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Cebatoriene D, Vilkeviciute A, Gedvilaite G, Bruzaite A, Kriauciuniene L, Zaliuniene D, Liutkeviciene R. CFH (rs1061170, rs1410996), KDR (rs2071559, rs1870377) and KDR and CFH Serum Levels in AMD Development and Treatment Efficacy. Biomedicines 2024; 12:948. [PMID: 38790910 PMCID: PMC11117782 DOI: 10.3390/biomedicines12050948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is a major global health problem as it is the leading cause of irreversible loss of central vision in the aging population. Av-vascular endothelial growth factor (anti-VEGF) therapies have been shown to be effective, but they do not respond optimally to all patients. OBJECTIVE This study investigates the genetic factors associated with susceptibility to AMD and response to treatment, focusing on key polymorphisms in the CFH (rs1061170, rs1410996) and KDR (rs2071559, rs1870377) genes and the association of CFH and KDR serum levels in patients with AMD. RESULTS A cohort of 255 patients with early AMD, 252 patients with exudative AMD, and 349 healthy controls underwent genotyping analysis, which revealed significant associations between CFH polymorphisms and the risk of exudative AMD. The CFH rs1061170 CC genotype was associated with an increased risk of early AMD (p = 0.046). For exudative AMD, the CFH rs1061170 TC + CC genotype increased odds (p < 0.001), while the rs1410996 GA + AA genotype decreased odds (p < 0.001). Haplotypes of CFH SNPs were associated with decreased odds of AMD. In terms of response to treatment, none of the SNPs were associated with the response to anti-VEGF treatment. We also found that both early and exudative AMD patients had lower CFH serum levels compared to the control group (p = 0.038 and p = 0.006, respectively). Exudative AMD patients with the CT genotype of CFH rs1061170 had lower CFH serum levels compared to the control group (p = 0.035). Exudative AMD patients with the GG genotype of CFH rs1410996 also had lower CFH serum levels compared to the control group (p = 0.021). CONCLUSIONS CFH polymorphisms influence susceptibility to AMD but do not correlate with a response to anti-VEGF therapy. Further research is imperative to fully evaluate the developmental significance, treatment efficacy, and predictive role in influencing susceptibility to anti-VEGF therapy for KDR and CFH.
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Affiliation(s)
- Dzastina Cebatoriene
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, LT-44307 Kaunas, Lithuania
| | - Alvita Vilkeviciute
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Greta Gedvilaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Akvile Bruzaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Loresa Kriauciuniene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Dalia Zaliuniene
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Rasa Liutkeviciene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
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Riley-Gillis B, Huh H, Shen J, den Hollander AI. Genetic and molecular biomarkers for geographic atrophy. Acta Ophthalmol 2023; 101:869-880. [PMID: 37933607 DOI: 10.1111/aos.15803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/14/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023]
Abstract
Geographic atrophy (GA) is characterized by atrophy of the retina, retinal pigment epithelium and choriocapillaris, causing a gradual loss of vision over time. Treatment options to prevent initiation or progression of GA are limited; two recently FDA-approved inhibitors of the complement system (pegcetacoplan, avacincaptad pegol) showed a modest decrease in GA lesion growth in phase 3 clinical trials. Exploration of genetic and molecular biomarkers in GA plays a critical role in our battle against this blinding disease to improve early disease detection, to find more effective therapies, and to provide personalized care to patients. In this review, we provide a comprehensive overview of the current literature investigating genetic and molecular biomarkers for GA. Genetic studies identified multiple genes and variants that play a role in progression to GA and GA lesion growth, involving pathways such as complement activation, extracellular matrix interaction and lipid metabolism. The number of published studies assessing molecular biomarkers for GA initiation and progression in ocular matrices is limited. Several studies evaluated molecular biomarkers in the systemic circulation, showing higher levels of complement activation and a causal role of lipid subfractions in GA. Larger, well-powered studies are needed to identify novel and validate existing biomarkers, and to investigate the potential of combining genetic and molecular markers with imaging techniques for more accurate diagnosis and monitoring of GA. The development of personalized medicine approaches based on individual genetic and molecular profiles could hold promise for more effective and targeted treatments for this devastating disease.
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Affiliation(s)
| | - Hannah Huh
- AbbVie, Local Delivery Translational Sciences, Irvine, California, USA
| | - Jie Shen
- AbbVie, Local Delivery Translational Sciences, Irvine, California, USA
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Pan Y, Fu Y, Baird PN, Guymer RH, Das T, Iwata T. Exploring the contribution of ARMS2 and HTRA1 genetic risk factors in age-related macular degeneration. Prog Retin Eye Res 2023; 97:101159. [PMID: 36581531 DOI: 10.1016/j.preteyeres.2022.101159] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of severe irreversible central vision loss in individuals over 65 years old. Genome-wide association studies (GWASs) have shown that the region at chromosome 10q26, where the age-related maculopathy susceptibility (ARMS2/LOC387715) and HtrA serine peptidase 1 (HTRA1) genes are located, represents one of the strongest associated loci for AMD. However, the underlying biological mechanism of this genetic association has remained elusive. In this article, we extensively review the literature by us and others regarding the ARMS2/HTRA1 risk alleles and their functional significance. We also review the literature regarding the presumed function of the ARMS2 protein and the molecular processes of the HTRA1 protein in AMD pathogenesis in vitro and in vivo, including those of transgenic mice overexpressing HtrA1/HTRA1 which developed Bruch's membrane (BM) damage, choroidal neovascularization (CNV), and polypoidal choroidal vasculopathy (PCV), similar to human AMD patients. The elucidation of the molecular mechanisms of the ARMS2 and HTRA1 susceptibility loci has begun to untangle the complex biological pathways underlying AMD pathophysiology, pointing to new testable paradigms for treatment.
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Affiliation(s)
- Yang Pan
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1, Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Yingbin Fu
- Department of Ophthalmology, Baylor College of Medicine, One Baylor Plaza, NC506, Houston, TX, 77030, USA
| | - Paul N Baird
- Department of Surgery, (Ophthalmology), Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - Robyn H Guymer
- Department of Surgery, (Ophthalmology), Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia; Centre for Eye Research Australia, Royal Victorian Eye & Ear Hospital, East Melbourne, Victoria, 3002, Australia
| | - Taraprasad Das
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, Kallam Anji Reddy Campus, L. V. Prasad Eye Institute, Hyderabad, 500034, India
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1, Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
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4
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Merle DA, Sen M, Armento A, Stanton CM, Thee EF, Meester-Smoor MA, Kaiser M, Clark SJ, Klaver CCW, Keane PA, Wright AF, Ehrmann M, Ueffing M. 10q26 - The enigma in age-related macular degeneration. Prog Retin Eye Res 2023; 96:101154. [PMID: 36513584 DOI: 10.1016/j.preteyeres.2022.101154] [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: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Despite comprehensive research efforts over the last decades, the pathomechanisms of age-related macular degeneration (AMD) remain far from being understood. Large-scale genome wide association studies (GWAS) were able to provide a defined set of genetic aberrations which contribute to disease risk, with the strongest contributors mapping to distinct regions on chromosome 1 and 10. While the chromosome 1 locus comprises factors of the complement system with well-known functions, the role of the 10q26-locus in AMD-pathophysiology remains enigmatic. 10q26 harbors a cluster of three functional genes, namely PLEKHA1, ARMS2 and HTRA1, with most of the AMD-associated genetic variants mapping to the latter two genes. High linkage disequilibrium between ARMS2 and HTRA1 has kept association studies from reliably defining the risk-causing gene for long and only very recently the genetic risk region has been narrowed to ARMS2, suggesting that this is the true AMD gene at this locus. However, genetic associations alone do not suffice to prove causality and one or more of the 14 SNPs on this haplotype may be involved in long-range control of gene expression, leaving HTRA1 and PLEKHA1 still suspects in the pathogenic pathway. Both, ARMS2 and HTRA1 have been linked to extracellular matrix homeostasis, yet their exact molecular function as well as their role in AMD pathogenesis remains to be uncovered. The transcriptional regulation of the 10q26 locus adds an additional level of complexity, given, that gene-regulatory as well as epigenetic alterations may influence expression levels from 10q26 in diseased individuals. Here, we provide a comprehensive overview on the 10q26 locus and its three gene products on various levels of biological complexity and discuss current and future research strategies to shed light on one of the remaining enigmatic spots in the AMD landscape.
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Affiliation(s)
- David A Merle
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department of Ophthalmology, Medical University of Graz, 8036, Graz, Austria.
| | - Merve Sen
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Angela Armento
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eric F Thee
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Simon J Clark
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands; Department of Ophthalmology, Radboudumc, 6525EX, Nijmegen, Netherlands; Institute of Molecular and Clinical Ophthalmology Basel, CH-4031, Basel, Switzerland
| | - Pearse A Keane
- Institute for Health Research, Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany.
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Cruz-Aguilar M, Groman-Lupa S, Jiménez-Martínez MC. MicroRNAs as potential biomarkers and therapeutic targets in age-related macular degeneration. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1023782. [PMID: 38983087 PMCID: PMC11182111 DOI: 10.3389/fopht.2023.1023782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/30/2023] [Indexed: 07/11/2024]
Abstract
Age-related macular degeneration (AMD) involves degenerative and neovascular alteration in the macular region of the retina resulting in central vision loss. AMD can be classified into dry (dAMD) and wet AMD (wAMD). There is no established treatment for dAMD, and therapies available for wAMD have limited success. Diagnosis in early AMD stages is difficult due to the absence of clinical symptoms. Currently, imaging tests are used in the diagnosis of AMD, but cannot predict the clinical course. The clinical limitations to establishing a diagnosis of AMD have led to exploration for innovative and more sensitive tests to support the diagnosis and prognosis of the disease. MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules that negatively regulate genes by post-transcriptional gene silencing. Because these molecules are dysregulated in various processes implicated in the pathogenesis of AMD, they could contribute to the early detection of the disease and monitoring of its progression. Studies of miRNA profiling have indicated several miRNAs as potential diagnostic biomarkers of AMD, but no approved biomarker is available at present for early AMD detection. Thus, understanding the function of miRNAs in AMD and their use as potential biomarkers may lead to future advances in diagnosis and treatment. Here we present a brief review of some of the miRNAs involved in regulating pathological processes associated with AMD and discuss several candidate miRNAs proposed as biomarkers or therapeutic targets for AMD.
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Affiliation(s)
- Marisa Cruz-Aguilar
- Department of Immunology and Research Unit, Institute of Ophthalmology "Conde de Valenciana Foundation", Ciudad de México, Mexico
| | - Sergio Groman-Lupa
- Retina Service, Codet Vision Institute, Tijuana, Baja California, Mexico
| | - María C Jiménez-Martínez
- Department of Immunology and Research Unit, Institute of Ophthalmology "Conde de Valenciana Foundation", Ciudad de México, Mexico
- Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico, Ciudad de México, Mexico
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6
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Shughoury A, Sevgi DD, Ciulla TA. Molecular Genetic Mechanisms in Age-Related Macular Degeneration. Genes (Basel) 2022; 13:1233. [PMID: 35886016 PMCID: PMC9316037 DOI: 10.3390/genes13071233] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Age-related macular degeneration (AMD) is among the leading causes of irreversible blindness worldwide. In addition to environmental risk factors, such as tobacco use and diet, genetic background has long been established as a major risk factor for the development of AMD. However, our ability to predict disease risk and personalize treatment remains limited by our nascent understanding of the molecular mechanisms underlying AMD pathogenesis. Research into the molecular genetics of AMD over the past two decades has uncovered 52 independent gene variants and 34 independent loci that are implicated in the development of AMD, accounting for over half of the genetic risk. This research has helped delineate at least five major pathways that may be disrupted in the pathogenesis of AMD: the complement system, extracellular matrix remodeling, lipid metabolism, angiogenesis, and oxidative stress response. This review surveys our current understanding of each of these disease mechanisms, in turn, along with their associated pathogenic gene variants. Continued research into the molecular genetics of AMD holds great promise for the development of precision-targeted, personalized therapies that bring us closer to a cure for this debilitating disease.
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Affiliation(s)
- Aumer Shughoury
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.S.); (D.D.S.)
| | - Duriye Damla Sevgi
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.S.); (D.D.S.)
| | - Thomas A. Ciulla
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.S.); (D.D.S.)
- Clearside Biomedical, Inc., Alpharetta, GA 30005, USA
- Midwest Eye Institute, Indianapolis, IN 46290, USA
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7
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Biomarkers as Predictive Factors of Anti-VEGF Response. Biomedicines 2022; 10:biomedicines10051003. [PMID: 35625740 PMCID: PMC9139112 DOI: 10.3390/biomedicines10051003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
Age-related macular degeneration is the main cause of irreversible vision in developed countries, and intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections are the current gold standard treatment today. Although anti-VEGF treatment results in important improvements in the course of this disease, there is a considerable number of patients not responding to the standardized protocols. The knowledge of how a patient will respond or how frequently retreatment might be required would be vital in planning treatment schedules, saving both resource utilization and financial costs, but today, there is not an ideal biomarker to use as a predictive response to ranibizumab therapy. Whole blood and blood mononuclear cells are the samples most studied; however, few reports are available on other important biofluid samples for studying this disease, such as aqueous humor. Moreover, the great majority of studies carried out to date were focused on the search for SNPs in genes related to AMD risk factors, but miRNAs, proteomic and metabolomics studies have rarely been conducted in anti-VEGF-treated samples. Here, we propose that genomic, proteomic and/or metabolomic markers could be used not alone but in combination with other methods, such as specific clinic characteristics, to identify patients with a poor response to anti-VEGF treatment to establish patient-specific treatment plans.
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8
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Ganjdanesh A, Zhang J, Chew EY, Ding Y, Huang H, Chen W. LONGL-Net: temporal correlation structure guided deep learning model to predict longitudinal age-related macular degeneration severity. PNAS NEXUS 2022; 1:pgab003. [PMID: 35360552 PMCID: PMC8962776 DOI: 10.1093/pnasnexus/pgab003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/15/2021] [Indexed: 01/28/2023]
Abstract
Age-related macular degeneration (AMD) is the principal cause of blindness in developed countries, and its prevalence will increase to 288 million people in 2040. Therefore, automated grading and prediction methods can be highly beneficial for recognizing susceptible subjects to late-AMD and enabling clinicians to start preventive actions for them. Clinically, AMD severity is quantified by Color Fundus Photographs (CFP) of the retina, and many machine-learning-based methods are proposed for grading AMD severity. However, few models were developed to predict the longitudinal progression status, i.e. predicting future late-AMD risk based on the current CFP, which is more clinically interesting. In this paper, we propose a new deep-learning-based classification model (LONGL-Net) that can simultaneously grade the current CFP and predict the longitudinal outcome, i.e. whether the subject will be in late-AMD in the future time-point. We design a new temporal-correlation-structure-guided Generative Adversarial Network model that learns the interrelations of temporal changes in CFPs in consecutive time-points and provides interpretability for the classifier's decisions by forecasting AMD symptoms in the future CFPs. We used about 30,000 CFP images from 4,628 participants in the Age-Related Eye Disease Study. Our classifier showed average 0.905 (95% CI: 0.886-0.922) AUC and 0.762 (95% CI: 0.733-0.792) accuracy on the 3-class classification problem of simultaneously grading current time-point's AMD condition and predicting late AMD progression of subjects in the future time-point. We further validated our model on the UK Biobank dataset, where our model showed average 0.905 accuracy and 0.797 sensitivity in grading 300 CFP images.
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Affiliation(s)
- Alireza Ganjdanesh
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jipeng Zhang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ying Ding
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Heng Huang
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Chen
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Russo C, Morello G, Malaguarnera R, Piro S, Furno DL, Malaguarnera L. Candidate genes of SARS-CoV-2 gender susceptibility. Sci Rep 2021; 11:21968. [PMID: 34753980 PMCID: PMC8578384 DOI: 10.1038/s41598-021-01131-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV-2) initiated a global viral pandemic since late 2019. Understanding that Coronavirus disease (COVID-19) disproportionately affects men than women results in great challenges. Although there is a growing body of published study on this topic, effective explanations underlying these sex differences and their effects on the infection outcome still remain uncertain. We applied a holistic bioinformatics method to investigate molecular variations of known SARS-CoV-2 interacting human proteins mainly expressed in gonadal tissues (testis and ovary), allowing for the identification of potential genetic targets for this infection. Functional enrichment and interaction network analyses were also performed to better investigate the biological differences between testicular and ovarian responses in the SARS-CoV-2 infection, paying particular attention to genes linked to immune-related pathways, reactions of host cells after intracellular infection, steroid hormone biosynthesis, receptor signaling, and the complement cascade, in order to evaluate their potential association with sexual difference in the likelihood of infection and severity of symptoms. The analysis revealed that within the testis network TMPRSS2, ADAM10, SERPING1, and CCR5 were present, while within the ovary network we found BST2, GATA1, ENPEP, TLR4, TLR7, IRF1, and IRF2. Our findings could provide potential targets for forthcoming experimental investigation related to SARS-CoV-2 treatment.
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Affiliation(s)
- Cristina Russo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giovanna Morello
- Institute for Research and Biomedical Innovation (IRIB), Italian National Research Council (CNR), Catania, Italy.
| | | | - Salvatore Piro
- Department of Clinical and Molecular Medicine, University of Catania, Catania, Italy
| | - Debora Lo Furno
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Lucia Malaguarnera
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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May A, Su F, Dinh B, Ehlen R, Tran C, Adivikolanu H, Shaw PX. Ongoing controversies and recent insights of the ARMS2-HTRA1 locus in age-related macular degeneration. Exp Eye Res 2021; 210:108605. [PMID: 33930395 DOI: 10.1016/j.exer.2021.108605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 01/17/2023]
Abstract
Age-related macular degeneration (AMD) is the most common cause of central vision loss among elderly populations in industrialized countries. Genome-wide association studies have consistently associated two genomic loci with progression to late-stage AMD: the complement factor H (CFH) locus on chromosome 1q31 and the age-related maculopathy susceptibility 2-HtrA serine peptidase 1 (ARMS2-HTRA1) locus on chromosome 10q26. While the CFH risk variant has been shown to alter complement activity, the ARMS2-HTRA1 risk haplotype remains enigmatic due to high linkage disequilibrium and inconsistent functional findings spanning two genes that are plausibly causative for AMD risk. In this review, we detail the genetic and functional evidence used to support either ARMS2 or HTRA1 as the causal gene for AMD risk, emphasizing both the historical development and the current understanding of the ARMS2-HTRA1 locus in AMD pathogenesis. We conclude by summarizing the evidence in favor of HTRA1 and present our hypothesis whereby HTRA1-derived ECM fragments mediate AMD pathogenesis.
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Affiliation(s)
- Adam May
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Fei Su
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Brian Dinh
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Rachael Ehlen
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Christina Tran
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Harini Adivikolanu
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Peter X Shaw
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
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11
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Ratnapriya R, Acar İE, Geerlings MJ, Branham K, Kwong A, Saksens NTM, Pauper M, Corominas J, Kwicklis M, Zipprer D, Starostik MR, Othman M, Yashar B, Abecasis GR, Chew EY, Ferrington DA, Hoyng CB, Swaroop A, den Hollander AI. Family-based exome sequencing identifies rare coding variants in age-related macular degeneration. Hum Mol Genet 2021; 29:2022-2034. [PMID: 32246154 PMCID: PMC7390936 DOI: 10.1093/hmg/ddaa057] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified 52 independent variants at 34 genetic loci that are associated with age-related macular degeneration (AMD), the most common cause of incurable vision loss in the elderly worldwide. However, causal genes at the majority of these loci remain unknown. In this study, we performed whole exome sequencing of 264 individuals from 63 multiplex families with AMD and analyzed the data for rare protein-altering variants in candidate target genes at AMD-associated loci. Rare coding variants were identified in the CFH, PUS7, RXFP2, PHF12 and TACC2 genes in three or more families. In addition, we detected rare coding variants in the C9, SPEF2 and BCAR1 genes, which were previously suggested as likely causative genes at respective AMD susceptibility loci. Identification of rare variants in the CFH and C9 genes in our study validated previous reports of rare variants in complement pathway genes in AMD. We then extended our exome-wide analysis and identified rare protein-altering variants in 13 genes outside the AMD-GWAS loci in three or more families. Two of these genes, SCN10A and KIR2DL4, are of interest because variants in these genes also showed association with AMD in case-control cohorts, albeit not at the level of genome-wide significance. Our study presents the first large-scale, exome-wide analysis of rare variants in AMD. Further independent replications and molecular investigation of candidate target genes, reported here, would assist in gaining novel insights into mechanisms underlying AMD pathogenesis.
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Affiliation(s)
- Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - İlhan E Acar
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Maartje J Geerlings
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Alan Kwong
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicole T M Saksens
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Marc Pauper
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Jordi Corominas
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - David Zipprer
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Margaret R Starostik
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Beverly Yashar
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily Y Chew
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory (NNRL), National Eye Institute, Bethesda, MD 20892, USA
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6500, The Netherlands
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12
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Ohishi K, Hosono K, Obana A, Noda A, Hiramitsu T, Hotta Y, Minoshima S. Identification of susceptibility loci for light-induced visual impairment in rats. Exp Eye Res 2021; 210:108688. [PMID: 34237304 DOI: 10.1016/j.exer.2021.108688] [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: 03/17/2021] [Revised: 06/14/2021] [Accepted: 06/29/2021] [Indexed: 12/01/2022]
Abstract
Bright light exposure in animals results in the selective degeneration of the outer retina, known as "retinal photic injury" (RPI). The susceptibility to RPI differs among rat strains. WKY rats display susceptibility to RPI with extensive retinal degeneration observed in the sagittal eye specimen, whereas LEW strain rats are resistant to it, showing only slight or no degeneration. In the present study, we first established an ethological screening method using the Morris water maze to discern differential susceptibility among the living rats. WKY and LEW were crossed to produce the first filial generation (F1) offspring. Maze-trained individuals were exposed to bright, white light. The screening test results demonstrated that the susceptibility to light-induced visual impairment in rats is a dominant Mendelian susceptibility trait, as F1 rats were susceptible to visual impairment like WKY rats. Therefore, F1 rats were backcrossed with recessive LEW to produce the first backcross offspring (BC1). Subsequent recurrent backcrossing while selecting for the susceptibility, indicated a segregation ratio of ca. 24% in BC1 and BC2 generations, indicating the involvement of two or more genes in the susceptibility. Further, microsatellite analysis of BC1-to-BC4 individuals using microsatellite markers mapped two susceptibility loci on chromosome segments 5q36 and 19q11-q12, named RPI susceptibility (Rpi)1 and Rpi2, respectively. This study provides an insight into mechanisms underlying differential susceptibility, which could help decipher the mechanism underlying the onset/progression of human age-related macular degeneration.
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Affiliation(s)
- Kentaro Ohishi
- Department of Photomedical Genomics, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.
| | - Katsuhiro Hosono
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Akira Obana
- Hamamatsu BioPhotonics Innovation Chair, Institute for Medical Photonics Research, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan; Department of Ophthalmology, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Akio Noda
- Department of Integrated Human Sciences (Mathematics), Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Tadahisa Hiramitsu
- Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shinsei Minoshima
- Department of Photomedical Genomics, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
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13
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Dere E, Crowell S, Maia M, Schuetz C, Lai P, Bantseev V, Booler H. Nonclinical Safety Assessment of FHTR2163, An Antigen-Binding Fragment Against HTRA1 for the Treatment of Geographic Atrophy. Toxicol Pathol 2021; 49:610-620. [PMID: 33297886 DOI: 10.1177/0192623320976095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
FHTR2163 is an antigen-binding fragment of a humanized immunoglobulin G1 monoclonal antibody directed against high-temperature requirement A serine peptidase 1 (HTRA1) that is being developed as a potential intravitreal (ITV) treatment for patients with geographic atrophy (GA), an advanced form of dry age-related macular degeneration. The nonclinical toxicology program was designed to assess the safety and tolerability of HTRA1 inhibition following ITV administration of FHTR2163 to support ITV administration in patients with GA. FHTR2163 was well tolerated in a single-dose ITV-administered 8-day toxicity study in cynomolgus monkeys following a 50 µL high (>700 mOsm/kg) osmolality formulation up to 12.5 mg/eye; however, 100 µL (2× 50 µL injections) of a high-osmolality formulation resulted in transient retinal detachment. Repeat-dose ITV administration every 2 weeks of FHTR2163 was well tolerated in 8- and 26-week studies with ITV injection of 100 µL (2× 50 μL) of iso-osmolar formulation up to 15 mg/eye, or 50 µL of the high-osmolality formulation up to 12.5 mg/eye. Observed transient and reversible ocular effects included inflammation and perivascular infiltrates, consistent with an immune response attributed to the administration of heterologous (humanized) protein. Overall, FHTR2163 was well tolerated, and the nonclinical package supported the continued clinical development of FHTR2163 in patients with GA.
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Affiliation(s)
- Edward Dere
- Department of Safety Assessment, 7412Genentech Inc., South San Francisco, CA, USA
| | - Susan Crowell
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, 7412Genentech Inc., South San Francisco, CA, USA
| | - Mauricio Maia
- Department of Bioanalytical Sciences, 7412Genentech Inc., South San Francisco, CA, USA
| | - Chris Schuetz
- Department of Safety Assessment, 7412Genentech Inc., South San Francisco, CA, USA
| | - Phillip Lai
- Department of Early Clinical Development OMNI, 7412Genentech Inc., South San Francisco, CA, USA
| | - Vladimir Bantseev
- Department of Safety Assessment, 7412Genentech Inc., South San Francisco, CA, USA
| | - Helen Booler
- Department of Safety Assessment, 7412Genentech Inc., South San Francisco, CA, USA
- Department of BIOmics and Pathology, F. Hoffmann-La Roche, Ltd., Basel, Switzerland
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14
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Yan Q, Jiang Y, Huang H, Swaroop A, Chew EY, Weeks DE, Chen W, Ding Y. Genome-Wide Association Studies-Based Machine Learning for Prediction of Age-Related Macular Degeneration Risk. Transl Vis Sci Technol 2021; 10:29. [PMID: 34003914 PMCID: PMC7900884 DOI: 10.1167/tvst.10.2.29] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/17/2020] [Indexed: 11/24/2022] Open
Abstract
Purpose Because age-related macular degeneration (AMD) is a progressive disorder and advanced AMD is currently hard to cure, an accurate and informative prediction of a person's AMD risk using genetic information is desirable for early diagnosis and potential individualized clinical management. The objective of this study was to develop and validate novel prediction models for AMD risk using large genome-wide association studies datasets with different machine learning approaches. Methods Genotype data from 32,215 Caucasian individuals with age of ≥50 years from the International AMD Genomics Consortium in dbGaP were used to establish and test prediction models for AMD risk. Four different machine learning approaches-neural network, lasso regression, support vector machine, and random forest-were implemented. A standard logistic regression model using a genetic risk score was also considered. Results All machine learning-based methods achieved satisfactory performance for predicting advanced AMD cases (vs. normal controls) (area under the curve = 0.81-0.82, Brier score = 0.17-0.18 in a separate test dataset) and any stage AMD (vs. normal controls) (area under the curve = 0.78-0.79, Brier score = 0.18-0.20 in a separate test dataset). The prediction performance was further validated in an independent dataset of 783 subjects from UK Biobank (area under the curve = 0.67). Conclusions By applying multiple state-of-art machine learning approaches on large AMD genome-wide association studies datasets, the predictive models we established can provide an accurate estimation of an individual's AMD risk profile based on genetic information along with age. The online prediction interface is available at: https://yanq.shinyapps.io/no_vs_amd_NN/. Translational Relevance The accurate and individualized risk prediction model interface will greatly improve early diagnosis and enhance tailored clinical management of AMD.
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Affiliation(s)
- Qi Yan
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
- Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yale Jiang
- Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Heng Huang
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, PA, USA
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, PA, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y. Chew
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel E. Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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15
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AMD Genetics: Methods and Analyses for Association, Progression, and Prediction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1256:191-200. [PMID: 33848002 DOI: 10.1007/978-3-030-66014-7_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Age-related macular degeneration (AMD) is a multifactorial neurodegenerative disease, which is a leading cause of vision loss among the elderly in the developed countries. As one of the most successful examples of genome-wide association study (GWAS), a large number of genetic studies have been conducted to explore the genetic basis for AMD and its progression, of which over 30 loci were identified and confirmed. In this chapter, we review the recent development and findings of GWAS for AMD risk and progression. Then, we present emerging methods and models for predicting AMD development or its progression using large-scale genetic data. Finally, we discuss a set of novel statistical and analytical methods that were recently developed to tackle the challenges such as analyzing bilateral correlated eye-level outcomes that are subject to censoring with high-dimensional genetic data. Future directions for analytical studies of AMD genetics are also proposed.
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16
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Kalteh S, Saadat M. Lack of association between three common genetic variations of XPC and susceptibility to age-related macular degeneration, a preliminary study. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Numerous association studies have indicated that genetic alterations in genes involved in DNA repair processes are associated with the risk of age-related macular degeneration (ARMD). There is no published study on the relationship between common xeroderma pigmentosum complementation group C (XPC, MIM 613208) polymorphisms and susceptibility to ARMD. The aim of this study is to determine whether three common (Ala499Val, Lys939Gln, and PAT) genetic variants of XPC are associated with the risk of developing ARMD. A total of 120 ARMD patients and 118 healthy controls were included in the study. Genotyping analyses were carried out by PCR-based methods.
Results
Our analysis revealed that there was no relationship between the XPC polymorphisms and susceptibility to ARMD. In both case and control groups, strong linkage disequilibrium existed between three common (Ala499Val, Lys939Gln, and PAT) genetic polymorphisms of XPC. Statistical analysis showed no association between the haplotypes and the risk of ARMD.
Conclusions
The present data indicated that the common polymorphisms of XPC are not susceptible genetic variations for ARMD.
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17
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Jiang Y, Chiu CY, Yan Q, Chen W, Gorin MB, Conley YP, Lakhal-Chaieb ML, Cook RJ, Amos CI, Wilson AF, Bailey-Wilson JE, McMahon FJ, Vazquez AI, Yuan A, Zhong X, Xiong M, Weeks DE, Fan R. Gene-Based Association Testing of Dichotomous Traits With Generalized Functional Linear Mixed Models Using Extended Pedigrees: Applications to Age-Related Macular Degeneration. J Am Stat Assoc 2020; 116:531-545. [PMID: 34321704 PMCID: PMC8315575 DOI: 10.1080/01621459.2020.1799809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 07/09/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Genetics plays a role in age-related macular degeneration (AMD), a common cause of blindness in the elderly. There is a need for powerful methods for carrying out region-based association tests between a dichotomous trait like AMD and genetic variants on family data. Here, we apply our new generalized functional linear mixed models (GFLMM) developed to test for gene-based association in a set of AMD families. Using common and rare variants, we observe significant association with two known AMD genes: CFH and ARMS2. Using rare variants, we find suggestive signals in four genes: ASAH1, CLEC6A, TMEM63C, and SGSM1. Intriguingly, ASAH1 is down-regulated in AMD aqueous humor, and ASAH1 deficiency leads to retinal inflammation and increased vulnerability to oxidative stress. These findings were made possible by our GFLMM which model the effect of a major gene as a fixed mean, the polygenic contributions as a random variation, and the correlation of pedigree members by kinship coefficients. Simulations indicate that the GFLMM likelihood ratio tests (LRTs) accurately control the Type I error rates. The LRTs have similar or higher power than existing retrospective kernel and burden statistics. Our GFLMM-based statistics provide a new tool for conducting family-based genetic studies of complex diseases. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
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Affiliation(s)
- Yingda Jiang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Chi-Yang Chiu
- Division of Biostatistics, Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Baltimore, MD
| | - Qi Yan
- Division of Pulmonary Medicine, Allergy and Immunology, Children’s Hospital of Pittsburgh at The University of Pittsburgh, Pittsburgh, PA
| | - Wei Chen
- Division of Pulmonary Medicine, Allergy and Immunology, Children’s Hospital of Pittsburgh at The University of Pittsburgh, Pittsburgh, PA
| | - Michael B. Gorin
- Department of Ophthalmology, David Geffen School of Medicine, UCLA Stein Eye Institute, Los Angeles, CA
| | - Yvette P. Conley
- Department of Health Promotion and Development, University of Pittsburgh, Pittsburgh, PA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | - Richard J. Cook
- Department of Statistics and Actuarial Science, Waterloo, ON, Canada
| | | | - Alexander F. Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Baltimore, MD
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Baltimore, MD
| | - Francis J. McMahon
- Human Genetics Branch and Genetic Basis of Mood and Anxiety Disorders Section, National Institute of Mental Health, NIH, Bethesda, MD
| | - Ana I. Vazquez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI
| | - Ao Yuan
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC
| | - Xiaogang Zhong
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC
| | - Momiao Xiong
- Human Genetics Center, University of Texas, Houston, TX
| | - Daniel E. Weeks
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Ruzong Fan
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Baltimore, MD
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC
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18
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: https:/doi.org/10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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19
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Gupta MK, Rajeswari J, Reddy PR, Kumar KS, Chamundeswaramma KV, Vadde R. Genetic Marker Identification for the Detection of Early-Onset Gastric Cancer Through Genome-Wide Association Studies. RECENT ADVANCEMENTS IN BIOMARKERS AND EARLY DETECTION OF GASTROINTESTINAL CANCERS 2020:191-211. [DOI: 10.1007/978-981-15-4431-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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Oura Y, Nakamura M, Takigawa T, Fukushima Y, Wakabayashi T, Tsujikawa M, Nishida K. High-Temperature Requirement A 1 Causes Photoreceptor Cell Death in Zebrafish Disease Models. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:2729-2744. [PMID: 30273602 DOI: 10.1016/j.ajpath.2018.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/28/2018] [Accepted: 08/23/2018] [Indexed: 02/06/2023]
Abstract
Age-related macular degeneration (AMD) is an important cause of blindness. It is characterized by a retinal pigment epithelium (RPE) disorder that leads to death of photoreceptor cells (PRCs). AMD has a strong genetic association with high-temperature requirement A 1 (HTRA1). The relationship between HTRA1 and the AMD phenotype is unknown. In this study, we show that the expression of HTRA1 in PRCs, as well as in RPE, is increased by the disease-associated HTRA1 mutation and aging. Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay and quantitative PCR of apoptosis-associated caspases confirmed that PRC-specific overexpression of HTRA1 induced PRC death. Transgenic zebrafish overexpressing human HTRA1 in rod PRCs showed morphologic changes of the RPE, including PRC death and lipofuscin accumulation, features similar to those of early AMD. htra1 expression was also increased in a retinitis pigmentosa zebrafish model compared with wild type. In both fish lines, PRC death was rescued by the suppression of htra1 by the inhibitor 6-boroV. AKT-forkhead box O3 signaling downstream of HTRA1 was activated via a tumor growth factor β signal, resulting in PRC death. These findings suggest that HTRA1 derived from PRCs is associated with early AMD via PRC death. HTRA1 is a potentially effective target for neuroprotective therapy of early AMD and other degenerative diseases of PRCs.
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Affiliation(s)
- Yoshihito Oura
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan
| | - Machiko Nakamura
- Pain and Neuroscience Laboratories, Daiichi Sankyo Co, Ltd, Tokyo, Japan
| | - Tohru Takigawa
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan
| | - Yoko Fukushima
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan
| | - Taku Wakabayashi
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan
| | - Motokazu Tsujikawa
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan.
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Medical School, Suita, Japan
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21
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Md Bakri N, Ramachandran V, Hoo FK, Subrayan V, Isa H, Ngah NF, Mohamad NA, Ching SM, Chan YM, Ismail P, Ismail F, Sukiman ES, Wan Sulaiman WA. Copy number variation in VEGF gene as a biomarker of susceptibility to age-related macular degeneration. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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22
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Warwick A, Lotery A. Genetics and genetic testing for age-related macular degeneration. Eye (Lond) 2018; 32:849-857. [PMID: 29125146 PMCID: PMC5944647 DOI: 10.1038/eye.2017.245] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022] Open
Abstract
Considerable advances have been made in our understanding of age-related macular degeneration (AMD) genetics over the past decade. The genetic associations discovered to date are estimated to account for approximately half of AMD heritability, and functional studies of these variants have revealed new insights into disease pathogenesis, leading to the development of potential novel therapies. There is furthermore growing interest in genetic testing for predicting an individual's risk of AMD and offering personalised preventive or therapeutic treatments. We review the progress made so far in AMD genetics and discuss the possible applications for genetic testing.
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Affiliation(s)
| | - A Lotery
- Clinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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Seddon JM. Macular Degeneration Epidemiology: Nature-Nurture, Lifestyle Factors, Genetic Risk, and Gene-Environment Interactions - The Weisenfeld Award Lecture. Invest Ophthalmol Vis Sci 2018; 58:6513-6528. [PMID: 29288272 PMCID: PMC5749242 DOI: 10.1167/iovs.17-23544] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Johanna M Seddon
- Ophthalmic Epidemiology and Genetics Service, Tufts Medical Center, Boston, Massachusetts, United States.,Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, United States.,Sackler School of Graduate Biomedical Sciences and Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States
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24
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Askou AL, Alsing S, Holmgaard A, Bek T, Corydon TJ. Dissecting microRNA dysregulation in age-related macular degeneration: new targets for eye gene therapy. Acta Ophthalmol 2018; 96:9-23. [PMID: 28271607 DOI: 10.1111/aos.13407] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/02/2017] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression in humans. Overexpression or depletion of individual miRNAs is associated with human disease. Current knowledge suggests that the retina is influenced by miRNAs and that dysregulation of miRNAs as well as alterations in components of the miRNA biogenesis machinery are involved in retinal diseases, including age-related macular degeneration (AMD). Furthermore, recent studies have indicated that the vitreous has a specific panel of circulating miRNAs and that this panel varies according to the specific pathological stress experienced by the retinal cells. MicroRNA (miRNA) profiling indicates subtype-specific miRNA profiles for late-stage AMD highlighting the importance of proper miRNA regulation in AMD. This review will describe the function of important miRNAs involved in inflammation, oxidative stress and pathological neovascularization, the key molecular mechanisms leading to AMD, and focus on dysregulated miRNAs as potential therapeutic targets in AMD.
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Affiliation(s)
| | - Sidsel Alsing
- Department of Biomedicine; Aarhus University; Aarhus C Denmark
| | | | - Toke Bek
- Department of Ophthalmology; Aarhus University Hospital; Aarhus C Denmark
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25
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Jahanfar F, Hamishehkar H. Exploring the association of rs10490924 polymorphism with age-related macular degeneration: An in silico approach. J Mol Graph Model 2018; 80:52-58. [PMID: 29316486 DOI: 10.1016/j.jmgm.2017.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. ARMS2 gene encodes a putative small (11 kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of A69S mutation, we performed a detailed analysis of an ARMS2 sequence with a broad set of bioinformatics tools. In silico analysis was followed to predict the tertiary structure, putative binding site regions, and binding site residues. Also, the effects of this mutation on protein stability, aggregation propensity, and homodimerization were analyzed. Next, a molecular dynamic simulation was carried out to understand the dynamic behavior of wild-type, A69S, and phosphorylated A69S structures. The results showed alterations in the putative post-translational modification sites on the ARMS2 protein, due to the mutation. Furthermore, the stability of protein and putative homodimer conformations were affected by the mutation. Molecular dynamic simulation results revealed that A69S mutation enhances the rigidity of the ARMS2 structure and residue serine at position 69 is buried and may not be phosphorylated; however, phosphorylated serine enhances the flexibility of the ARMS2 structure. In conclusion, our study provides new insights into the deleterious effects of A69S mutation on the ARMS2 structure.
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Affiliation(s)
- Farhad Jahanfar
- Biotechnology Research Center and Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Hamishehkar
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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26
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Exploring the association of rs10490924 polymorphism with age-related macular degeneration: An in silico approach. J Mol Graph Model 2017; 77:280-285. [PMID: 28915445 DOI: 10.1016/j.jmgm.2017.09.003] [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: 04/20/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/21/2022]
Abstract
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools. In silico analysis was followed to predict the tertiary structure, putative binding site regions, and binding site residues. Also, the effects of this mutation on protein stability, aggregation propensity, and homodimerization were analyzed. Next, a molecular dynamic simulation was carried out to understand the dynamic behavior of wild-type, A69S, and phosphorylated A69S structures. The results showed alterations in the putative post-translational modification sites on the ARMS2 protein, due to the mutation. Furthermore, the stability of protein and putative homodimer conformations were affected by the mutation. Molecular dynamic simulation results revealed that the A69S mutation enhances the rigidity of the ARMS2 structure and residue serine at position 69 is buried and may not be phosphorylated; however, phosphorylated serine enhances the flexibility of the ARMS2 structure. In conclusion, our study provides new insights into the deleterious effects of the A69S mutation on the ARMS2 structure.
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27
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Tan PL, Garrett ME, Willer JR, Campochiaro PA, Campochiaro B, Zack DJ, Ashley-Koch AE, Katsanis N. Systematic Functional Testing of Rare Variants: Contributions of CFI to Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2017; 58:1570-1576. [PMID: 28282489 PMCID: PMC6022411 DOI: 10.1167/iovs.16-20867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purpose Genome-wide association (GWAS) and sequencing studies for AMD have highlighted the importance of coding variants at loci that encode components of the complement pathway. However, assessing the contribution of such alleles to AMD, especially when they are rare, remains coarse, in part because of the persistent challenge in establishing their functional relevance. Others and we have shown previously that rare alleles in complement factor I (CFI) can be tested functionally using a surrogate in vivo assay of retinal vascularization in zebrafish embryos. Here, we have implemented and scaled these tools to assess the overall contribution of rare alleles in CFI to AMD. Methods We performed targeted sequencing of CFI in 731 AMD patients, followed by replication in a second patient cohort of 511 older healthy individuals. Systematic functional testing of all alleles and post-hoc statistical analysis of functional variants was also performed. Results We discovered 20 rare coding nonsynonymous variants, including the previously reported G119R allele. In vivo testing led to the identification of nine variants that alter CFI; six of which are associated with hypoactive complement factor I (FI). Post-hoc analysis in ethnically matched, population controls showed six of these to be present exclusively in cases. Conclusions Taken together, our data argue that multiple rare and ultra-rare alleles in CFI contribute to AMD pathogenesis; they improve the precision of the assessment of the contribution of CFI to AMD; and they offer a rational route to establishing both causality and direction of allele effect for genes associated with this disorder.
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Affiliation(s)
- Perciliz L Tan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States 2Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States
| | - Melanie E Garrett
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States
| | - Peter A Campochiaro
- Departments of Ophthalmology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - Betsy Campochiaro
- Departments of Ophthalmology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - Donald J Zack
- Departments of Ophthalmology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States 4Center for Stem Cells and Ocular Regenerative Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States 5Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - Allison E Ashley-Koch
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States 6Departments of Medicine, Molecular Genetics and Microbiology, Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, United States 2Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States
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28
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Bonyadi M, Foruzandeh Z, Mohammadian T, Fotouhi N, Soheilian M, Jabbarpoor Bonyadi MH, Javadzadeh A, Moein H, Yaseri M. Evaluation of CC-cytokine ligand 2 and complementary factor H Y402H polymorphisms and their interactional association with age-related macular degeneration. Acta Ophthalmol 2016; 94:e779-e785. [PMID: 27316788 DOI: 10.1111/aos.13143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 04/30/2016] [Indexed: 12/15/2022]
Abstract
PURPOSE To evaluate the association of CC-cytokine ligand 2 CCL2-2518 (rs1024611) single nucleotide polymorphism, complement factor H (CFH Y402H) and their possible interaction in developing advanced age-related macular degeneration (AMD). METHODS In this case-control study, DNA samples from 266 patients with advanced AMD and 229 healthy controls were genotyped for CCL2 polymorphism and also 254 patients and 164 healthy controls were genotyped for CFH polymorphism. The possible associations of these polymorphisms with susceptibility to AMD independently and in different joint combinations were evaluated. RESULTS The genotype frequency for CFH was found to be significantly different between AMD and normal controls (31.5% versus 20.7%, OR = 3.56, p < 0.001 for CC and 52.4% versus 41.5%, OR = 2.96, p < 0.001 for CT genotype). However, no significant association between CCL2 polymorphism and AMD was observed in this cohort (OR = 1.15 and OR = 0.8, p = 0.172). Interestingly, studying the joint effects of two genotypes (TT genotype of CFH Y402H and AG genotype of CCL2-2518) showed more significant protective effect against AMD (p = 0.0001), while the risk effect of CC and CT genotypes of CFH was only visible in the presence of AA genotype of CCL2-2518 (p = 0.044 and p = 0.05). CONCLUSION Complement factor H Y402H polymorphism is strongly associated with advanced type AMD. Although this study revealed no association of CCL2-2518 with AMD, the risk effect of CFH genotypes was only visible in the presence of AA genotype of CCL2-2518. AG genotype of CCL2-2518 in combination with TT genotype of CFH Y402H showed significant protective effect against AMD.
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Affiliation(s)
- Mortaza Bonyadi
- Center of Excellence for Biodiversity; Faculty of Natural Sciences; University of Tabriz; Tabriz Iran
- Liver and Gastrointestinal Disease Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Zahra Foruzandeh
- Center of Excellence for Biodiversity; Faculty of Natural Sciences; University of Tabriz; Tabriz Iran
| | - Tahereh Mohammadian
- Center of Excellence for Biodiversity; Faculty of Natural Sciences; University of Tabriz; Tabriz Iran
| | - Nikou Fotouhi
- Center of Excellence for Biodiversity; Faculty of Natural Sciences; University of Tabriz; Tabriz Iran
| | - Masoud Soheilian
- Ocular Tissue Engineering Research Center; Ophthalmic Research Center; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Mohammad Hossein Jabbarpoor Bonyadi
- Center of Excellence for Biodiversity; Faculty of Natural Sciences; University of Tabriz; Tabriz Iran
- Ocular Tissue Engineering Research Center; Ophthalmic Research Center; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Alireza Javadzadeh
- Department of Ophthalmology; Tabriz University of Medical Sciences; Tabriz Iran
| | - Hamidreza Moein
- Ocular Tissue Engineering Research Center; Ophthalmic Research Center; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Mehdi Yaseri
- Department of Biostatistics and Epidemiology; Tehran University of Medical Sciences; Tehran Iran
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29
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Wagner EK, Raychaudhuri S, Villalonga MB, Java A, Triebwasser MP, Daly MJ, Atkinson JP, Seddon JM. Mapping rare, deleterious mutations in Factor H: Association with early onset, drusen burden, and lower antigenic levels in familial AMD. Sci Rep 2016; 6:31531. [PMID: 27572114 PMCID: PMC5004131 DOI: 10.1038/srep31531] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/21/2016] [Indexed: 02/02/2023] Open
Abstract
The genetic architecture of age-related macular degeneration (AMD) involves numerous genetic variants, both common and rare, in the coding region of complement factor H (CFH). While these variants explain high disease burden in some families, they fail to explain the pathology in all. We selected families whose AMD was unexplained by known variants and performed whole exome sequencing to probe for other rare, highly penetrant variants. We identified four rare loss-of-function variants in CFH associated with AMD. Missense variant CFH 1:196646753 (C192F) segregated perfectly within a family characterized by advanced AMD and drusen temporal to the macula. Two families, each comprising a pair of affected siblings with extensive extramacular drusen, carried essential splice site variant CFH 1:196648924 (IVS6+1G>A) or missense variant rs139360826 (R175P). In a fourth family, missense variant rs121913058 (R127H) was associated with AMD. Most carriers had early onset bilateral advanced AMD and extramacular drusen. Carriers tended to have low serum Factor H levels, especially carriers of the splice variant. One missense variant (R127H) has been previously shown not to be secreted. The two other missense variants were produced recombinantly: compared to wild type, one (R175P) had no functional activity and the other (C192F) had decreased secretion.
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Affiliation(s)
- Erin K. Wagner
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Mercedes B. Villalonga
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Anuja Java
- Washington University School of Medicine, Department of Medicine, Division of Nephrology, Saint Louis, MO 63110, USA
| | - Michael P. Triebwasser
- Washington University School of Medicine, Department of Medicine, Division of Rheumatology, Saint Louis, MO 63110, USA
| | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA 02115, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John P. Atkinson
- Washington University School of Medicine, Department of Medicine, Division of Rheumatology, Saint Louis, MO 63110, USA
| | - Johanna M. Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA 02111, USA
- Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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Polley S, Cipriani V, Khan JC, Shahid H, Moore AT, Yates JRW, Hollox EJ. Analysis of copy number variation at DMBT1 and age-related macular degeneration. BMC MEDICAL GENETICS 2016; 17:44. [PMID: 27416785 PMCID: PMC4946147 DOI: 10.1186/s12881-016-0311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 07/07/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND DMBT1 is a gene that shows extensive copy number variation (CNV) that alters the number of bacteria-binding domains in the protein and has been shown to activate the complement pathway. It lies next to the ARMS2/HTRA1 genes in a region of chromosome 10q26, where single nucleotide variants have been strongly associated with age-related macular degeneration (AMD), the commonest cause of blindness in Western populations. Complement activation is thought to be a key factor in the pathogenesis of this condition. We sought to investigate whether DMBT1 CNV plays any role in the susceptibility to AMD. METHODS We analysed long-range linkage disequilibrium of DMBT1 CNV1 and CNV2 with flanking single nucleotide polymorphisms (SNPs) using our previously published CNV and HapMap Phase 3 SNP data in the CEPH Europeans from Utah (CEU). We then typed a large cohort of 860 AMD patients and 419 examined age-matched controls for copy number at DMBT1 CNV1 and CNV2 and combined these data with copy numbers from a further 480 unexamined controls. RESULTS We found weak linkage disequilibrium between DMBT1 CNV1 and CNV2 with the SNPs rs1474526 and rs714816 in the HTRA1/ARMS2 region. By directly analysing copy number variation, we found no evidence of association of CNV1 or CNV2 with AMD. CONCLUSIONS We have shown that copy number variation at DMBT1 does not affect risk of developing age-related macular degeneration and can therefore be ruled out from future studies investigating the association of structural variation at 10q26 with AMD.
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Affiliation(s)
- Shamik Polley
- Department of Genetics, University of Leicester, Leicester, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Jane C Khan
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Australia
| | - Humma Shahid
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Department of Ophthamology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
- Department of Ophthalmology UCSF Medical School, San Francisco, USA
| | - John R W Yates
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK.
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Abstract
Age-related macular degeneration (AMD), widely prevalent across the globe, is a major stakeholder among adult visual morbidity and blindness, not only in the Western world but also in Asia. Several risk factors have been identified, including critical genetic factors, which were never imagined 2 decades ago. The etiopathogenesis is emerging to demonstrate that immune and complement-related inflammation pathway members chronically exposed to environmental insults could justifiably influence disease morbidity and treatment outcomes. Approximately half a dozen physiological and biochemical cascades are disrupted in the AMD disease genesis, eventually leading to the distortion and disruption of the subretinal space, subretinal pigment epithelium, and Bruch membrane, thus setting off chaos and disorder for signs and symptoms to manifest. Approximately 3 dozen genetic factors have so far been identified, including the recent ones, through powerful genomic technologies and large robust sample sizes. The noteworthy genetic variants (common and rare) are complement factor H, complement factor H-related genes 1 to 5, C3, C9, ARMS2/HTRA1, vascular endothelial growth factor A, vascular endothelial growth factor receptor 2/KDR, and rare variants (show causal link) such as TIMP3, fibrillin, COL4A3, MMP19, and MMP9. Despite the enormous amount of scientific information generated over the years, diagnostic genetic or biomarker tests are still not available for clinicians to understand the natural course of the disease and its management in a patient. However, further research in the field should reduce this gap not only by aiding the clinician but also through the possibilities of clinical intervention with complement pathway-related inhibitors entering preclinical and clinical trials in the near future.
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Tan PL, Bowes Rickman C, Katsanis N. AMD and the alternative complement pathway: genetics and functional implications. Hum Genomics 2016; 10:23. [PMID: 27329102 PMCID: PMC4915094 DOI: 10.1186/s40246-016-0079-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 12/22/2022] Open
Abstract
Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses. Here, we review the genetic architecture of AMD, considering the contribution of both common and rare alleles to susceptibility, and we explore the possible mechanistic links between photoreceptor degeneration and the alternative complement pathway, a cascade that has emerged as the most potent genetic driver of this disorder.
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Affiliation(s)
- Perciliz L Tan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Catherine Bowes Rickman
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Ophthalmology, Duke Eye Center, Duke University, Durham, NC, 27710, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, 27710, USA. .,Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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33
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Karkhane R, Ahmadraji A, Riazi Esfahani M, Roohipour R, Alami Harandi Z, Lashay A, Kermani MS, Roozafzoon R, Khoshzaban A. Complement factor H and LOC387715/ARMS2/HTRA1 variant's frequencies and phenotypic associations in neovascular age-related macular degeneration, a pilot study. J Curr Ophthalmol 2016; 28:32-6. [PMID: 27239600 PMCID: PMC4881216 DOI: 10.1016/j.joco.2016.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/15/2015] [Indexed: 11/30/2022] Open
Abstract
Purpose To evaluate the frequency of 12 single nucleotide polymorphisms (SNPs) of complement factor H (CFH) and LOC387715/ARMS2/HRTA1 and their association with some of the presenting clinical features of neovascular age-related macular degeneration (AMD). Methods In this prospective non-comparative case series forty four naïve patients with neovascular AMD were genotyped using sequencing or Sequenom iPLEX technology. Descriptive tests were used for displaying the magnitude of each allele, gender distribution, and age at diagnosis. Fisher exact test was used to evaluate the correlation between visual acuity (VA) and different alleles. Also Kruskal-Wallis test was used for comparison between age at the time of diagnosis and different alleles. Results The most frequent SNP among studied patients was rs1061147 with 100% frequency rate. The least common was rs2672598 with a frequency of 52.27%. Only the allele rs800292 of CFH locus on 1q32 was associated with VA better than 20/200 (p value = 0.034). The frequency of this allele was 77.27% (34 patients) in this study. There was no significant association between any of alleles, and VA worse than 20/200(p > 0.05). Fifteen patients had bilateral exudative AMD (34.09%). There was no significant difference between alleles in bilateral neovascular AMD and unilateral disease. Also bilateral and unilateral patients were not different in terms of age, gender or VA (p value: 0.330, 0.764 and 0.456 respectively). There was also no significant association between any of SNPs and bilaterality of disease. Conclusion We designated the frequencies of SNPs of CFH and LOC387715/ARMS2/HRTA1 in neovascular AMD in a sample of Iranian patients. Only the allele rs800292 of CFH locus on chromosome 1q32 was associated with better VA.
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Affiliation(s)
- Reza Karkhane
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Aliasghar Ahmadraji
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Riazi Esfahani
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramak Roohipour
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Alami Harandi
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Lashay
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Sharifzadeh Kermani
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Roozafzoon
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahad Khoshzaban
- Stem Cell Preparation Unit, Eye Research Center, Farabi Eye Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Cooke Bailey JN, Hoffman JD, Sardell RJ, Scott WK, Pericak-Vance MA, Haines JL. The Application of Genetic Risk Scores in Age-Related Macular Degeneration: A Review. J Clin Med 2016; 5:jcm5030031. [PMID: 26959068 PMCID: PMC4810102 DOI: 10.3390/jcm5030031] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/19/2016] [Accepted: 02/29/2016] [Indexed: 01/08/2023] Open
Abstract
Age-related macular degeneration (AMD), a highly prevalent and impactful disease of aging, is inarguably influenced by complex interactions between genetic and environmental factors. Various risk scores have been tested that assess measurable genetic and environmental contributions to disease. We herein summarize and review the ability and utility of these numerous models for prediction of AMD and suggest additional risk factors to be incorporated into clinically useful predictive models of AMD.
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Affiliation(s)
- Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA.
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA.
| | - Rebecca J Sardell
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
| | - William K Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA.
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
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35
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Sparrow JR, Duncker T. Fundus Autofluorescence and RPE Lipofuscin in Age-Related Macular Degeneration. J Clin Med 2015; 3:1302-21. [PMID: 25774313 PMCID: PMC4358814 DOI: 10.3390/jcm3041302] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genes that increase susceptibility to age-related macular degeneration (AMD) have been identified; however, since many individuals carrying these risk alleles do not develop disease, other contributors are involved. One additional factor, long implicated in the pathogenesis of AMD, is the lipofuscin of retinal pigment epithelium (RPE). The fluorophores that constitute RPE lipofuscin also serve as a source of autofluorescence (AF) that can be imaged by confocal laser ophthalmoscopy. The AF originating from lipofuscin is excited by the delivery of short wavelength (SW) light. A second autofluorescence is emitted from the melanin of RPE (and choroid) upon near-infrared (NIR-AF) excitation. SW-AF imaging is currently used in the clinical management of retinal disorders and the advantages of NIR-AF are increasingly recognized. Here we visit the damaging properties of RPE lipofuscin that could be significant when expressed on a background of genetic susceptibility. To advance interpretations of disease-related patterns of fundus AF in AMD, we also consider the photochemical and spectrophotometric features of the lipofuscin compounds responsible for generating the fluorescence emission.
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Affiliation(s)
- Janet R. Sparrow
- Department of Ophthalmology, Columbia University Medical Center, 635 W. 165th Street, New York, NY 10032, USA; E-Mail:
- Department of Pathology and Cell Biology, Columbia University Medical Center, 630 168th Street, New York, NY 10032, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-212-305-0044
| | - Tobias Duncker
- Department of Ophthalmology, Columbia University Medical Center, 635 W. 165th Street, New York, NY 10032, USA; E-Mail:
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Reichel E, Aldave AJ, Schaumberg DA, Singh R, Henderson BA. Genetic testing for age-related macular degeneration: progress and perspectives. EXPERT REVIEW OF OPHTHALMOLOGY 2015. [DOI: 10.1586/17469899.2015.1059752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Black JRM, Clark SJ. Age-related macular degeneration: genome-wide association studies to translation. Genet Med 2015; 18:283-9. [PMID: 26020418 PMCID: PMC4823638 DOI: 10.1038/gim.2015.70] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/20/2015] [Indexed: 02/01/2023] Open
Abstract
In recent years, genome-wide association studies (GWAS), which are able to analyze the contribution to disease of genetic variations that are common within a population, have attracted considerable investment. Despite identifying genetic variants for many conditions, they have been criticized for yielding data with minimal clinical utility. However, in this regard, age-related macular degeneration (AMD), the most common form of blindness in the Western world, is a striking exception. Through GWAS, common genetic variants at a number of loci have been discovered. Two loci in particular, including genes of the complement cascade on chromosome 1 and the ARMS2/HTRA1 genes on chromosome 10, have been shown to convey significantly increased susceptibility to developing AMD. Today, although it is possible to screen individuals for a genetic predisposition to the disease, effective interventional strategies for those at risk of developing AMD are scarce. Ongoing research in this area is nonetheless promising. After providing brief overviews of AMD and common disease genetics, we outline the main recent advances in the understanding of AMD, particularly those made through GWAS. Finally, the true merit of these findings and their current and potential translational value is examined.Genet Med 18 4, 283-289.
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Affiliation(s)
- James R M Black
- Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Simon J Clark
- Centre for Ophthalmology and Vision Sciences, Institute of Human Development, University of Manchester, Manchester, UK
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Pei X, Ma K, Xu J, Wang N, Liu N. Inhibition of cell proliferation and migration after HTRA1 knockdown in retinal pigment epithelial cells. Graefes Arch Clin Exp Ophthalmol 2015; 253:565-72. [PMID: 25550099 DOI: 10.1007/s00417-014-2901-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/06/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022] Open
Abstract
PURPOSE The purpose of this study was to investigate the role of HtrA serine peptidase 1 (HTRA1) in the proliferation and migration of cells of the human retinal pigment epithelial cell line ARPE-19, and the possible mechanisms involved. METHODS ARPE-19 cells were transduced by a recombinant lentiviral vector carrying HTRA1-shRNA to knockdown HTRA1 expression. Subsequent HTRA1 gene and HTRA1 protein levels in these cells and control cells were detected by quantitative real-time PCR and Western blot, respectively. Changes in cell proliferation and migration associated with the inhibition of HTRA1 expression were assessed, as well as changes in the mRNA levels of transforming growth factor beta 1 (TGFB1), bone morphogenetic protein 4 (BMP4), and bone morphogenetic protein 2 (BMP2). RESULTS The recombinant lentivirus carrying HTRA1-shRNA was successfully generated, as evidenced by reduced levels of HTRA1 mRNA and HTRA1 protein in ARPE-19 cells. The knockdown of HTRA1 in ARPE-19 cells was associated with reduced cellular proliferation and migration, and increased mRNA levels of TGF-β1, BMP4, and BMP2. CONCLUSIONS Silence of the HTRA1 gene was associated with significantly higher levels of TGF-β1, BMP4, and BMP2 mRNA and reduction in the proliferation and migration of ARPE-19 cells.
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Affiliation(s)
- Xueting Pei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, No. 1 Dongjiaominxiang, Dongcheng District, Beijing, China,
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Tsuchihashi T, Mori K, Horie-Inoue K, Okazaki Y, Awata T, Inoue S, Yoneya S. Prognostic phenotypic and genotypic factors associated with photodynamic therapy response in patients with age-related macular degeneration. Clin Ophthalmol 2014; 8:2471-8. [PMID: 25525324 PMCID: PMC4266424 DOI: 10.2147/opth.s71305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND This study aimed to demonstrate the phenotypic and genotypic factors associated with photodynamic therapy (PDT) for age-related macular degeneration (AMD). METHODS The study included 149 patients with exudative AMD treated by PDT. Eight phenotypic factors and ten genotypic factors for three single nucleotide polymorphisms (SNPs; rs800292, rs1061170, rs1410996) in the complement factor H (CFH) gene, rs 11200638-SNP in the high temperature requirement A-1 (HTRA1) gene, two SNPs (rs699947, rs2010963) in the vascular endothelial growth factor (VEGF) gene, and four SNPs (rs12948385, rs12150053, rs9913583, rs1136287) in the pigment epithelium-derived factor (PEDF) gene were evaluated. RESULTS A significant association with best-corrected visual acuity change was demonstrated in the greatest linear dimension, presence or absence of pigment epithelial detachment, and HTRA1-rs11200638 genotype statistically (P=3.67×10(-4), 1.95×10(-2), 1.24×10(-3), respectively). Best-corrected visual acuity in patients with AA genotype of HTRA1-rs11200638 significantly decreased compared with that in patients with GG genotype (P=1.33×10(-3)). Logistic regression analyses demonstrated HTRA1-rs11200638 genotype was most strongly associated with best-corrected visual acuity outcome from baseline at 12 months after photodynamic therapy (P=4.60×10(-3); odds ratio 2.363; 95% confidence interval 1.303-4.285). CONCLUSION The HTRA1-rs11200638 variant showed the most significant association. Therefore, this variant may be used as a prognostic factor to estimate the PDT response with significant predictive power.
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Affiliation(s)
- Takashi Tsuchihashi
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Keisuke Mori
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Iruma, Saitama, Japan
| | - Takuya Awata
- Division of Endocrinology and Diabetes, Department of Medicine, Saitama Medical University, Iruma, Saitama, Japan
- Division of RI Laboratory, Biomedical Research Center, Saitama Medical University, Iruma, Saitama, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shin Yoneya
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Current knowledge and trends in age-related macular degeneration: genetics, epidemiology, and prevention. Retina 2014; 34:423-41. [PMID: 24285245 DOI: 10.1097/iae.0000000000000036] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE To address the most dynamic and current issues concerning human genetics, risk factors, pharmacoeconomics, and prevention regarding age-related macular degeneration. METHODS An online review of the database Pubmed and Ovid was performed, searching for the key words: age-related macular degeneration, AMD, pharmacoeconomics, risk factors, VEGF, prevention, genetics and their compound phrases. The search was limited to articles published since 1985 to date. All returned articles were carefully screened and their references were manually reviewed for additional relevant data. The webpage www.clinicaltrials.gov was also accessed in search of relevant research trials. RESULTS A total of 366 articles were reviewed, including 64 additional articles extracted from the references and 25 webpages and online databases from different institutions. At the end, only 244 references were included in this review. CONCLUSION Age-related macular degeneration is a complex multifactorial disease that has an uneven manifestation around the world but with one common denominator, it is increasing and spreading. The economic burden that this disease poses in developed nations will increase in the coming years. Effective preventive therapies need to be developed in the near future.
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Horie-Inoue K, Inoue S. Genomic aspects of age-related macular degeneration. Biochem Biophys Res Commun 2014; 452:263-75. [PMID: 25111812 DOI: 10.1016/j.bbrc.2014.08.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/04/2014] [Indexed: 11/29/2022]
Abstract
Age-related macular degeneration (AMD) is a major late-onset posterior eye disease that causes central vision to deteriorate among elderly populations. The predominant lesion of AMD is the macula, at the interface between the outer retina and the inner choroid. Recent advances in genetics have revealed that inflammatory and angiogenic pathways play critical roles in the pathophysiology of AMD. Genome-wide association studies have identified ARMS2/HTRA1 and CFH as major AMD susceptibility genes. Genetic studies for AMD will contribute to the prevention of central vision loss, the development of new treatment, and the maintenance of quality of vision for productive aging.
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Affiliation(s)
- Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan.
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan; Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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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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Querques G, Souied EH. The role of omega-3 and micronutrients in age-related macular degeneration. Surv Ophthalmol 2014; 59:532-9. [DOI: 10.1016/j.survophthal.2014.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 12/27/2022]
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Malek G, Lad EM. Emerging roles for nuclear receptors in the pathogenesis of age-related macular degeneration. Cell Mol Life Sci 2014; 71:4617-36. [PMID: 25156067 DOI: 10.1007/s00018-014-1709-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/20/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of vision loss in the elderly in the Western world. Over the last 30 years, our understanding of the pathogenesis of the disease has grown exponentially thanks to the results of countless epidemiology, genetic, histological, and biochemical studies. This information, in turn, has led to the identification of multiple biologic pathways potentially involved in development and progression of AMD, including but not limited to inflammation, lipid and extracellular matrix dysregulation, and angiogenesis. Nuclear receptors are a superfamily of transcription factors that have been shown to regulate many of the pathogenic pathways linked with AMD and as such they are emerging as promising targets for therapeutic intervention. In this review, we will present the fundamental phenotypic features of AMD and discuss our current understanding of the pathobiological disease mechanisms. We will introduce the nuclear receptor superfamily and discuss the current literature on their effects on AMD-related pathophysiology.
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Affiliation(s)
- Goldis Malek
- Department of Ophthalmology, Duke University School of Medicine, 2351 Erwin Road, AERI Room 4006, Durham, NC, 27710, USA,
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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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Askou AL. Development of gene therapy for treatment of age-related macular degeneration. Acta Ophthalmol 2014; 92 Thesis3:1-38. [PMID: 24953666 DOI: 10.1111/aos.12452] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intraocular neovascular diseases are the leading cause of blindness in the Western world in individuals over the age of 50. Age-related macular degeneration (AMD) is one of these diseases. Exudative AMD, the late-stage form, is characterized by abnormal neovessel development, sprouting from the choroid into the avascular subretinal space, where it can suddenly cause irreversible damage to the vulnerable photoreceptor (PR) cells essential for our high-resolution, central vision. The molecular basis of AMD is not well understood, but several growth factors have been implicated including vascular endothelial growth factor (VEGF), and the advent of anti-VEGF therapy has markedly changed the outcome of treatment. However, common to all current therapies for exudative AMD are the complications of repeated monthly intravitreal injections, which must be continued throughout one's lifetime to maintain visual benefits. Additionally, some patients do not benefit from established treatments. Strategies providing long-term suppression of inappropriate ocular angiogenesis are therefore needed, and gene therapy offers a potential powerful technique. This study aimed to develop a strategy based on RNA interference (RNAi) for the sustained attenuation of VEGF. We designed a panel of anti-VEGF short hairpin RNAs (shRNA), and based on the most potent shRNAs, microRNA (miRNA)-mimicked hairpins were developed. We demonstrated an additive VEGF silencing effect when we combined the miRNAs in a tricistronic miRNA cluster. To meet the requirements for development of medical treatments for AMD with long-term effects, the shRNA/miRNA is expressed from vectors based on adeno-associated virus (AAV) or lentivirus (LV). Both vector systems have been found superior in terms of transduction efficiency and persistence in gene expression in retinal cells. The capacity of AAV-encoded RNAi effector molecules to silence endogenous VEGF gene expression was evaluated in mouse models, including the model of laser-induced choroidal neovascularization (CNV), and we found that subretinal administration of self-complementary (sc)-AAV2/8 encoding anti-VEGF shRNAs can impair vessel formation. In parallel, a significant reduction of endogenous VEGF was demonstrated following injection of scAAV2/8 vectors expressing multiple anti-VEGF miRNAs into murine hind limb muscles. Furthermore, in an ongoing project we have designed versatile, multigenic LV vectors with combined expression of multiple miRNAs and proteins, including pigment epithelium-derived factor (PEDF), a multifunctional, secreted protein that has anti-angiogenic and neurotrophic functions. Co-expression of miRNAs and proteins from a single viral vector increases safety by minimizing the viral load necessary to obtain a therapeutic effect and thereby reduces the risk of insertional mutagenesis as well as the immune response against viral proteins. Our results show co-expression of functional anti-VEGF-miRNAs and PEDF in cell studies, and in vivo studies reveal an efficient retinal pigment epithelium (RPE)-specific gene expression following the incorporation of the vitelliform macular dystrophy 2 (VMD2) promoter, demonstrating the potential applicability of our multigenic LV vectors in ocular anti-VEGF gene therapy, including combination therapy for treatment of exudative AMD. In conclusion, these highly promising data clearly demonstrate that viral-encoded RNAi effector molecules can be used for the inhibition of neovascularization and will, in combination with the growing interest of applying DNA- or RNA-based technologies in the clinic, undoubtedly contribute to the development of efficacious long-term gene therapy treatment of intraocular neovascular diseases.
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Fritsche LG, Fariss RN, Stambolian D, Abecasis GR, Curcio CA, Swaroop A. Age-related macular degeneration: genetics and biology coming together. Annu Rev Genomics Hum Genet 2014; 15:151-71. [PMID: 24773320 DOI: 10.1146/annurev-genom-090413-025610] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic and genomic studies have enhanced our understanding of complex neurodegenerative diseases that exert a devastating impact on individuals and society. One such disease, age-related macular degeneration (AMD), is a major cause of progressive and debilitating visual impairment. Since the pioneering discovery in 2005 of complement factor H (CFH) as a major AMD susceptibility gene, extensive investigations have confirmed 19 additional genetic risk loci, and more are anticipated. In addition to common variants identified by now-conventional genome-wide association studies, targeted genomic sequencing and exome-chip analyses are uncovering rare variant alleles of high impact. Here, we provide a critical review of the ongoing genetic studies and of common and rare risk variants at a total of 20 susceptibility loci, which together explain 40-60% of the disease heritability but provide limited power for diagnostic testing of disease risk. Identification of these susceptibility loci has begun to untangle the complex biological pathways underlying AMD pathophysiology, pointing to new testable paradigms for treatment.
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Affiliation(s)
- Lars G Fritsche
- Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109; ,
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Kuo JZ, Wong TY, Ong FS. Genetic risk, ethnic variations and pharmacogenetic biomarkers in age-related macular degeneration and polypoidal choroidal vasculopathy. EXPERT REVIEW OF OPHTHALMOLOGY 2014; 8:127-140. [PMID: 24860613 DOI: 10.1586/eop.13.3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jane Z Kuo
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 ; Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 ; Department of Ophthalmology, Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Taiwan
| | - Tien Y Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore ; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Frank S Ong
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 ; Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
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Sobrin L, Seddon JM. Nature and nurture- genes and environment- predict onset and progression of macular degeneration. Prog Retin Eye Res 2013; 40:1-15. [PMID: 24374240 DOI: 10.1016/j.preteyeres.2013.12.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/09/2013] [Accepted: 12/12/2013] [Indexed: 12/19/2022]
Abstract
Age-related macular degeneration (AMD) is a common cause of irreversible visual loss and the disease burden is rising world-wide as the population ages. Both environmental and genetic factors contribute to the development of this disease. Among environmental factors, smoking, obesity and dietary factors including antioxidants and dietary fat intake influence onset and progression of AMD. There are also several lines of evidence that link cardiovascular, immune and inflammatory biomarkers to AMD. The genetic etiology of AMD has been and continues to be an intense and fruitful area of investigation. Genome-wide association studies have revealed numerous common variants associated with AMD and sequencing is increasing our knowledge of how rare genetic variants strongly impact disease. Evidence for interactions between environmental, therapeutic and genetic factors is emerging and elucidating the mechanisms of this interplay remains a major challenge in the field. Genotype-phenotype associations are evolving. The knowledge of non-genetic, modifiable risk factors along with information about heritability and genetic risk variants for this disease acquired over the past 25 years have greatly improved patient management and our ability to predict which patients will develop or progress to advanced forms of AMD. Personalized medicine and individualized prevention and treatment strategies may become a reality in the near future.
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Affiliation(s)
- Lucia Sobrin
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Johanna M Seddon
- Ophthalmic Epidemiology and Genetics Service, New England Eye Center, Tufts Medical Center, Boston, MA, USA; Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA; Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, USA.
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50
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Wang G. Chromosome 10q26 locus and age-related macular degeneration: a progress update. Exp Eye Res 2013; 119:1-7. [PMID: 24291204 DOI: 10.1016/j.exer.2013.11.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 12/18/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of late-onset central vision loss in developed countries. Both genetic and environmental factors contribute to the onset of AMD. Variation at a locus on chromosome 10q26 has been consistently associated with this disease and represents one of the two strongest genetic effects being identified in AMD. At least three genes are located within the bounds of the locus: pleckstrin homology domain containing family A member 1 (PLEKHA1), age-related maculopathy susceptibility 2 (ARMS2) and high-temperature requirement A serine peptidase 1 (HTRA1), all of which are associated with AMD. Due to the strong linkage disequilibrium (LD) across this region, statistical genetic analysis alone is incapable of distinguishing the effect of an individual gene in the locus. Uncertainty remains, however, in regards to which gene is responsible for the linkage and association of the locus with AMD. Investigating functional consequences of the associated variants and related genes tends to be essential to identifying the biologically responsible gene(s) underlying AMD. This review examines the recent progress and current uncertainty on the genetic and functional analyses of the 10q26 locus in AMD with a focus on ARMS2 and HTRA1. A discussion, which entails the possible multi-faceted approaches for pinpointing the gene(s) in the locus underlying the pathogenesis of AMD, is also included.
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Affiliation(s)
- Gaofeng Wang
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 N.W. 10th Avenue, BRB 525, M860, Miami, FL 33136, United States.
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