japan
- Department of Cohort Genome Information Analysis, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Ophthalmic imaging and information analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kosuke Fujita
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Mai Takahashi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazuko Omodaka
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Ophthalmic imaging and information analytics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Makoto Araie
- Kanto Central Hospital of The Mutual Aid Association of Public School Teachers, Tokyo, Japan
| | - Kenji Kashiwagi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Makoto Aihara
- Department of Ophthalmology, University of Tokyo School of Medicine, Tokyo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Fumihiko Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mitsuko Takamoto
- Department of Ophthalmology, University of Tokyo School of Medicine, Tokyo, Japan
| | | | | | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Medical Biochemistry, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Miyagi, Japan
- Department of Cohort Genome Information Analysis, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
- Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
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Expression QTL analysis of glaucoma endophenotypes in the Norfolk Island isolate provides evidence that immune-related genes are associated with optic disc size. J Hum Genet 2017; 63:83-87. [PMID: 29215094 DOI: 10.1038/s10038-017-0374-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022]
Abstract
Primary open-angle glaucoma (POAG) is influenced by both genetic and environmental factors. Despite significant progress in identifying genetic variants associated with POAG, there remains a substantial amount of unexplained heritability. Study design features that may enhance knowledge of the genetic architecture include focusing on multiple quantitative traits related to ocular disorders (i.e. endophenotypes), targeting genetic variants that directly influence gene expression (i.e. cis-eQTLs) and utilising genetically isolated populations to reduce genetic and environmental noise and thus enhance association signals. In this study we performed heritability and blood-based eQTL association analysis of five key POAG endophenotypes in 330 individuals from the Norfolk Island (NI) isolate. Results showed evidence of heritability for all five traits, with H2 estimates ranging from 0.35 for intraocular pressure (IOP) to 0.82 for central corneal thickness (CCT) (P < 0.05). The primary finding was for BTN3A2, whereby both cis-SNP and transcript were significantly associated with disc size within a conditional regression model. Specifically, this model included rs853676 (β = 0.23,P = 0.008) and transcript (β = 0.23, P = 0.03). We also observed a cis-SNP association between optic disc size and LPCAT2 independent of transcript (P = 0.0004). These genes have specific functions in immune system pathways and suggest a role for an inherited immune component of POAG risk. This study also demonstrates an alternate approach to understanding the functional genetic basis of POAG and ocular health more generally.
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Wang J, Yu L, Zhang D, Wang S, Zhao J. Analysis of gene expression in intracranial aneurysms. Chin Neurosurg J 2017. [DOI: 10.1186/s41016-017-0098-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Restrepo NA, Cooke Bailey JN. Primary Open-Angle Glaucoma Genetics in African Americans. CURRENT GENETIC MEDICINE REPORTS 2017; 5:167-174. [PMID: 29276656 PMCID: PMC5739069 DOI: 10.1007/s40142-017-0131-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Individuals of African descent are at highest risk for developing primary open-angle glaucoma (POAG), a devastating disease and major contributor of blindness worldwide. Currently, there is a large dearth of knowledge in this area despite a critical need for better understanding the underlying genetic and environmental factors afflicting this population. Here we highlight the current literature exploring the genetics of POAG in African Americans. RECENT FINDINGS Current studies have yet to replicate European POAG index variants (i.e. CDKN2B-AS1 and SIX1/SIX6) in African Americans or to definitely exclude that these loci contribute to risk in African descent populations. Recent studies have evaluated clinical features that may account for some differences in POAG risk between African Americans and European Americans. SUMMARY In summary, little headway has been made in elucidating the genetics of primary open-angle glaucoma in African Americans and other individuals of African descent.
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Affiliation(s)
- Nicole A. Restrepo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
| | - Jessica N. Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
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Kondkar AA, Azad TA, Almobarak FA, Kalantan H, Sultan T, Alsabaani NA, Al-Obeidan SA, Abu-Amero KK. Polymorphism rs10483727 in the SIX1/SIX6 Gene Locus Is a Risk Factor for Primary Open Angle Glaucoma in a Saudi Cohort. Genet Test Mol Biomarkers 2017; 22:74-78. [PMID: 29190129 DOI: 10.1089/gtmb.2017.0159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIMS Variant rs10483727 in the SIX1/SIX6 locus has been significantly associated with primary open angle glaucoma (POAG) in multiple ethnic groups. We conducted a case-control study to investigate the association between this variant and POAG in a Saudi cohort. MATERIALS AND METHODS Polymorphism rs10483727 was genotyped by using a TaqMan® assay in 186 subjects comprising 92 unrelated POAG cases and 94 controls all of Saudi origin. RESULTS The "C" allele frequency was 0.33 and 0.45 among POAG cases and controls, respectively (odds ratio [OR] = 0.58, 95% confidence interval [CI] = 0.38-0.89; p = 0.013), suggesting a protective effect; and the "T" allele was associated with increased susceptibility to POAG (OR = 1.7, 95% CI = 1.11-2.58; p = 0.013). Genotype distribution was also significantly associated with POAG (χ2 = 6.41, df = 2, p = 0.041). Endophenotype traits such as intraocular pressure and cup/disk ratio did not show any significant genotype distribution in POAG cases. A binary logistic regression analysis used to evaluate the effects of age, gender, and genotype on the likelihood of having POAG showed that genotype distribution (p = 0.012) significantly affected the disease outcome as compared with age (p = 0.055) and sex (p = 0.432). CONCLUSION The "T" allele of the rs10483727 polymorphism is an independent significant risk factor for POAG in the Saudi population.
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Affiliation(s)
- Altaf A Kondkar
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Taif A Azad
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Faisal A Almobarak
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Hatem Kalantan
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Tahira Sultan
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Nasser A Alsabaani
- 2 Ophthalmology Department, College of Medicine, King Khalid University , Abha, Saudi Arabia
| | - Saleh A Al-Obeidan
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Khaled K Abu-Amero
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia .,3 Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago , Chicago, Illinois
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