1
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Polygenic Risk Score Impact on Susceptibility to Age-Related Macular Degeneration in Polish Patients. J Clin Med 2022; 12:jcm12010295. [PMID: 36615095 PMCID: PMC9821027 DOI: 10.3390/jcm12010295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
Age-related macular degeneration (AMD) is a common retina degenerative disease with a complex genetic and environmental background. This study aimed to determine the polygenic risk score (PRS) stratification between the AMD case and control patients. The PRS model was established on the targeted sequencing data of a cohort of 471 patients diagnosed with AMD and 167 healthy controls without symptoms of retinal degeneration. The highest predictive value to the target dataset was achieved for a 22-variant model with a p-value lower than threshold PT = 0.0123. The median PRS for cases was higher by 1.1 than for control samples (95% CI: (−1.19; −0.85)). The patients in the highest quantile had a significantly higher relative risk of developing AMD than those in the lowest reference quantile (OR = 35.13, 95% CI: (7.9; 156.1), p < 0.001). The diagnostic ability was investigated using ROC analysis with AUC = 0.76 (95% CI: (0.72; 0.80)). The polygenic susceptibility to AMD may be the starting point to expand AMD diagnostics based on rare highly penetrant variants and investigate associations with disease progression and treatment response in Polish patients in future studies.
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2
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Waksmunski AR, Kinzy TG, Cruz LA, Nealon CL, Halladay CW, Simpson P, Canania RL, Anthony SA, Roncone DP, Sawicki Rogers L, Leber JN, Dougherty JM, Greenberg PB, Sullivan JM, Wu WC, Iyengar SK, Crawford DC, Peachey NS, Cooke Bailey JN. Glaucoma Genetic Risk Scores in the Million Veteran Program. Ophthalmology 2022; 129:1263-1274. [PMID: 35718050 PMCID: PMC9997524 DOI: 10.1016/j.ophtha.2022.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) is a degenerative eye disease for which early treatment is critical to mitigate visual impairment and irreversible blindness. POAG-associated loci individually confer incremental risk. Genetic risk score(s) (GRS) could enable POAG risk stratification. Despite significantly higher POAG burden among individuals of African ancestry (AFR), GRS are limited in this population. A recent large-scale, multi-ancestry meta-analysis identified 127 POAG-associated loci and calculated cross-ancestry and ancestry-specific effect estimates, including in European ancestry (EUR) and AFR individuals. We assessed the utility of the 127-variant GRS for POAG risk stratification in EUR and AFR Veterans in the Million Veteran Program (MVP). We also explored the association between GRS and documented invasive glaucoma surgery (IGS). DESIGN Cross-sectional study. PARTICIPANTS MVP Veterans with imputed genetic data, including 5830 POAG cases (445 with IGS documented in the electronic health record) and 64 476 controls. METHODS We tested unweighted and weighted GRS of 127 published risk variants in EUR (3382 cases and 58 811 controls) and AFR (2448 cases and 5665 controls) Veterans in the MVP. Weighted GRS were calculated using effect estimates from the most recently published report of cross-ancestry and ancestry-specific meta-analyses. We also evaluated GRS in POAG cases with documented IGS. MAIN OUTCOME MEASURES Performance of 127-variant GRS in EUR and AFR Veterans for POAG risk stratification and association with documented IGS. RESULTS GRS were significantly associated with POAG (P < 5 × 10-5) in both groups; a higher proportion of EUR compared with AFR were consistently categorized in the top GRS decile (21.9%-23.6% and 12.9%-14.5%, respectively). Only GRS weighted by ancestry-specific effect estimates were associated with IGS documentation in AFR cases; all GRS types were associated with IGS in EUR cases. CONCLUSIONS Varied performance of the GRS for POAG risk stratification and documented IGS association in EUR and AFR Veterans highlights (1) the complex risk architecture of POAG, (2) the importance of diverse representation in genomics studies that inform GRS construction and evaluation, and (3) the necessity of expanding diverse POAG-related genomic data so that GRS can equitably aid in screening individuals at high risk of POAG and who may require more aggressive treatment.
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Affiliation(s)
- Andrea R Waksmunski
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Tyler G Kinzy
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio; Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - Lauren A Cruz
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Cari L Nealon
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - Christopher W Halladay
- Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, Rhode Island
| | - Piana Simpson
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | | | - Scott A Anthony
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - David P Roncone
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - Lea Sawicki Rogers
- Ophthalmology Section, VA Western NY Healthcare System, Buffalo, New York
| | - Jenna N Leber
- Ophthalmology Section, VA Western NY Healthcare System, Buffalo, New York
| | | | - Paul B Greenberg
- Ophthalmology Section, Providence VA Medical Center, Providence, Rhode Island; Division of Ophthalmology, Alpert Medical School, Brown University, Providence, Rhode Island
| | - Jack M Sullivan
- Ophthalmology Section, VA Western NY Healthcare System, Buffalo, New York; Research Service, VA Western NY Healthcare System, Buffalo, New York
| | - Wen-Chih Wu
- Cardiology Section, Medical Service, Providence VA Medical Center, Providence, Rhode Island
| | - Sudha K Iyengar
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio; Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio; Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio
| | - Neal S Peachey
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio; Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Jessica N Cooke Bailey
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio; Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio.
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3
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Pauly D, Agarwal D, Dana N, Schäfer N, Biber J, Wunderlich KA, Jabri Y, Straub T, Zhang NR, Gautam AK, Weber BHF, Hauck SM, Kim M, Curcio CA, Stambolian D, Li M, Grosche A. Cell-Type-Specific Complement Expression in the Healthy and Diseased Retina. Cell Rep 2019; 29:2835-2848.e4. [PMID: 31775049 PMCID: PMC6911814 DOI: 10.1016/j.celrep.2019.10.084] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Complement dysregulation is a feature of many retinal diseases, yet mechanistic understanding at the cellular level is limited. Given this knowledge gap about which retinal cells express complement, we performed single-cell RNA sequencing on ~92,000 mouse retinal cells and validated our results in five major purified retinal cell types. We found evidence for a distributed cell-type-specific complement expression across 11 cell types. Notably, Müller cells are the major contributor of complement activators c1s, c3, c4, and cfb. Retinal pigment epithelium (RPE) mainly expresses cfh and the terminal complement components, whereas cfi and cfp transcripts are most abundant in neurons. Aging enhances c1s, cfb, cfp, and cfi expression, while cfh expression decreases. Transient retinal ischemia increases complement expression in microglia, Müller cells, and RPE. In summary, we report a unique complement expression signature for murine retinal cell types suggesting a well-orchestrated regulation of local complement expression in the retinal microenvironment. Overshooting complement activity contributes to retinal degeneration. Pauly et al. demonstrate a distinct complement expression profile of retinal cell types that changes with aging and during retinal degeneration. This prompts the intriguing concept of a local retinal complement activation possibly independent of the systemic components typically produced by the liver.
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Affiliation(s)
- Diana Pauly
- Experimental Ophthalmology, University Hospital Regensburg, Regensburg 93053, Germany.
| | - Divyansh Agarwal
- Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas Dana
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole Schäfer
- Experimental Ophthalmology, University Hospital Regensburg, Regensburg 93053, Germany
| | - Josef Biber
- Department of Physiological Genomics, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany
| | - Kirsten A Wunderlich
- Department of Physiological Genomics, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany
| | - Yassin Jabri
- Experimental Ophthalmology, University Hospital Regensburg, Regensburg 93053, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Avneesh K Gautam
- Department of Medicine, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg 93053, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Research Center for Environmental Health (GmbH), Munich 80939, Germany
| | - Mijin Kim
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine A Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL 35294-0019, USA
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Antje Grosche
- Department of Physiological Genomics, Biomedical Center, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany.
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4
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Akhter MS, Singh S, Yadegari H, Ivaskevicius V, Oldenburg J, Biswas A. Exploring the structural similarity yet functional distinction between coagulation factor XIII-B and complement factor H sushi domains. J Thromb Thrombolysis 2019; 48:95-102. [PMID: 30915671 DOI: 10.1007/s11239-019-01841-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coagulation factor XIII (FXIII) covalently crosslinks pre-formed fibrin clots preventing their premature fibrinolysis. In plasma, FXIII circulates as a zymogenic heterotetramer composed of catalytic FXIII-A subunits, and carrier/regulatory FXIII-B subunits. FXIII-A is a well characterized component of this complex, and has been associated with several pleiotropic roles outside coagulation as well. In comparison only protective/regulatory roles towards the FXIII-A subunit have been identified for FXIII-B. Strong homology between FXIII-B and complement regulator Complement factor H suggests a putative role of FXIII-B in complement activation. In the current study we have analyzed the similarities and yet functional divergence of these two proteins using in silico sequence alignment and structural analysis. We have evaluated complement activation post reconstitution of FXIII components into FXIII deficient and CFH deficient plasma. We have also transiently expressed FXIII-B in SH-SY5Y cell lines and evaluated its effect on the endogenous complement activation. Our investigations show no effect of FXIII-B subunit on the rate of complement activation. Therefore we conclude that at a physiological level, FXIII-B subunit plays no role in the complement system, although a vestigial function in altered pathological states might still exist.
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Affiliation(s)
- Mohammad Suhail Akhter
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany
- College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sneha Singh
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany
| | - Hamideh Yadegari
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany
| | - Vytautas Ivaskevicius
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, Sigmund Freud Str. 25, 53127, Bonn, Germany.
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5
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Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Lloyd KCK, Murphy CJ, Moshiri A. Identification of genes required for eye development by high-throughput screening of mouse knockouts. Commun Biol 2018; 1:236. [PMID: 30588515 PMCID: PMC6303268 DOI: 10.1038/s42003-018-0226-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from the International Mouse Phenotyping Consortium, a large-scale functional genetic screen with the goal of generating and phenotyping a null mutant for every mouse gene. Of 4364 genes evaluated, 347 were identified to influence ocular phenotypes, 75% of which are entirely novel in ocular pathology. This discovery greatly increases the current number of genes known to contribute to ophthalmic disease, and it is likely that many of the genes will subsequently prove to be important in human ocular development and disease. Bret Moore et al. from the International Mouse Phenotyping Consortium report the identification of 347 mouse genes that influence ocular phenotypes when knocked out. 75% of the identified genes have not previously been associated with any ocular pathology.
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Affiliation(s)
- Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lionel Sebbag
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Sydney G Edwards
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Ann Cooper
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ewan Straiton
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Christopher Reilly
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Stephen M Griffey
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lynette Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - David Clary
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Michel J Roux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Hamid Meziane
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Celeste Owen
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Mohammed Eskandarian
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan J Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vivek Philip
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Sharon Clementson-Mobbs
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Russell Joynson
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | | | | | - Damian Smedley
- Clinical Pharmacology, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J K Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 08826, South Korea
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, I-00015, Monterotondo Scalo, Italy
| | - Mark Moore
- International Mouse Phenotyping Consortium, San Anselmo, CA, 94960, USA
| | | | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | | | - Mark P Krebs
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA. .,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
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6
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Benson MD, Khor CC, Gage PJ, Lehmann OJ. A targeted approach to genome-wide studies reveals new genetic associations with central corneal thickness. Mol Vis 2017; 23:952-962. [PMID: 29296075 PMCID: PMC5741379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/13/2017] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To evaluate the ability of a targeted genome-wide association study (GWAS) to identify genes associated with central corneal thickness (CCT). METHODS A targeted GWAS was used to investigate whether ten candidate genes with known roles in corneal development were associated with CCT in two Singaporean populations. The single nucleotide polymorphisms (SNPs) within a 500 kb interval encompassing each candidate were analyzed, and in light of the resulting data, members of the Wnt pathway were subsequently screened using similar methodology. RESULTS Variants within the 500 kb interval encompassing three candidate genes, DKK1 (rs1896368, p=1.32×10-3), DKK2 (rs17510449, p=7.34×10-4), and FOXO1 (rs7326616, p=1.56×10-4 and rs4943785, p=1.19×10-3), were statistically significantly associated with CCT in the Singapore Indian population. DKK2 was statistically significantly associated with CCT in a separate Singapore Malaysian population (rs10015200, p=2.26×10-3). Analysis of Wnt signaling pathway genes in each population demonstrated that TCF7L2 (rs3814573, p=1.18×10-3), RYK (rs6763231, p=1.12×10-3 and rs4854785, p=1.11×10-3), and FZD8 (rs640827, p=5.17×10-4) were statistically significantly associated with CCT. CONCLUSIONS The targeted GWAS identified four genes (DKK1, DKK2, RYK, and FZD8) with novel associations with CCT and confirmed known associations with two genes, FOXO1 and TCF7L2. All six participate in the Wnt pathway, supporting a broader role for Wnt signaling in regulating the thickness of the cornea. In parallel, this study demonstrated that a hypothesis-driven candidate gene approach can identify associations in existing GWAS data sets.
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Affiliation(s)
- Matthew D. Benson
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, Canada
| | | | - Philip J. Gage
- Department of Ophthalmology and Visual Science, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Ordan J. Lehmann
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, Canada,Department of Medical Genetics, University of Alberta, Edmonton, Canada
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Ghorbanpour E, Pasalar P, Yazdani S, Moazzeni H, Elahi E. FMNL2 with Functions Related to the Cytoskeleton is Partially Regulated by PAX6. J Ophthalmic Vis Res 2017; 12:407-412. [PMID: 29090051 PMCID: PMC5644408 DOI: 10.4103/jovr.jovr_8_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Purpose: We aimed to assess whether the transcription factor PAX6 affects transcription of FMNL2. PAX6 is a transcription factor with significant roles in development of the eye and eye-related functions. FMNL2 encodes a member of the formin family of proteins and has roles in polymerization of actin and features of the cytoskeleton. The state of the cytoskeleton affects the flow of aqueous humor, disruption of which is a cornerstone of glaucoma pathology. Methods: Initially, bioinformatics were used extensively to identify FMNL2 as an appropriate candidate gene for possible targeting by PAX6. Subsequently, direct targeting of the promoter of FMNL2 by PAX6 was tested using the dual luciferase assay. The experiment was performed by cloning a promoter region of FMNL2 that contains PAX6 binding sitesupstream of a firefly luciferase gene and comparison of expression of luciferase in the presence and absence of PAX6 expression vectors in the HEK293T cell line. The effect of PAX6 on endogenous expression of FMNL2 in primary trabecular meshwork (TM) cells was assessed by real-time polymerase chain reaction. Results: Dual luciferase assays in HEK293T cells clearly demonstrated that PAX6 directly affects the FMNL2 promoter to increase expression of downstream sequences. However, overexpression of PAX6 in TM cells caused mild but statistically significant downregulation of endogenous FMNL2 as assessed by real-time polymerase chain reaction. Conclusion: It is concluded that PAX6 can indeed directly affect transcription of FMNL2. However, regulation of FMNL2 expression in TM cells is complicated and not limited to the direct effects of PAX6.
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Affiliation(s)
- Elham Ghorbanpour
- Department of Medical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvin Pasalar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahin Yazdani
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Moazzeni
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elahe Elahi
- Department of Cell and Molecular Biology, School of Biology, University College of Science, University of Tehran, Tehran, Iran.,Department of Biotechnology, University College of Science, University of Tehran, Tehran, Iran
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Fini ME, Schwartz SG, Gao X, Jeong S, Patel N, Itakura T, Price MO, Price FW, Varma R, Stamer WD. Steroid-induced ocular hypertension/glaucoma: Focus on pharmacogenomics and implications for precision medicine. Prog Retin Eye Res 2017; 56:58-83. [PMID: 27666015 PMCID: PMC5237612 DOI: 10.1016/j.preteyeres.2016.09.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 02/06/2023]
Abstract
Elevation of intraocular pressure (IOP) due to therapeutic use of glucocorticoids is called steroid-induced ocular hypertension (SIOH); this can lead to steroid-induced glaucoma (SIG). Glucocorticoids initiate signaling cascades ultimately affecting expression of hundreds of genes; this provides the potential for a highly personalized pharmacological response. Studies attempting to define genetic risk factors were undertaken early in the history of glucocorticoid use, however scientific tools available at that time were limited and progress stalled. In contrast, significant advances were made over the ensuing years in defining disease pathophysiology. As the genomics age emerged, it appeared the time was right to renew investigation into genetics. Pharmacogenomics is an unbiased discovery approach, not requiring an underlying hypothesis, and provides a way to pinpoint clinically significant genes and pathways that could not have been discovered any other way. Results of the first genome-wide association study to identify polymorphisms associated with SIOH, and follow-up on two novel genes linked to the disorder, GPR158 and HCG22, is discussed in the second half of the article. However, knowledge of genetic variants determining response to steroids in the eye also has value in its own right as a predictive and diagnostic tool. This article concludes with a discussion of how the Precision Medicine Initiative®, announced by U.S. President Obama in his 2015 State of the Union address, is beginning to touch the practice of ophthalmology. It is argued that SIOH/SIG may provide one of the next opportunities for effective application of precision medicine.
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Affiliation(s)
- M Elizabeth Fini
- USC Institute for Genetic Medicine and Department of Cell & Neurobiology, Keck School of Medicine of USC, University of Southern California, 2250 Alcatraz St., Suite 240, Los Angeles, CA, 90089, USA.
| | - Stephen G Schwartz
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 3880 Tamiami Trail North, Naples, FL, 34103, USA.
| | - Xiaoyi Gao
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, 1905 W Taylor St., Suite 235, Chicago, IL, 60612, USA.
| | - Shinwu Jeong
- USC Institute for Genetic Medicine, USC Roski Eye Institute and Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California, 2250 Alcatraz St., Suite 240, Los Angeles, CA, 90089, USA.
| | - Nitin Patel
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, 2250 Alcatraz St., Suite 240, Los Angeles, CA, 90089, USA.
| | - Tatsuo Itakura
- USC Institute for Genetic Medicine, Keck School of Medicine of USC, University of Southern California, 2250 Alcatraz St., Suite 240, Los Angeles, CA, 90089, USA.
| | - Marianne O Price
- Cornea Research Foundation of America, 9002 North Meridian Street, Indianapolis, IN, 46260, USA.
| | - Francis W Price
- Price Vision Group, 9002 North Meridian Street, Indianapolis, IN, 46260, USA.
| | - Rohit Varma
- Office of the Dean, USC Roski Eye Institute and Department of Ophthalmology, Keck School of Medicine of USC, University of Southern California, 1975 Zonal Ave., KAM 500, Los Angeles, CA, 90089, USA.
| | - W Daniel Stamer
- Department of Ophthalmology and Department of Biomedical Engineering, Duke University, AERI Room 4008, 2351 Erwin Rd, Durham, NC, 27705, USA.
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Ethnicity and Deprivation are Associated With Blindness Among Adults With Primary Glaucoma in Nigeria: Results From the Nigeria National Blindness and Visual Impairment Survey. J Glaucoma 2016; 25:e861-e872. [PMID: 27479370 DOI: 10.1097/ijg.0000000000000487] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE We explored the risk factors for glaucoma blindness among adults aged 40 years and above with primary glaucoma in Nigeria. PARTICIPANTS AND METHODS A total of 13,591 participants aged 40 years and above were examined in the Nigeria Blindness Survey; 682 (5.02%; 95 CI, 4.60%-5.47%) had glaucoma by ISGEO's criteria. This was a case-control study (n=890 eyes of 629 persons): glaucoma blind persons were cases and glaucoma not-blind were controls. Education and occupation were used to determine socioeconomic status scores, which were divided into 3 tertiles (affluent, medium, deprived). We assessed sociodemographic, biophysical, and ocular factors by logistic regression analysis for association with glaucoma blindness. Multinomial regression analysis was also performed with nonglaucoma as the reference category. RESULTS A total of 119/629 (18.9%; 95% CI, 15.9%-22.4%) persons were blind in both eyes; 510 were controls. There was interethnic variation in odds of blindness; age, male sex, socioeconomic status, prior diagnosis of glaucoma, hypertension, intraocular pressure, and lens opacity were associated with glaucoma blindness. Axial length, mean ocular perfusion pressure, and angle-closure glaucoma were associated with blind glaucoma eyes. In multivariate analysis, Igbo ethnicity (OR=2.79; 95% CI, 1.03-7.57) had higher risk as was being male (OR=4.59; 95% CI, 1.73-12.16) and unmarried (OR=2.50; 95% CI, 1.03-6.07). Deprivation (OR=3.57; 95% CI, 1.46-8.72), prior glaucoma diagnosis (OR=5.89; 95% CI, 1.79-19.40), and intraocular pressure (OR=1.07; 95% CI, 1.04-1.09) were also independent risk factors for glaucoma blindness. CONCLUSION Approximately 1 in 5 people with primary glaucoma were blind. Male sex, ethnicity and deprivation were strongly associated with blindness. Services for glaucoma need to improve in Nigeria, focusing on poor communities and men.
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Abstract
Genes carrying mutations associated with genetic diseases are present in all human cells; yet, clinical manifestations of genetic diseases are usually highly tissue-specific. Although some disease genes are expressed only in selected tissues, the expression patterns of disease genes alone cannot explain the observed tissue specificity of human diseases. Here we hypothesize that for a disease to manifest itself in a particular tissue, a whole functional subnetwork of genes (disease module) needs to be expressed in that tissue. Driven by this hypothesis, we conducted a systematic study of the expression patterns of disease genes within the human interactome. We find that genes expressed in a specific tissue tend to be localized in the same neighborhood of the interactome. By contrast, genes expressed in different tissues are segregated in distinct network neighborhoods. Most important, we show that it is the integrity and the completeness of the expression of the disease module that determines disease manifestation in selected tissues. This approach allows us to construct a disease-tissue network that confirms known and predicts unexpected disease-tissue associations.
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Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases. PLoS One 2016; 11:e0156252. [PMID: 27243976 PMCID: PMC4887111 DOI: 10.1371/journal.pone.0156252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 05/11/2016] [Indexed: 02/08/2023] Open
Abstract
Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulations-based structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis, and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas.
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12
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Liu H, Yang ZK, Li Y, Zhang WJ, Wang YT, Duan XC. ABCB1 variants confer susceptibility to primary open-angle glaucoma and predict individual differences to latanoprost treatment. Biomed Pharmacother 2016; 80:115-120. [DOI: 10.1016/j.biopha.2016.02.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 02/24/2016] [Accepted: 02/24/2016] [Indexed: 01/06/2023] Open
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13
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Williams PA, Tribble JR, Pepper KW, Cross SD, Morgan BP, Morgan JE, John SWM, Howell GR. Inhibition of the classical pathway of the complement cascade prevents early dendritic and synaptic degeneration in glaucoma. Mol Neurodegener 2016; 11:26. [PMID: 27048300 PMCID: PMC4822272 DOI: 10.1186/s13024-016-0091-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022] Open
Abstract
Background Glaucoma is a complex, multifactorial disease characterised by the loss of retinal ganglion cells and their axons leading to a decrease in visual function. The earliest events that damage retinal ganglion cells in glaucoma are currently unknown. Retinal ganglion cell death appears to be compartmentalised, with soma, dendrite and axon changes potentially occurring through different mechanisms. There is mounting evidence from other neurodegenerative diseases suggesting that neuronal dendrites undergo a prolonged period of atrophy, including the pruning of synapses, prior to cell loss. In addition, recent evidence has shown the role of the complement cascade in synaptic pruning in glaucoma and other diseases. Results Using a genetic (DBA/2J mouse) and an inducible (rat microbead) model of glaucoma we first demonstrate that there is loss of retinal ganglion cell synapses and dendrites at time points that precede axon or soma loss. We next determine the role of complement component 1 (C1) in early synaptic loss and dendritic atrophy during glaucoma. Using a genetic knockout of C1qa (D2.C1qa-/- mouse) or pharmacological inhibition of C1 (in the rat bead model) we show that inhibition of C1 is sufficient to preserve dendritic and synaptic architecture. Conclusions This study further supports assessing the potential for complement-modulating therapeutics for the prevention of retinal ganglion cell degeneration in glaucoma.
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Affiliation(s)
| | - James R Tribble
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | | | - Stephen D Cross
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - B Paul Morgan
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - James E Morgan
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Simon W M John
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,Department of Ophthalmology, Tufts University of Medicine, Boston, MA, 02111, USA. .,The Howard Hughes Medical Institute, Bar Harbor, ME, 04609, USA.
| | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA, USA.
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14
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Liu XL, Jia QJ, Wang LN, Liu ZM, Liu H, Duan XC, Lyu XM. Roles of CYP2C19 Gene Polymorphisms in Susceptibility to POAG and Individual Differences in Drug Treatment Response. Med Sci Monit 2016; 22:310-5. [PMID: 26822491 PMCID: PMC4737058 DOI: 10.12659/msm.894868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background The aim of this study was to investigate the roles of cytochrome P450 2C19 (CYP2C19) polymorphisms in primary open-angle glaucoma (POAG) susceptibility and individual responses to drug treatment. Material/Methods This case-control study consisted of 93 cases with POAG and 125 controls. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to analyze CYP2C19 single-nucleotide polymorphisms (SNPs). After timolol treatment, patients were classified into side effect (SE) group and non-side effect (NSE) group. According to drug treatment responses, patients were divided into 3 groups: excellent group (Ex) (IOP ≥8 mm Hg); utility group (Ut) (5 <IOP ≤8 mm Hg), and ineffective group (In) (IOP ≤5 mm Hg). Data analysis was performed using SPSS software. Results We found no statistical differences in the alleles and genotypes frequencies of CYP2C19 between the case group and the control group (both P>0.05). Frequencies of extensive metabolizer phenotype and poor metabolizer phenotype or poor metabolizer phenotype and intermediate metabolizer phenotype were significantly different between the SE group and NSE group (both P<0.05). The distribution of intermediate metabolizer phenotype and extensive metabolizer phenotype were significantly different among Ex group, Ut group, and In group (all P<0.05). Conclusions We found no evidence that CYP2C19 polymorphisms are associated with susceptibility to POAG. However, different CYP2C19 metabolizer phenotypes were identified and observed to have important effects on the individual differences in drug treatment response.
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Affiliation(s)
- Xiang-Long Liu
- Department of Ophthalmology, Affiliated Hospital of Beihua University, Jilin City, Jilin, China (mainland)
| | - Qiu-Ju Jia
- Department of Ophthalmology, Central Hospital of Jilin, Jilin City, Jilin, China (mainland)
| | - Li-Na Wang
- Department of Ophthalmology, China-Japan Union Hospital of Jilin University, Jilin City, Jilin, China (mainland)
| | - Zong-Ming Liu
- Department of Anesthesiology, Jilin Cancer Hospital, Changchun, Jilin, China (mainland)
| | - Hai Liu
- Department of Ophthalmology, The First People's Hospital of Yueyang, Yueyang, Hunan, China (mainland)
| | - Xuan-Chu Duan
- Department of Ophthalmology, The First People's Hospital of Yueyang, Yueyang, Hunan, China (mainland)
| | - Xue-Man Lyu
- Department of Ophthalmology, China-Japan Union Hospital of Jilin University, Jilin City, Jilin, China (mainland)
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King R, Lu L, Williams RW, Geisert EE. Transcriptome networks in the mouse retina: An exon level BXD RI database. Mol Vis 2015; 21:1235-51. [PMID: 26604663 PMCID: PMC4626778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/22/2015] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Differences in gene expression provide diverse retina phenotypes and may also contribute to susceptibility to injury and disease. The present study defines the transcriptome of the retina in the BXD RI strain set, using the Affymetrix Mouse Gene 2.0 ST array to investigate all exons of traditional protein coding genes, non-coding RNAs, and microRNAs. These data are presented in a highly interactive database on the GeneNetwork website. METHODS In the Normal Retina Database, the mRNA levels of the transcriptome from retinas was quantified using the Affymetrix Mouse Gene 2.0 ST array. This database consists of data from male and female mice. The data set includes a total of 52 BXD RI strains, the parental strains (C57BL/6J and DBA/2J), and a reciprocal cross. RESULTS In combination with GeneNetwork, the Department of Defense (DoD) Congressionally Directed Medical Research Programs (CDMRP) Normal Retina Database provides a large resource for mapping, graphing, analyzing, and testing complex genetic networks. Protein-coding and non-coding RNAs can be used to map quantitative trait loci (QTLs) that contribute to expression differences among the BXD strains and to establish links between classical ocular phenotypes associated with differences in the genomic sequence. Using this resource, we extracted transcriptome signatures for retinal cells and defined genetic networks associated with the maintenance of the normal retina. Furthermore, we examined differentially expressed exons within a single gene. CONCLUSIONS The high level of variation in mRNA levels found among the BXD RI strains makes it possible to identify expression networks that underline differences in retina structure and function. Ultimately, we will use this database to define changes that occur following blast injury to the retina.
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Affiliation(s)
- Rebecca King
- Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA
| | - Lu Lu
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN
| | - Robert W. Williams
- Department of Anatomy and Neurobiology and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN
| | - Eldon E. Geisert
- Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA
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Neamatzadeh H, Soleimanizad R, Atefi A, Zare-Shehneh M, Gharibi S, Shekari A, Rahimzadeh AB. Association between p53 codon 72 (Arg72Pro) polymorphism and primary open-angle glaucoma in Iranian patients. IRANIAN BIOMEDICAL JOURNAL 2015; 19:51-6. [PMID: 25605490 PMCID: PMC4322233 DOI: 10.6091/ibj.1379.2014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Glaucomatous neuropathy is a type of cell death due to apoptosis. The p53 gene is one of the regulatory genes of apoptosis. Recently, the association between the p53 gene encoding for proline at codon 72 and primary open-angle glaucoma (POAG) has been studied in some ethnic groups. This study is the first association analysis of POAG and p53 codon 72 polymorphism in Iranian patients. METHODS A cohort of 65 unrelated patients with POAG (age range from 12-62 years, mean ± SD of 40.16 ± 17.51 years) and 65 unrelated control subjects (without glaucoma, age range of 14-63 years, mean ± SD of 35.64 ± 13.61 years) were selected. In Iranian POAG patients and normal healthy controls, the p53 codon 72 polymorphism in exon 4 was amplified using polymerase chain reaction. The amplified DNA fragments were digested with the BstUI restriction enzyme, and the digestion patterns were used to identify the alleles for the polymorphic site. RESULTS Comparisons revealed significant differences in allele and genotype frequencies of Pro72Arg between POAG patients and control group. A higher risk of POAG was associated with allele Pro (OR = 2.1, 95% CI = 1.2-3.4) and genotype Pro/Pro (OR = 3.9, 95% CI = 0.13-12.7). CONCLUSION The p53 Pro72 allele was more frequent in Iranian POAG patients than in the control group (P<0.05). The present findings show that the individuals with the Pro/Pro genotype may be more likely to develop POAG. However, additional studies are necessary to confirm this association.
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Affiliation(s)
- Hossein Neamatzadeh
- Hematology, Oncology and Genetic Research Center, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd, Iran
| | - Reza Soleimanizad
- Dept. of Ophthalmology, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd; Iran
| | - Aref Atefi
- Dept. of Microbial Biotechnology, Payam Noor University, Tehran, Iran
| | - Masoud Zare-Shehneh
- Dept. of Medical Genetics, Shahid Sadoughi University of Medical Sciences and Health Services,
Yazd, Iran
| | - Saba Gharibi
- Dept. of Medical Genetics, Shahid Sadoughi University of Medical Sciences and Health Services,
Yazd, Iran
| | - Abolfazl Shekari
- Dept. of Medical Genetics, Zanjan University of Medical Sciences, Zanjan, Iran
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Deletion of myosin VI causes slow retinal optic neuropathy and age-related macular degeneration (AMD)-relevant retinal phenotype. Cell Mol Life Sci 2015; 72:3953-69. [PMID: 25939269 PMCID: PMC4575690 DOI: 10.1007/s00018-015-1913-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 11/16/2022]
Abstract
The unconventional myosin VI, a member of the actin-based motor protein family of myosins, is expressed in the retina. Its deletion was previously shown to reduce amplitudes of the a- and b-waves of the electroretinogram. Analyzing wild-type and myosin VI-deficient Snell’s Waltzer mice in more detail, the expression pattern of myosin VI in retinal pigment epithelium, outer limiting membrane, and outer plexiform layer could be linked with differential progressing ocular deficits. These encompassed reduced a-waves and b-waves and disturbed oscillatory potentials in the electroretinogram, photoreceptor cell death, retinal microglia infiltration, and formation of basal laminar deposits. A phenotype comprising features of glaucoma (neurodegeneration) and age-related macular degeneration could thus be uncovered that suggests dysfunction of myosin VI and its variable cargo adaptor proteins for membrane sorting and autophagy, as possible candidate mediators for both disease forms.
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Dong Y, Li ZD, Fang XY, Shi XF, Chen S, Tang X. Association between SERPING1 rs2511989 polymorphism and age-related macular degeneration: Meta-analysis. Int J Ophthalmol 2015; 8:385-94. [PMID: 25938061 DOI: 10.3980/j.issn.2222-3959.2015.02.31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/19/2014] [Indexed: 11/02/2022] Open
Abstract
AIM To investigate the association between SERPING1 rs2511989 (G>A) polymorphism and age-related macular degeneration (AMD). METHODS A number of electronic databases (up to July 15, 2014) were searched independently by two investigators. A Meta-analysis was performed on the association between SERPING1 rs2511989 polymorphism and AMD. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated. RESULTS Eight studies with 16 cohorts consisting of 9163 cases and 6813 controls were included in this Meta-analysis. There was no significant association between rs2511989 polymorphism and AMD under all genetic models in overall estimates (A vs G: OR= 0.938, 95%CI =0.858-1.025; AA vs GG:OR =0.871, 95%CI =0.719-1.056; AG vs GG: OR =0.944, 95%CI =0.845-1.054; AA+AG vs GG: OR =0.927, 95% CI =0.823-1.044; AA vs AG+GG: OR =0.890, 95%CI =0.780-1.034). Cumulative Meta-analyses also showed a trend of no association between rs2511989 polymorphism and AMD as information accumulated by year. Subgroup analysis and Meta-regression analysis indicated that age-matching status was the main source of heterogeneity. Sensitivity analysis found the results in overall comparisons and subgroup comparisons of white subjects under the allele model were found to have significantly statistical differences after studies deviating from Hardy-Weinberg equilibrium (HWE) were excluded (overall: OR=0.918, 95%CI = 0.844-0.999, P =0.049; whites: OR =0.901, 95%CI = 0.817-0.994, P =0.038). However, the results were not sufficiently robust for further sensitivity analysis and statistical differences disappeared on applying Bonferroni correction (with a significance level set at 0.05/25). CONCLUSION This Meta-analysis indicates that SERPING1 rs2511989 polymorphism and AMD tend to have no association with each other. Age matching status is a big confounding factor, and more studies with subtle designs are warranted in future.
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Affiliation(s)
- Yi Dong
- Tianjin Medical University, Tianjin 300070, China ; Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Ze-Dong Li
- Tianjin Medical University, Tianjin 300070, China ; Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Xin-Yu Fang
- Department of Epidemiology and Statistics, School of Public Health, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Xue-Feng Shi
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Song Chen
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
| | - Xin Tang
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Hospital, Tianjin 300020, China
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Guo H, Li M, Wang Z, Liu Q, Wu X. Association of MYOC and APOE promoter polymorphisms and primary open-angle glaucoma: a meta-analysis. Int J Clin Exp Med 2015; 8:2052-2064. [PMID: 25932136 PMCID: PMC4402783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Primary open-angle glaucoma (POAG) is the most common form of glaucoma with a genetic predisposition. The relationship between polymorphisms in MYOC or APOE promoter region and POAG has been addressed in many case-control studies, but the published results were not consistent. METHODS A meta-analysis assessing the association between five single nucleotide polymorphisms (SNPs) (in MYOC promoter: rs12035719 and rs2075648; in APOE promoter: rs405509, rs769446 and rs449647) and the risk of POAG was performed based on included studies from literature research. In fixed effect model or random effect model, the Mantel-Haenszel (M-H) pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to evaluate the genetic association. Stratification analysis was also conducted to test the association within Asian or Caucasian populations. RESULTS Twenty five case-control studies within multiple populations were identified and no publish bias was observed. Significant association was detected between POAG risk and MYOC rs2075648 in Caucasian (GA+AA vs. GG, OR=0.587, 95% CI=0.437-0.788, P < 0.001). For other SNPs and in other ethnic populations, no statistic evidence was detected for significant association between them and the development of POAG. CONCLUSIONS This meta-analysis suggested a genetic association between one of MYOC polymorphism (rs2075648) and the risk of POAG only in Caucasian population. The significant heterogeneity for this locus might imply the different POAG genetic basis among different populations.
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Affiliation(s)
- Hui Guo
- Department of Ophthalmology, Qilu Hospital of Shandong UniversityJinan, China
| | - Minghao Li
- School of Medicine, Shandong UniversityJinan, China
| | - Zhe Wang
- School of Medicine, Shandong UniversityJinan, China
| | - Qiji Liu
- Department of Medical Genetics, Key Laboratory for Experimental Teratology of The Ministry of Education, Shandong University School of MedicineJinan, China
| | - Xinyi Wu
- Department of Ophthalmology, Qilu Hospital of Shandong UniversityJinan, China
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Doucette LP, Rasnitsyn A, Seifi M, Walter MA. The interactions of genes, age, and environment in glaucoma pathogenesis. Surv Ophthalmol 2015; 60:310-26. [PMID: 25907525 DOI: 10.1016/j.survophthal.2015.01.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 12/30/2022]
Abstract
Glaucoma, a progressive degenerative condition that results in the death of retinal ganglion cells, is one of the leading causes of blindness, affecting millions worldwide. The mechanisms underlying glaucoma are not well understood, although years of studies have shown that the largest risk factors are elevated intraocular pressure, age, and genetics. Eleven genes and multiple loci have been identified as contributing factors. These genes act by a number of mechanisms, including mechanical stress, ischemic/oxidative stress, and neurodegeneration. We summarize the recent advances in the understanding of glaucoma and propose a unified hypothesis for glaucoma pathogenesis. Glaucoma does not result from a single pathological mechanism, but rather a combination of pathways that are influenced by genes, age, and environment. In particular, we hypothesize that, in the presence of genetic risk factors, exposure to environment stresses results in an earlier age of onset for glaucoma. This hypothesis is based upon the overlap of the molecular pathways in which glaucoma genes are involved. Because of the interactions between these processes, it is likely that there are common therapies that may be effective for different subtypes of glaucoma.
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Affiliation(s)
- Lance P Doucette
- Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta T6G 2H7, Canada
| | - Alexandra Rasnitsyn
- Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta T6G 2H7, Canada
| | - Morteza Seifi
- Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta T6G 2H7, Canada
| | - Michael A Walter
- Faculty of Medicine and Dentistry, Department of Medical Genetics, Edmonton, Alberta T6G 2H7, Canada.
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Genome-wide association studies: getting to pathogenesis, the role of inflammation/complement in age-related macular degeneration. Cold Spring Harb Perspect Med 2014; 4:a017186. [PMID: 25213188 DOI: 10.1101/cshperspect.a017186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Age-related macular degeneration (AMD) is a chronic, degenerative, and significant cause of visual impairment and blindness in the elderly. Genetic and epidemiological studies have confirmed that AMD has a strong genetic component, which has encouraged the application of increasingly sophisticated genetic techniques to uncover the important underlying genetic variants. Although various genes and pathways have been implicated in the risk for AMD, complement activation has been emphasized repeatedly throughout the literature as having a major role both physiologically and genetically in susceptibility to and pathogenesis of this disease. This article explores the research efforts that brought about the discovery and characterization of the role of inflammatory and immune processes (specifically complement) in AMD. The focus herein is on the genetic evidence for the role of complement in AMD as supported specifically by genome-wide association (GWA) studies, which interrogate hundreds of thousands of variants across the genome in a hypothesis-free approach, and other genetic interrogation methods.
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The impact of the human genome project on complex disease. Genes (Basel) 2014; 5:518-35. [PMID: 25032678 PMCID: PMC4198915 DOI: 10.3390/genes5030518] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/03/2014] [Accepted: 06/24/2014] [Indexed: 02/06/2023] Open
Abstract
In the decade that has passed since the initial release of the Human Genome, numerous advancements in science and technology within and beyond genetics and genomics have been encouraged and enhanced by the availability of this vast and remarkable data resource. Progress in understanding three common, complex diseases: age-related macular degeneration (AMD), Alzheimer's disease (AD), and multiple sclerosis (MS), are three exemplars of the incredible impact on the elucidation of the genetic architecture of disease. The approaches used in these diseases have been successfully applied to numerous other complex diseases. For example, the heritability of AMD was confirmed upon the release of the first genome-wide association study (GWAS) along with confirmatory reports that supported the findings of that state-of-the art method, thus setting the foundation for future GWAS in other heritable diseases. Following this seminal discovery and applying it to other diseases including AD and MS, the genetic knowledge of AD expanded far beyond the well-known APOE locus and now includes more than 20 loci. MS genetics saw a similar increase beyond the HLA loci and now has more than 100 known risk loci. Ongoing and future efforts will seek to define the remaining heritability of these diseases; the next decade could very well hold the key to attaining this goal.
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Wang Y, Zhou YF, Zhao BY, Gu ZY, Li SL. Apolipoprotein E gene ε4ε4 is associated with elevated risk of primary open angle glaucoma in Asians: a meta-analysis. BMC MEDICAL GENETICS 2014; 15:60. [PMID: 24885013 PMCID: PMC4035820 DOI: 10.1186/1471-2350-15-60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/02/2022]
Abstract
Background Epidemiological studies have evaluated the association between Apolipoprotein E (APOE) gene ε2/ε3/ε4 polymorphism and glaucoma susceptibility. However, the published data are still inconclusive. The aim of the present study is to evaluate the impact of APOE gene ε2/ε3/ε4 polymorphism on glaucoma risk by using meta-analysis. Methods A comprehensive literature search of PubMed, EMBASE, Cochrane, Elsevier Science Direct and CNKI databases was conducted to identify relevant articles, with the last report up to January 5, 2014. Pooled odds ratio (OR) and 95% confidence interval (CI) were used to assess the strength of association by using the fixed or random effect model. Results Fifteen separate studies including 2,700 cases and 2,365 controls were included in the meta-analysis. We did not detect a significant association between APOE gene ε2/ε3/ε4 polymorphism and glaucoma in overall population (P > 0.0083). In Asians, we detected an association of the ε4ε4 genotype with elevated risk for glaucoma (OR = 5.22, 95% CI = 1.85-14.68, P = 0.002), mainly for primary open angle glaucoma (OR = 4.98, 95% CI = 1.75-14.20, P = 0.003). Conclusions The meta-analysis suggests that APOE gene ε4ε4 may be associated with elevated risk for primary open angle glaucoma in Asians. However, more epidemiologic studies based on larger sample size, case–control design and stratified by ethnicity as well as types of glaucoma are suggested to further clarify the relationship between APOE gene ε2/ε3/ε4 polymorphism and genetic predisposition to glaucoma.
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Affiliation(s)
| | | | | | | | - Shou-Ling Li
- Department of Ophthalmology, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei 230022, Anhui, China.
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Buys ES, Potter LR, Pasquale LR, Ksander BR. Regulation of intraocular pressure by soluble and membrane guanylate cyclases and their role in glaucoma. Front Mol Neurosci 2014; 7:38. [PMID: 24904270 PMCID: PMC4032937 DOI: 10.3389/fnmol.2014.00038] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/21/2014] [Indexed: 01/01/2023] Open
Abstract
Glaucoma is a progressive optic neuropathy characterized by visual field defects that ultimately lead to irreversible blindness (Alward, 2000; Anderson et al., 2006). By the year 2020, an estimated 80 million people will have glaucoma, 11 million of which will be bilaterally blind. Primary open-angle glaucoma (POAG) is the most common type of glaucoma. Elevated intraocular pressure (IOP) is currently the only risk factor amenable to treatment. How IOP is regulated and can be modulated remains a topic of active investigation. Available therapies, mostly geared toward lowering IOP, offer incomplete protection, and POAG often goes undetected until irreparable damage has been done, highlighting the need for novel therapeutic approaches, drug targets, and biomarkers (Heijl et al., 2002; Quigley, 2011). In this review, the role of soluble (nitric oxide (NO)-activated) and membrane-bound, natriuretic peptide (NP)-activated guanylate cyclases that generate the secondary signaling molecule cyclic guanosine monophosphate (cGMP) in the regulation of IOP and in the pathophysiology of POAG will be discussed.
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Affiliation(s)
- Emmanuel S Buys
- Department of Anesthesia, Critical Care, and Pain Medicine, Anesthesia Center for Critical Care Research, Harvard Medical School, Massachusetts General Hospital Boston, MA, USA
| | - Lincoln R Potter
- Department of Pharmacology, University of Minnesota Medical School Minneapolis, MN, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Glaucoma Service Mass Eye and Ear Infirmary and Channing Division of Network Medicine, Harvard Medical School, Brigham and Women's Hospital Boston, MA, USA
| | - Bruce R Ksander
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Schepens Eye Research Institute, Harvard Medical School Boston, MA, USA
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Aboobakar IF, Allingham RR. Developments in Ocular Genetics: 2013 Annual Review. Asia Pac J Ophthalmol (Phila) 2014; 3:181-93. [PMID: 25097799 PMCID: PMC4119463 DOI: 10.1097/apo.0000000000000063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE To highlight major advancements in ocular genetics from the year 2013. DESIGN Literature review. METHODS A literature search was conducted on PubMed to identify articles pertaining to genetic influences on human eye diseases. This review focuses on manuscripts published in print or online in the English language between January 1, 2013 and December 31, 2013. A total of 120 papers from 2013 were included in this review. RESULTS Significant progress has been made in our understanding of the genetic basis of a broad group of ocular disorders, including glaucoma, age-related macular degeneration, cataract, diabetic retinopathy, keratoconus, Fuchs' endothelial dystrophy, and refractive error. CONCLUSIONS The latest next-generation sequencing technologies have become extremely effective tools for identifying gene mutations associated with ocular disease. These technological advancements have also paved the way for utilization of genetic information in clinical practice, including disease diagnosis, prediction of treatment response and molecular interventions guided by gene-based knowledge.
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Affiliation(s)
- Inas F Aboobakar
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
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Kaurani L, Vishal M, Kumar D, Sharma A, Mehani B, Sharma C, Chakraborty S, Jha P, Ray J, Sen A, Dash D, Ray K, Mukhopadhyay A. Gene-rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins. Invest Ophthalmol Vis Sci 2014; 55:3258-64. [PMID: 24764060 DOI: 10.1167/iovs.14-14339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Large copy number variations (CNV) can contribute to increased burden for neurodegenerative diseases. In this study, we analyzed the genome-wide burden of large CNVs > 100 kb in primary open angle glaucoma (POAG), a neurodegenerative disease of the eye that is the largest cause of irreversible blindness. METHODS Genome-wide analysis of CNVs > 100 kb were analyzed in a total of 1720 individuals, including an Indian cohort (347 POAG cases and 345 controls) and a Caucasian cohort (624 cases and 404 controls). All the CNV data were obtained from experiments performed on Illumina 660W-Quad (infinium) arrays. RESULTS We observed that for both the populations CNVs > 1 Mb was significantly enriched for gene-rich regions unique to the POAG cases (P < 10(-11)). In the Indian cohort CNVs > 1 Mb (39 calls) in patients influenced 125 genes while in controls 31 such CNVs influenced only 5 genes with no overlap. In both cohorts we observed 1.9-fold gene enrichment in patients for deletions compared to duplications, while such a bias was not observed in controls (0.3-fold). Overall duplications > 1 Mb were more than deletions (Del/Dup = 0.82) confirming that the enrichment of gene-rich deletions in patients was associated with the disease. Of the 39 CNVs > 1 Mb from Indian patients, 28 (72%) also were implicated in other neurodegenerative disorders, like autism, schizophrenia, sensorineural hearing loss, and so forth. We found one large duplication encompassing CNTN4 gene in Indian and Caucasian POAG patients that was absent in the controls. CONCLUSIONS To our knowledge, our study is the first report on large CNV bias for gene-rich regions in glaucomatous neurodegeneration, implicating its impact across populations of contrasting ethnicities. We identified CNTN4 as a novel candidate gene for POAG.
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Affiliation(s)
- Lalit Kaurani
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mansi Vishal
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Dhirendra Kumar
- G. N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anchal Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Bharati Mehani
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Charu Sharma
- Mathematics Department, Shiv Nadar University, Uttar Pradesh, India
| | - Subhadip Chakraborty
- Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | - Pankaj Jha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Jharna Ray
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, India
| | | | - Debasis Dash
- G. N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Kunal Ray
- Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Arijit Mukhopadhyay
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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Lack of association of apolipoprotein E (Apo E) ε2/ε3/ε4 polymorphisms with primary open-angle glaucoma: a meta-analysis from 1916 cases and 1756 controls. PLoS One 2013; 8:e72644. [PMID: 24023758 PMCID: PMC3759379 DOI: 10.1371/journal.pone.0072644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023] Open
Abstract
Background A number of case-control studies were conducted to investigate the association of apolipoprotein E (Apo E) polymorphisms with primary open angle glaucoma (POAG). But the results remain controversial. This meta-analysis aims to comprehensively evaluate the relationship between a common ε2/ε3/ε4 polymorphism in Apo E gene on the risk of POAG. Method A comprehensive literature search for studies published up to April 2013 was performed. Summary odds ratios (ORs) and 95% confidence intervals (CI) were calculated employing random-effects models irrespective of between-study heterogeneity. Publication bias of literatures was evaluated using funnel plots and Egger's test. Results A total of 12 studies including 1916 cases and 1756 controls meeting the predefined criteria were involved in this meta-analysis. Overall, the Apo E ε2 allele and ε4 allele were not associated with POAG, compared with those carrying ε3 allele, with ORs of 0.98 (95% CI, 0.79 to 1.23; P = 0.872) and 1.05 (95% CI, 0.78 to 1.41; P = 0.743), respectively. Genotypic analysis also found no significant association between the ε4 carriers (ε3/ε4+ε4/ε4), ε2 carriers (ε2/ε3+ε2/ε2) and POAG, compared with participants with Apo E ε3/3, with ORs of 0.91 (95% CI, 0.66 to 1.25; P = 0.543) and 1.08 (95% CI, 0.74 to 1.57; P = 0.694), respectively. In the subgroup analysis by ethnicity, source of controls, genotyping methods, Hardy-Weinberg equilibrium or not, or type of the POAG, still no obvious associations were found. Conclusions This meta-analysis suggests that Apo E ε2/ε3/ε4 polymorphisms may not be associated with the risk of POAG. However, well-designed studies with larger sample size and more ethnic groups are required to further validate the results.
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