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Cipriani V, Tierney A, Griffiths JR, Zuber V, Sergouniotis PI, Yates JRW, Moore AT, Bishop PN, Clark SJ, Unwin RD. Beyond factor H: The impact of genetic-risk variants for age-related macular degeneration on circulating factor-H-like 1 and factor-H-related protein concentrations. Am J Hum Genet 2021; 108:1385-1400. [PMID: 34260948 PMCID: PMC8387294 DOI: 10.1016/j.ajhg.2021.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/27/2021] [Indexed: 01/04/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of vision loss; there is strong genetic susceptibility at the complement factor H (CFH) locus. This locus encodes a series of complement regulators: factor H (FH), a splice variant factor-H-like 1 (FHL-1), and five factor-H-related proteins (FHR-1 to FHR-5), all involved in the regulation of complement factor C3b turnover. Little is known about how AMD-associated variants at this locus might influence FHL-1 and FHR protein concentrations. We have used a bespoke targeted mass-spectrometry assay to measure the circulating concentrations of all seven complement regulators and demonstrated elevated concentrations in 352 advanced AMD-affected individuals for all FHR proteins (FHR-1, p = 2.4 × 10-10; FHR-2, p = 6.0 × 10-10; FHR-3, p = 1.5 × 10-5; FHR-4, p = 1.3 × 10-3; FHR-5, p = 1.9 × 10-4) and FHL-1 (p = 4.9 × 10-4) when these individuals were compared to 252 controls, whereas no difference was seen for FH (p = 0.94). Genome-wide association analyses in controls revealed genome-wide-significant signals at the CFH locus for all five FHR proteins, and univariate Mendelian-randomization analyses strongly supported the association of FHR-1, FHR-2, FHR-4, and FHR-5 with AMD susceptibility. These findings provide a strong biochemical explanation for how genetically driven alterations in circulating FHR proteins could be major drivers of AMD and highlight the need for research into FHR protein modulation as a viable therapeutic avenue for AMD.
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Affiliation(s)
- Valentina Cipriani
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, United Kingdom; UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, United Kingdom; Moorfields Eye Hospital National Health Service Foundation Trust, London, EC1V 2PD, United Kingdom; UCL Genetics Institute, University College London, London, WC1E 6BT, United Kingdom.
| | - Anna Tierney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9NY, United Kingdom
| | - John R Griffiths
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9NY, United Kingdom
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, United Kingdom
| | - Panagiotis I Sergouniotis
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, United Kingdom; Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University National Health Service Foundation Trust, Manchester, M13 9WL, United Kingdom
| | - John R W Yates
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, United Kingdom; Moorfields Eye Hospital National Health Service Foundation Trust, London, EC1V 2PD, United Kingdom; Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, United Kingdom; Moorfields Eye Hospital National Health Service Foundation Trust, London, EC1V 2PD, United Kingdom; Ophthalmology Department, University of California San Francisco, San Francisco, CA 94143-0730, USA
| | - Paul N Bishop
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, United Kingdom; Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, United Kingdom
| | - Simon J Clark
- University Eye Clinic, Department for Ophthalmology, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany; Institute for Ophthalmic Research, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre and Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, M13 9NQ, United Kingdom.
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Lorés-Motta L, van Beek AE, Willems E, Zandstra J, van Mierlo G, Einhaus A, Mary JL, Stucki C, Bakker B, Hoyng CB, Fauser S, Clark SJ, de Jonge MI, Nogoceke E, Koertvely E, Jongerius I, Kuijpers TW, den Hollander AI. Common haplotypes at the CFH locus and low-frequency variants in CFHR2 and CFHR5 associate with systemic FHR concentrations and age-related macular degeneration. Am J Hum Genet 2021; 108:1367-1384. [PMID: 34260947 PMCID: PMC8387287 DOI: 10.1016/j.ajhg.2021.06.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Age-related macular degeneration (AMD) is the principal cause of blindness in the elderly population. A strong effect on AMD risk has been reported for genetic variants at the CFH locus, encompassing complement factor H (CFH) and the complement-factor-H-related (CFHR) genes, but the underlying mechanisms are not fully understood. We aimed to dissect the role of factor H (FH) and FH-related (FHR) proteins in AMD in a cohort of 202 controls and 216 individuals with AMD. We detected elevated systemic levels of FHR-1 (p = 1.84 × 10-6), FHR-2 (p = 1.47 × 10-4), FHR-3 (p = 1.05 × 10-5) and FHR-4A (p = 1.22 × 10-2) in AMD, whereas FH concentrations remained unchanged. Common AMD genetic variants and haplotypes at the CFH locus strongly associated with FHR protein concentrations (e.g., FH p.Tyr402His and FHR-2 concentrations, p = 3.68 × 10-17), whereas the association with FH concentrations was limited. Furthermore, in an International AMD Genomics Consortium cohort of 17,596 controls and 15,894 individuals with AMD, we found that low-frequency and rare protein-altering CFHR2 and CFHR5 variants associated with AMD independently of all previously reported genome-wide association study (GWAS) signals (p = 5.03 × 10-3 and p = 2.81 × 10-6, respectively). Low-frequency variants in CFHR2 and CFHR5 led to reduced or absent FHR-2 and FHR-5 concentrations (e.g., p.Cys72Tyr in CFHR2 and FHR-2, p = 2.46 × 10-16). Finally, we showed localization of FHR-2 and FHR-5 in the choriocapillaris and in drusen. Our study identifies FHR proteins as key proteins in the AMD disease mechanism. Consequently, therapies that modulate FHR proteins might be effective for treating or preventing progression of AMD. Such therapies could target specific individuals with AMD on the basis of their genotypes at the CFH locus.
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Affiliation(s)
- Laura Lorés-Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525EX, the Netherlands; Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Anna E van Beek
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, 1066CX, the Netherlands; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, 1105 AZ, the Netherlands; Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, 4051, Switzerland; University of Basel, Basel, 4051, Switzerland
| | - Esther Willems
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525GA, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525GA, the Netherlands
| | - Judith Zandstra
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, 1066CX, the Netherlands; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, 1105 AZ, the Netherlands
| | - Gerard van Mierlo
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, 1066CX, the Netherlands
| | - Alfred Einhaus
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Jean-Luc Mary
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Corinne Stucki
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Bjorn Bakker
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525EX, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525EX, the Netherlands
| | - Sascha Fauser
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Simon J Clark
- University Eye Clinic, Department for Ophthalmology, University of Tübingen, 72076, Germany; Institue for Ophthalmic Research, Eberhard Karls University of Tübingen, 72076, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, M139PL, United Kingdom
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, 6525GA, the Netherlands
| | - Everson Nogoceke
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Elod Koertvely
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Ilse Jongerius
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, 1066CX, the Netherlands; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, 1105 AZ, the Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, 1105 AZ, the Netherlands; Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, 1066CX, the Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525EX, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6525GA, the Netherlands.
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Martínez-Velasco A, Perez-Ortiz AC, Antonio-Aguirre B, Martínez-Villaseñor L, Lira-Romero E, Palacio-Pastrana C, Zenteno JC, Ramirez I, Zepeda-Palacio C, Mendoza-Velásquez C, Camacho-Ordóñez A, Ortiz Bibriesca DM, Estrada-Mena FJ. Assessment of CFH and HTRA1 polymorphisms in age-related macular degeneration using classic and machine-learning approaches. Ophthalmic Genet 2020; 41:539-547. [PMID: 32838591 DOI: 10.1080/13816810.2020.1804945] [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] [Received: 07/03/2020] [Accepted: 07/26/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND CFH and HTRA1 are pivotal genes driving increased risk for age-related macular degeneration (AMD) among several populations. Here, we performed a hospital-based case-control study to evaluate the effects of three single nucleotide polymorphisms (SNPs) among Hispanics from Mexico. MATERIALS AND METHODS 122 cases and 249 controls were genotyped using Taqman probes. Experienced ophthalmologists diagnosed AMD following the American Association of Ophthalmology guidelines. We studied CFH (rs1329428, rs203687) and HTRA1 (rs11200638) SNPs thoroughly by logistic regression models (assuming different modes of inheritance) and machine learning-based methods (ML). RESULTS HTRA1 rs11200638 is the most significant polymorphism associated with AMD in our studied population. In a multivariate regression model adjusted for clinically and statistically meaningful covariates, the A/G and A/A genotypes increased the odds of disease by a factor of 2.32 and 7.81, respectively (P < .05) suggesting a multiplicative effect of the polymorphic A allele. Furthermore, this observation remains statistically meaningful in the allelic, dominant, and recessive models, and ML algorithms. When stratifying by phenotype, this polymorphism was significantly associated with increased odds for geographic atrophy (GA) in a recessive mode of inheritance (12.4, p < .05). CONCLUSIONS In sum, this work supports a strong association between HTRA1 genetic variants and AMD in Hispanics from Mexico, especially with GA. Moreover, ML was able to replicate the results of conventional biostatistics methods unbiasedly.
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Affiliation(s)
| | - Andric C Perez-Ortiz
- Universidad Panamericana. Facultad De Ciencias De La Salud. Ciudad De México, México
- Transplant Center, Division of Surgery, Massachusetts General Hospital , Boston, MA, USA
| | - Bani Antonio-Aguirre
- Universidad Panamericana. Facultad De Ciencias De La Salud. Ciudad De México, México
| | | | - Esmeralda Lira-Romero
- Universidad Panamericana. Facultad De Ciencias De La Salud. Ciudad De México, México
| | - Claudia Palacio-Pastrana
- Department of Microsurgery of the Anterior Segment, Fundación Hospital Nuestra Señora De La Luz, IAP , Ciudad De México, México
- Department of Microsurgery of the Anterior Segment, Clínicas Oftalmologicas Salauno Salud, Hamburgo, Ciudad de México, México
| | | | - Israel Ramirez
- Universidad Panamericana. Facultad De Ciencias De La Salud. Ciudad De México, México
| | - Claudia Zepeda-Palacio
- Department of Microsurgery of the Anterior Segment, Fundación Hospital Nuestra Señora De La Luz, IAP , Ciudad De México, México
| | - Cristina Mendoza-Velásquez
- Department of Microsurgery of the Anterior Segment, Fundación Hospital Nuestra Señora De La Luz, IAP , Ciudad De México, México
| | - Azyadeh Camacho-Ordóñez
- Department of Microsurgery of the Anterior Segment, Fundación Hospital Nuestra Señora De La Luz, IAP , Ciudad De México, México
| | | | - F Javier Estrada-Mena
- Universidad Panamericana. Facultad De Ciencias De La Salud. Ciudad De México, México
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A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes. Proc Natl Acad Sci U S A 2020; 117:9942-9951. [PMID: 32321835 PMCID: PMC7211993 DOI: 10.1073/pnas.1913970117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of the alternative complement pathway due to impaired binding of complement factor H (CFH) to self-ligands or altered self-ligands (e.g. malondialdehyde [MDA]-modified molecules) involved in homeostasis can promote the development of complement-related diseases, such as age-related macular degeneration (AMD). We identified, in an unbiased GWAS approach, that common genetic variants within the CFH gene family (rs1061170 and the deletion of the complement factor H-related protein 1 and 3 genes [CFHR3 and CFHR1]) act as major modulators of CFH recruitment and its ability to regulate complement on MDA-epitopes. These findings demonstrate the importance of the genetic status within the CFH/CFHR3/CFHR1 locus in tissue homeostasis and provide a mechanistic explanation as to why deletion of CFHR3/CFHR1 is protective in AMD development. Genetic variants within complement factor H (CFH), a major alternative complement pathway regulator, are associated with the development of age-related macular degeneration (AMD) and other complementopathies. This is explained with the reduced binding of CFH or its splice variant factor H-like protein 1 (FHL-1) to self-ligands or altered self-ligands (e.g., malondialdehyde [MDA]-modified molecules) involved in homeostasis, thereby causing impaired complement regulation. Considering the critical role of CFH in inhibiting alternative pathway activation on MDA-modified surfaces, we performed an unbiased genome-wide search for genetic variants that modify the ability of plasma CFH to bind MDA in 1,830 individuals and characterized the mechanistic basis and the functional consequences of this. In a cohort of healthy individuals, we identified rs1061170 in CFH and the deletion of CFHR3 and CFHR1 as dominant genetic variants that modify CFH/FHL-1 binding to MDA. We further demonstrated that FHR1 and FHR3 compete with CFH for binding to MDA-epitopes and that FHR1 displays the highest affinity toward MDA-epitopes compared to CFH and FHR3. Moreover, FHR1 bound to MDA-rich areas on necrotic cells and prevented CFH from mediating its cofactor activity on MDA-modified surfaces, resulting in enhanced complement activation. These findings provide a mechanistic explanation as to why the deletion of CFHR3 and CFHR1 is protective in AMD and highlight the importance of genetic variants within the CFH/CFHR3/CFHR1 locus in the recognition of altered-self in tissue homeostasis.
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Cipriani V, Lorés-Motta L, He F, Fathalla D, Tilakaratna V, McHarg S, Bayatti N, Acar İE, Hoyng CB, Fauser S, Moore AT, Yates JRW, de Jong EK, Morgan BP, den Hollander AI, Bishop PN, Clark SJ. Increased circulating levels of Factor H-Related Protein 4 are strongly associated with age-related macular degeneration. Nat Commun 2020; 11:778. [PMID: 32034129 PMCID: PMC7005798 DOI: 10.1038/s41467-020-14499-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness. Genetic variants at the chromosome 1q31.3 encompassing the complement factor H (CFH, FH) and CFH related genes (CFHR1-5) are major determinants of AMD susceptibility, but their molecular consequences remain unclear. Here we demonstrate that FHR-4 plays a prominent role in AMD pathogenesis. We show that systemic FHR-4 levels are elevated in AMD (P-value = 7.1 × 10-6), whereas no difference is seen for FH. Furthermore, FHR-4 accumulates in the choriocapillaris, Bruch's membrane and drusen, and can compete with FH/FHL-1 for C3b binding, preventing FI-mediated C3b cleavage. Critically, the protective allele of the strongest AMD-associated CFH locus variant rs10922109 has the highest association with reduced FHR-4 levels (P-value = 2.2 × 10-56), independently of the AMD-protective CFHR1-3 deletion, and even in those individuals that carry the high-risk allele of rs1061170 (Y402H). Our findings identify FHR-4 as a key molecular player contributing to complement dysregulation in AMD.
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Affiliation(s)
- Valentina Cipriani
- William Harvey Research Institute, Clinical Pharmacology, Queen Mary University of London, London, EC1M 6BQ, UK.
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Laura Lorés-Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Fan He
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Dina Fathalla
- Systems Immunity URI, Division of Infection and Immunity, and UK DRI Cardiff, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Viranga Tilakaratna
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Selina McHarg
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Nadhim Bayatti
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - İlhan E Acar
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, 50924, Germany
- Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
- Ophthalmology Department, University of California San Francisco, San Francisco, CA, USA
| | - John R W Yates
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - B Paul Morgan
- Systems Immunity URI, Division of Infection and Immunity, and UK DRI Cardiff, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, 6525 HR, The Netherlands
| | - Paul N Bishop
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Simon J Clark
- Division of Evolution and Genomic Sciences, Faculty of Biology Medicine and Health, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Department of Ophthalmology, Research Institute of Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany.
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Sivakumaran TA, Igo RP, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BEK, Nickerson DA, Eichler EE, Iyengar SK. Correction: A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration. PLoS One 2018; 13:e0209943. [PMID: 30571798 PMCID: PMC6301675 DOI: 10.1371/journal.pone.0209943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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7
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Significant Association Between Variant in SGCD and Age-Related Macular Degeneration. Genes (Basel) 2018; 9:genes9100467. [PMID: 30257524 PMCID: PMC6210939 DOI: 10.3390/genes9100467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022] Open
Abstract
CFH and HTRA1 genes are traditional markers of increased risk of age-related macular degeneration (AMD) across populations. Recent findings suggest that additional genes—for instance, in the dystrophin-associated protein complex—might be promising markers for AMD. Here, we performed a case-control study to assess the effect of SGCD single nucleotide polymorphisms (SNPs), a member of this protein family, on AMD diagnosis and phenotype. We performed a case-control study of an under-studied population from Hispanics in Mexico City, with 134 cases with 134 unpaired controls. Cases were 60 years or older (Clinical Age-Related Maculopathy Staging (CARMS) grade 4–5, as assessed by experienced ophthalmologists following the American Association of Ophthalmology (AAO) guidelines), without other retinal disease or history of vitreous-retinal surgery. Controls were outpatients aged 60 years or older, with no drusen or retinal pigment epithelium (RPE) changes on a fundus exam and a negative family history of AMD. We examined SNPs in the SGCD gene (rs931798, rs140617, rs140616, and rs970476) by sequencing and real-time PCR. Genotyping quality checks and univariate analyses were performed with PLINK v1.90b3.42. Furthermore, logistic regression models were done in SAS v.9.4 and haplotype configurations in R v.3.3.1. After adjusting for clinical covariates, the G/A genotype of the SGCD gene (rs931798) significantly increases the odds of being diagnosed with AMD in 81% of cases (1.81; 95% CI 1.06–3.14; p = 0.031), especially the geographic atrophy phenotype (1.82; 95% CI 1.03–3.21; p = 0.038) compared to the G/G homozygous genotype. Moreover, the GATT haplotype in this gene (rs931798, rs140617, rs140616, and rs970476) is associated with lower odds of AMD (adjusted odds ratio (OR) 0.13; 95% CI 0.02–0.91; p = 0.041). SGCD is a promising gene for AMD research. Further corroboration in other populations is warranted, especially among other Hispanic ethnicities.
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Sánchez-Corral P, Pouw RB, López-Trascasa M, Józsi M. Self-Damage Caused by Dysregulation of the Complement Alternative Pathway: Relevance of the Factor H Protein Family. Front Immunol 2018; 9:1607. [PMID: 30050540 PMCID: PMC6052053 DOI: 10.3389/fimmu.2018.01607] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
The alternative pathway is a continuously active surveillance arm of the complement system, and it can also enhance complement activation initiated by the classical and the lectin pathways. Various membrane-bound and plasma regulatory proteins control the activation of the potentially deleterious complement system. Among the regulators, the plasma glycoprotein factor H (FH) is the main inhibitor of the alternative pathway and its powerful amplification loop. FH belongs to a protein family that also includes FH-like protein 1 and five factor H-related (FHR-1 to FHR-5) proteins. Genetic variants and abnormal rearrangements involving the FH protein family have been linked to numerous systemic and organ-specific diseases, including age-related macular degeneration, and the renal pathologies atypical hemolytic uremic syndrome, C3 glomerulopathies, and IgA nephropathy. This review covers the known and recently emerged ligands and interactions of the human FH family proteins associated with disease and discuss the very recent experimental data that suggest FH-antagonistic and complement-activating functions for the FHR proteins.
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Affiliation(s)
- Pilar Sánchez-Corral
- Complement Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Richard B Pouw
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Margarita López-Trascasa
- Complement Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain.,Department of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mihály Józsi
- Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary.,MTA-SE Research Group of Immunology and Hematology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
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9
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Understanding variable disease severity in X-linked retinoschisis: Does RS1 secretory mechanism determine disease severity? PLoS One 2018; 13:e0198086. [PMID: 29851975 PMCID: PMC5978886 DOI: 10.1371/journal.pone.0198086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/14/2018] [Indexed: 11/24/2022] Open
Abstract
X-linked retinoschisis (XLRS) is a retinal degenerative disorder caused by mutations in RS1 gene leading to splitting of retinal layers (schisis) which impairs visual signal processing. Retinoschisin (RS1) is an adhesive protein which is secreted predominantly by the photoreceptors and bipolar cells as a double-octameric complex. In general, XLRS patients show wide clinical heterogeneity, presenting practical challenges in disease management. Though researchers have attempted various approaches to offer an explanation for clinical heterogeneity, the molecular basis has not been understood yet. Therefore, this study aims at establishing a link between the phenotype and genotype based on the molecular mechanism exerted by the mutations. Twenty seven XLRS patients were enrolled, of which seven harboured novel mutations. The mutant constructs were genetically engineered and their secretion profiles were studied by in vitro cell culture experiments. Based on the secretory profile, the patients were categorized as either secreted or non-secreted group. Various clinical parameters such as visual acuity, location of schisis, foveal thickness and ERG parameters were compared between the two groups and control. Although the two groups showed severe disease phenotype in comparison with control, there was no significant difference between the two XLRS groups. However, the secreted group exhibited relatively severe disease indications. On the other hand molecular analysis suggests that most of the RS1 mutations result in intracellular retention of retinoschisin. Hence, clinical parameters of patients with non-secreted profile were analyzed which in turn revealed wide variability even within the group. Altogether, our results indicate that disease severity is not merely dependent on secretory profile of the mutations. Thus, we hypothesize that intricate molecular detail such as the precise localization of mutant protein in the cell as well as its ability to assemble into a functionally active oligomer might largely influence disease severity among XLRS patients.
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Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H ( CFH) gene family. Proc Natl Acad Sci U S A 2018; 115:E4433-E4442. [PMID: 29686068 DOI: 10.1073/pnas.1717600115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Structural variation and single-nucleotide variation of the complement factor H (CFH) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four CFH-related (CFHR) gene paralogs (CFHR2 and CFHR4 ∼25-35 Mya and CFHR1 and CFHR3 ∼7-13 Mya). Remarkably, all evolutionary breakpoints share a common ∼4.8-kbp segment corresponding to an ancestral CFHR gene promoter that has expanded independently throughout primate evolution. This segment is recurrently reused and juxtaposed with a donor duplication containing exons 8 and 9 from ancestral CFH, creating four CFHR fusion genes that include lineage-specific members of the gene family. Combined analysis of >5,000 AMD cases and controls identifies a significant burden of a rare missense mutation that clusters at the N terminus of CFH [P = 5.81 × 10-8, odds ratio (OR) = 9.8 (3.67-Infinity)]. A bipolar clustering pattern of rare nonsynonymous mutations in patients with AMD (P < 10-3) and AHUS (P = 0.0079) maps to functional domains that show evidence of positive selection during primate evolution. Our structural variation analysis in >2,400 individuals reveals five recurrent rearrangement breakpoints that show variable frequency among AMD cases and controls. These data suggest a dynamic and recurrent pattern of mutation critical to the emergence of new CFHR genes but also in the predisposition to complex human genetic disease phenotypes.
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11
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Pouw RB, Brouwer MC, van Beek AE, Józsi M, Wouters D, Kuijpers TW. Complement Factor H-Related Protein 4A Is the Dominant Circulating Splice Variant of CFHR4. Front Immunol 2018; 9:729. [PMID: 29719534 PMCID: PMC5913293 DOI: 10.3389/fimmu.2018.00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
Recent research has elucidated circulating levels of almost all factor H-related (FHR) proteins. Some of these proteins are hypothesized to act as antagonists of the important complement regulator factor H (FH), fine-tuning complement regulation on human surfaces. For the CFHR4 splice variants FHR-4A and FHR-4B, the individual circulating levels are unknown, with only total levels being described. Specific reagents for FHR-4A or FHR-4B are lacking due to the fact that the unique domains in FHR-4A show high sequence similarity with FHR-4B, making it challenging to distinguish them. We developed an assay that specifically measures FHR-4A using novel, well-characterized monoclonal antibodies (mAbs) that target unique domains in FHR-4A only. Using various FHR-4A/FHR-4B-specific mAbs, no FHR-4B was identified in any of the serum samples tested. The results demonstrate that FHR-4A is the dominant splice variant of CFHR4 in the circulation, while casting doubt on the presence of FHR-4B. FHR-4A levels (avg. 2.55 ± 1.46 µg/mL) were within the range of most of the previously reported levels for all other FHRs. FHR-4A was found to be highly variable among the population, suggesting a strong genetic regulation. These results shed light on the physiological relevance of the previously proposed role of FHR-4A and FHR-4B as antagonists of FH in the circulation.
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Affiliation(s)
- Richard B. Pouw
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children’s hospital, Academic Medical Center, Amsterdam, Netherlands
| | - Mieke C. Brouwer
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Anna E. van Beek
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children’s hospital, Academic Medical Center, Amsterdam, Netherlands
| | - Mihály Józsi
- MTA-ELTE “Lendület” Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Diana Wouters
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W. Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children’s hospital, Academic Medical Center, Amsterdam, Netherlands
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory of the Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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12
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Niche harmony search algorithm for detecting complex disease associated high-order SNP combinations. Sci Rep 2017; 7:11529. [PMID: 28912584 PMCID: PMC5599559 DOI: 10.1038/s41598-017-11064-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 08/17/2017] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association study is especially challenging in detecting high-order disease-causing models due to model diversity, possible low or even no marginal effect of the model, and extraordinary search and computations. In this paper, we propose a niche harmony search algorithm where joint entropy is utilized as a heuristic factor to guide the search for low or no marginal effect model, and two computationally lightweight scores are selected to evaluate and adapt to diverse of disease models. In order to obtain all possible suspected pathogenic models, niche technique merges with HS, which serves as a taboo region to avoid HS trapping into local search. From the resultant set of candidate SNP-combinations, we use G-test statistic for testing true positives. Experiments were performed on twenty typical simulation datasets in which 12 models are with marginal effect and eight ones are with no marginal effect. Our results indicate that the proposed algorithm has very high detection power for searching suspected disease models in the first stage and it is superior to some typical existing approaches in both detection power and CPU runtime for all these datasets. Application to age-related macular degeneration (AMD) demonstrates our method is promising in detecting high-order disease-causing models.
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13
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Liu Y, Allingham RR. Major review: Molecular genetics of primary open-angle glaucoma. Exp Eye Res 2017; 160:62-84. [PMID: 28499933 DOI: 10.1016/j.exer.2017.05.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/07/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common type, is a complex inherited disorder that is characterized by progressive retinal ganglion cell death, optic nerve head excavation, and visual field loss. The discovery of a large, and growing, number of genetic and chromosomal loci has been shown to contribute to POAG risk, which carry implications for disease pathogenesis. Differential gene expression analyses in glaucoma-affected tissues as well as animal models of POAG are enhancing our mechanistic understanding in this common, blinding disorder. In this review we summarize recent developments in POAG genetics and molecular genetics research.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States; James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States; Duke - National University of Singapore (Duke-NUS), Singapore.
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14
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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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Fratelli M, Bolis M, Kurosaki M, Dori M, Guarnaccia V, Spinelli O, Alberti M, Valoti E, Pileggi S, Noris M, Remuzzi G, Rambaldi A, Terao M, Garattini E. Association of CFHR1 homozygous deletion with acute myelogenous leukemia in the European population. Leuk Lymphoma 2016; 57:1234-7. [PMID: 26317246 DOI: 10.3109/10428194.2015.1082180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Maddalena Fratelli
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Marco Bolis
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Mami Kurosaki
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Martina Dori
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Valeria Guarnaccia
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Orietta Spinelli
- b Division of Hematology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Marta Alberti
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Elisabetta Valoti
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Silvana Pileggi
- d Laboratory of Clinical Drug Evaluation , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Marina Noris
- c Immunology and Genetics of Rare Diseases and Organ Transplantation, Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Ranica (BG) , Italy
| | - Giuseppe Remuzzi
- e Clinical Research Center for Rare Diseases "Aldo & Cele Daccò" , Ranica (BG) , Italy ;,f Centro Anna Maria Astori , Science and Technology Park Kilometro Rosso , Bergamo , Italy ; and.,g IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" and Unit of Nephrology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Alessandro Rambaldi
- b Division of Hematology , Azienda Ospedaliera Papa Giovanni XXIII , Bergamo , Italy
| | - Mineko Terao
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
| | - Enrico Garattini
- a Laboratory of Molecular Biology , IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156 , Milano , Italy
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16
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Morrison MA, Magalhaes TR, Ramke J, Smith SE, Ennis S, Simpson CL, Portas L, Murgia F, Ahn J, Dardenne C, Mayne K, Robinson R, Morgan DJ, Brian G, Lee L, Woo SJ, Zacharaki F, Tsironi EE, Miller JW, Kim IK, Park KH, Bailey-Wilson JE, Farrer LA, Stambolian D, DeAngelis MM. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world. Front Genet 2015. [PMID: 26217379 PMCID: PMC4496576 DOI: 10.3389/fgene.2015.00238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus.
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Affiliation(s)
- Margaux A Morrison
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital Dublin, Ireland ; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland
| | | | - Silvia E Smith
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital Dublin, Ireland
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul Metropolitan Government Seoul National University Boramae Medical Center Seoul, South Korea
| | - Caitlin Dardenne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Katie Mayne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Rosann Robinson
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Denise J Morgan
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Garry Brian
- The Fred Hollows Foundation New Zealand Auckland, New Zealand
| | - Lucy Lee
- The Fred Hollows Foundation New Zealand Auckland, New Zealand ; London School of Hygiene and Tropical Medicine, University of London London, UK
| | - Se J Woo
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Fani Zacharaki
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Evangelia E Tsironi
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Joan W Miller
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Ivana K Kim
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Kyu H Park
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Lindsay A Farrer
- Departments of Medicine, Ophthalmology, Neurology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health Boston, MA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania Philadelphia, PA, USA
| | - Margaret M DeAngelis
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
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17
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Ding X, Wang J, Zelikovsky A, Guo X, Xie M, Pan Y. Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:695-704. [PMID: 26357280 DOI: 10.1109/tcbb.2014.2363459] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single nucleotide polymorphisms, a dominant type of genetic variants, have been used successfully to identify defective genes causing human single gene diseases. However, most common human diseases are complex diseases and caused by gene-gene and gene-environment interactions. Many SNP-SNP interaction analysis methods have been introduced but they are not powerful enough to discover interactions more than three SNPs. The paper proposes a novel method that analyzes all SNPs simultaneously. Different from existing methods, the method regards an individual's genotype data on a list of SNPs as a point with a unit of energy in a multi-dimensional space, and tries to find a new coordinate system where the energy distribution difference between cases and controls reaches the maximum. The method will find different multiple SNPs combinatorial patterns between cases and controls based on the new coordinate system. The experiment on simulated data shows that the method is efficient. The tests on the real data of age-related macular degeneration (AMD) disease show that it can find out more significant multi-SNP combinatorial patterns than existing methods.
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18
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Klein R, Meuer SM, Myers CE, Buitendijk GHS, Rochtchina E, Choudhury F, de Jong PTVM, McKean-Cowdin R, Iyengar SK, Gao X, Lee KE, Vingerling JR, Mitchell P, Klaver CCW, Wang JJ, Klein BEK. Harmonizing the classification of age-related macular degeneration in the three-continent AMD consortium. Ophthalmic Epidemiol 2014; 21:14-23. [PMID: 24467558 DOI: 10.3109/09286586.2013.867512] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PURPOSE To describe methods to harmonize the classification of age-related macular degeneration (AMD) phenotypes across four population-based cohort studies: the Beaver Dam Eye Study (BDES), the Blue Mountains Eye Study (BMES), the Los Angeles Latino Eye Study (LALES), and the Rotterdam Study (RS). METHODS AMD grading protocols, definitions of categories, and grading forms from each study were compared to determine whether there were systematic differences in AMD severity definitions and lesion categorization among the three grading centers. Each center graded the same set of 60 images using their respective systems to determine presence and severity of AMD lesions. A common 5-step AMD severity scale and definitions of lesion measurement cutpoints and early and late AMD were developed from this exercise. RESULTS Applying this severity scale changed the age-sex adjusted prevalence of early AMD from 18.7% to 20.3% in BDES, from 4.7% to 14.4% in BMES, from 14.1% to 15.8% in LALES, and from 7.5% to 17.1% in RS. Age-sex adjusted prevalences of late AMD remained unchanged. Comparison of each center's grades of the 60 images converted to the consortium scale showed that exact agreement of AMD severity among centers varied from 61.0-81.4%, and one-step agreement varied from 84.7-98.3%. CONCLUSION Harmonization of AMD classification reduced categorical differences in phenotypic definitions across the studies, resulted in a new 5-step AMD severity scale, and enhanced similarity of AMD prevalence among the four cohorts. Despite harmonization it may still be difficult to remove systematic differences in grading, if present.
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Affiliation(s)
- Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health , Madison, Wisconsin , USA
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Klein BEK, Howard KP, Iyengar SK, Sivakumaran TA, Meyers KJ, Cruickshanks KJ, Klein R. Sunlight exposure, pigmentation, and incident age-related macular degeneration. Invest Ophthalmol Vis Sci 2014; 55:5855-61. [PMID: 25125603 DOI: 10.1167/iovs.14-14602] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Examine potential effects of sunlight exposure, hair color, eye color, and selected gene single-nucleotide polymorphisms (SNPs) on incidence of AMD. METHODS Subjects participated in up to five examinations over a 20-year period. Eye color, self-reported hair color as a teenager, and sunlight exposure were ascertained at the baseline examination. Presence and severity of AMD and its lesions were determined via fundus photographs. Genetic data were available on a subset of participants. The SNPs CFH Y402H rs1061170 and ARMS2 A69S rs10490924 were used to analyze genetic risk of AMD; OCA2 rs4778241 and HERC2 rs12913832 represented genetic determinants of eye color. RESULTS Incidence of early AMD was higher in blond/red-haired persons compared with brown/black-haired persons (hazard ratio [HR] 1.25, P = 0.02) and in persons with high sun exposure in their thirties (HR 1.41, P = 0.02). However, neither was significant after adjustment for multiple comparisons. Eye (HR 1.36, P = 0.006) and hair color (HR 1.42, P = 0.003) were associated with incidence of any retinal pigmentary abnormalities (RPAs). Both remained significant after adjustment for multiple comparisons. Neither presence of alleles for light-colored eyes nor those associated with high risk of late AMD altered the association of eye or hair color with early AMD. None of the characteristics studied were significantly associated with late AMD. CONCLUSIONS Modest associations of eye color, hair color, and HERC2 genotype with any RPAs were found. Genes for AMD did not affect these associations. Eye color phenotype was more strongly associated with outcomes than HERC2 or OCA2 genotype.
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Affiliation(s)
- Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Kerri P Howard
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Sudha K Iyengar
- Departments of Epidemiology & Biostatistics, Genetics & Genome Sciences and Ophthalmology & Visual Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Theru A Sivakumaran
- Departments of Epidemiology & Biostatistics, Genetics & Genome Sciences and Ophthalmology & Visual Sciences, Case Western Reserve University, Cleveland, Ohio, United States Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Kristin J Meyers
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Karen J Cruickshanks
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
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20
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Myers CE, Klein BEK, Gangnon R, Sivakumaran TA, Iyengar SK, Klein R. Cigarette smoking and the natural history of age-related macular degeneration: the Beaver Dam Eye Study. Ophthalmology 2014; 121:1949-55. [PMID: 24953792 DOI: 10.1016/j.ophtha.2014.04.040] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/18/2014] [Accepted: 04/25/2014] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To examine the association of current cigarette smoking and pack-years smoked with the incidence and progression of age-related macular degeneration (AMD) and to examine the interactions of current smoking and pack-years smoked with complement factor H (CFH, rs1061170) and age-related maculopathy susceptibility 2 (ARMS2, rs10490924) genotype. DESIGN A longitudinal population-based study of AMD in a representative American community. Examinations were performed every 5 years over a 20-year period. PARTICIPANTS A total of 4439 participants in the population-based Beaver Dam Eye Study (BDES). METHODS Age-related macular degeneration status was determined from grading retinal photographs. Multi-state models were used to model the relationship of current smoking and pack-years smoked and interactions with CFH and ARMS2 with the incidence and progression of AMD over the entire age range. MAIN OUTCOME MEASURES Incidence and progression of AMD over a 20-year period and interactions between current smoking and pack-years smoked with CFH and ARMS2 genotype. RESULTS The incidence of early AMD over the 20-year period was 24.4%, and the incidence of late AMD was 4.5%. Current smoking was associated with an increased risk of transitioning from minimal to moderate early AMD. A greater number of pack-years smoked was associated with an increased risk of transitioning from no AMD to minimal early AMD and from severe early AMD to late AMD. Current smoking and a greater number of pack-years smoked were associated with an increased risk of death. There were no statistically significant multiplicative interactions between current smoking or pack-years smoked and CFH or ARMS2 genotype. CONCLUSIONS Current smoking and a greater number of pack-years smoked increase the risk of the progression of AMD. This has important health care implications because smoking is a modifiable behavior.
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Affiliation(s)
- Chelsea E Myers
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Ronald Gangnon
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Theru A Sivakumaran
- Department of Epidemiology & Biostatistics, Genetics and Ophthalmology, Case Western Reserve University, Cleveland, Ohio
| | - Sudha K Iyengar
- Department of Epidemiology & Biostatistics, Genetics and Ophthalmology, Case Western Reserve University, Cleveland, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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Boddu S, Lee MD, Marsiglia M, Marmor M, Freund KB, Smith RT. Risk factors associated with reticular pseudodrusen versus large soft drusen. Am J Ophthalmol 2014; 157:985-993.e2. [PMID: 24491417 DOI: 10.1016/j.ajo.2014.01.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
PURPOSE To investigate genetic, environmental, and systemic risk factors in prospectively identified subjects with the age-related macular degeneration (AMD) phenotypes of (1) reticular pseudodrusen without large soft drusen and (2) large soft drusen without reticular pseudodrusen. DESIGN Prospective case-case comparison. METHODS In a clinical practice setting, patients with AMD were sequentially screened using clinical examination and scanning laser ophthalmoscopy imaging to prospectively identify subjects (n = 73) with the phenotypes of (1) reticular pseudodrusen without large soft drusen (n = 30) or (2) large soft drusen without reticular pseudodrusen (n = 43). Subjects were genotyped for 2 alleles associated with AMD, age-related maculopathy susceptibility 2 (ARMS2) and complement factor H (CFH). A questionnaire was administered to collect history of smoking, hypertension, diabetes, and hyperlipidemia, as well as personal and family history of AMD. RESULTS The reticular pseudodrusen group was older (median age 87 vs 81 years, P = .04) and had more female subjects (83.3% vs 48.8%, P = .003), later ages of AMD onset (83 vs 70 years, P = .0005), and a greater frequency of hypertension (76.7% vs 55.8%, P = .08). No significant differences were found in the distribution of the ARMS2 risk allele (P = .4) between the reticular pseudodrusen (homozygous = 20.0%; heterozygous = 56.7%) and large soft drusen (homozygous = 19.0%; heterozygous = 42.9%) phenotypes, or in the distribution of the CHF risk allele (P = .7) between the reticular pseudodrusen (homozygous = 26.7%; heterozygous = 56.7%) and large soft drusen (homozygous = 21.4%; heterozygous = 66.7%) phenotypes. CONCLUSIONS The reticular pseudodrusen phenotype was associated with increased age, later age of AMD onset, and female sex.
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Wang X, Geng P, Zhang Y, Zhang M. Association between complement factor H Val62Ile polymorphism and age-related macular degeneration susceptibility: a meta-analysis. Gene 2014; 538:306-12. [PMID: 24440287 DOI: 10.1016/j.gene.2014.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 10/12/2013] [Accepted: 01/08/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND An increasing body of studies has assessed the contribution of Val62Ile polymorphism to age-related macular degeneration (AMD) risk, but the exact association still remains uncertain. This meta-analysis was undertaken in order to further characterize the potential association between Val62Ile polymorphism and AMD risk in four different ethnic populations. METHODS A meta-analysis was performed using data available from 16 case-control studies evaluating correlation between the Val62Ile polymorphism and AMD in Caucasian, Chinese, Japanese and South Korean populations. Data extraction and study quality assessment were performed in duplicate. Summary odds ratios (ORs) and 95% confidence intervals (CIs) of allele contrast and genotype contrast were estimated using the random-effects model. The Q-statistic test was used to identify heterogeneity, and the funnel plot was adopted to evaluate publication bias. RESULTS Sixteen studies involving a total of 11,400 subjects based on the search criteria were included in the meta-analysis. In overall populations, the Val62Ile polymorphism seemed to be associated with AMD (ORAA vs. GG=0.40, 95% CI=0.28-0.59; ORAA+GA vs. GG=0.72, 95% CI=0.64-0.80; ORAA vs. GC+GG=0.50, 95% CI=0.36-0.70; ORA vs. G=0.68, 95% CI=0.58-0.78; ORGA vs. GG=0.71, 95% CI=0.65-0.77). Similarly, subgroup analysis also revealed that this polymorphism was related to AMD in all ethnicities. CONCLUSIONS This meta-analysis suggested that Val62Ile polymorphism was associated with susceptibility to AMD.
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Affiliation(s)
- Xin Wang
- Department of Ophthalmology, Chinese PLA General Hospital & Chinese PLA Medical School, 28 Fuxing Road, Beijing 100853, People's Republic of China; Department of Ophthalmology, The 306th Hospital of Chinese PLA, 9 North Anxiang Road, Beijing 100101, People's Republic of China
| | - Peiliang Geng
- Institute of Oncology, Key Laboratory of Oncology, Cancer Center, Division of Internal Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, 28 Fuxing Road, Beijing 100853, People's Republic of China
| | - Ying Zhang
- Department of Ophthalmology, Chinese PLA General Hospital & Chinese PLA Medical School, 28 Fuxing Road, Beijing 100853, People's Republic of China
| | - Maonian Zhang
- Department of Ophthalmology, Chinese PLA General Hospital & Chinese PLA Medical School, 28 Fuxing Road, Beijing 100853, People's Republic of China.
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Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics 2014; 30:1-8. [PMID: 23751181 PMCID: PMC3866549 DOI: 10.1093/bioinformatics/btt250] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 12/27/2022] Open
Abstract
MOTIVATION With high-throughput DNA sequencing costs dropping <$1000 for human genomes, data storage, retrieval and analysis are the major bottlenecks in biological studies. To address the large-data challenges, we advocate a clean separation between the evidence collection and the inference in variant calling. We define and implement a Genome Query Language (GQL) that allows for the rapid collection of evidence needed for calling variants. RESULTS We provide a number of cases to showcase the use of GQL for complex evidence collection, such as the evidence for large structural variations. Specifically, typical GQL queries can be written in 5-10 lines of high-level code and search large datasets (100 GB) in minutes. We also demonstrate its complementarity with other variant calling tools. Popular variant calling tools can achieve one order of magnitude speed-up by using GQL to retrieve evidence. Finally, we show how GQL can be used to query and compare multiple datasets. By separating the evidence and inference for variant calling, it frees all variant detection tools from the data intensive evidence collection and focuses on statistical inference. AVAILABILITY GQL can be downloaded from http://cseweb.ucsd.edu/~ckozanit/gql.
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Affiliation(s)
- Christos Kozanitis
- Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, San Diego, CA 92123 and Microsoft Research, 1065 La Avenida, Mountain View, CA 94043, USA
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Baird PN, Chakrabarti S. How genetic studies have advanced our understanding of age-related macular degeneration and their impact on patient care: a review. Clin Exp Ophthalmol 2013; 42:53-64. [DOI: 10.1111/ceo.12235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/15/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Paul N Baird
- Centre for Eye Research Australia; University of Melbourne; Melbourne Victoria Australia
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Ratnapriya R, Swaroop A. Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing. Genome Med 2013; 5:84. [PMID: 24112618 PMCID: PMC4066589 DOI: 10.1186/gm488] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inherited retinal degenerative diseases (RDDs) display wide variation in their mode of inheritance, underlying genetic defects, age of onset, and phenotypic severity. Molecular mechanisms have not been delineated for many retinal diseases, and treatment options are limited. In most instances, genotype-phenotype correlations have not been elucidated because of extensive clinical and genetic heterogeneity. Next-generation sequencing (NGS) methods, including exome, genome, transcriptome and epigenome sequencing, provide novel avenues towards achieving comprehensive understanding of the genetic architecture of RDDs. Whole-exome sequencing (WES) has already revealed several new RDD genes, whereas RNA-Seq and ChIP-Seq analyses are expected to uncover novel aspects of gene regulation and biological networks that are involved in retinal development, aging and disease. In this review, we focus on the genetic characterization of retinal and macular degeneration using NGS technology and discuss the basic framework for further investigations. We also examine the challenges of NGS application in clinical diagnosis and management.
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Affiliation(s)
- Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Marangoni D, Falsini B, Piccardi M, Ambrosio L, Minnella AM, Savastano MC, Bisti S, Maccarone R, Fadda A, Mello E, Concolino P, Capoluongo E. Functional effect of Saffron supplementation and risk genotypes in early age-related macular degeneration: a preliminary report. J Transl Med 2013; 11:228. [PMID: 24067115 PMCID: PMC3850693 DOI: 10.1186/1479-5876-11-228] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/13/2013] [Indexed: 01/28/2023] Open
Abstract
Background To determine whether the functional effects of oral supplementation with Saffron, a natural compound that proved to be neuroprotective in early age-related macular degeneration, are influenced by complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2) risk genotypes. Methods Thirty-three early AMD patients, screened for CFH (rs1061170) and ARMS2 (rs10490924) polymorphisms and receiving Saffron oral supplementation (20 mg/day) over an average period of treatment of 11 months (range, 6–12), were longitudinally evaluated by clinical examination and focal electroretinogram (fERG)-derived macular (18°) flicker sensitivity estimate. fERG amplitude and macular sensitivity, the reciprocal value of the estimated fERG amplitude threshold, were the main outcome measures. Results After three months of supplementation, mean fERG amplitude and fERG sensitivity improved significantly when compared to baseline values (p < 0.01). These changes were stable throughout the follow-up period. No significant differences in clinical and fERG improvements were observed across different CFH or ARMS2 genotypes. Conclusions The present results indicate that the functional effect of Saffron supplementation in individual AMD patients is not related to the major risk genotypes of disease.
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Affiliation(s)
- Dario Marangoni
- Dipartimento di Scienze Otorinolaringoiatriche e Oftalmologiche, Universita' Cattolica del Sacro Cuore, Lgo F, Vito 1, 00168 Roma, Italy.
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Ansari M, McKeigue PM, Skerka C, Hayward C, Rudan I, Vitart V, Polasek O, Armbrecht AM, Yates JRW, Vatavuk Z, Bencic G, Kolcic I, Oostra BA, Van Duijn CM, Campbell S, Stanton CM, Huffman J, Shu X, Khan JC, Shahid H, Harding SP, Bishop PN, Deary IJ, Moore AT, Dhillon B, Rudan P, Zipfel PF, Sim RB, Hastie ND, Campbell H, Wright AF. Genetic influences on plasma CFH and CFHR1 concentrations and their role in susceptibility to age-related macular degeneration. Hum Mol Genet 2013; 22:4857-69. [PMID: 23873044 PMCID: PMC3820139 DOI: 10.1093/hmg/ddt336] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
It is a longstanding puzzle why non-coding variants in the complement factor H (CFH) gene are more strongly associated with age-related macular degeneration (AMD) than functional coding variants that directly influence the alternative complement pathway. The situation is complicated by tight genetic associations across the region, including the adjacent CFH-related genes CFHR3 and CFHR1, which may themselves influence the alternative complement pathway and are contained within a common deletion (CNP147) which is associated with protection against AMD. It is unclear whether this association is mediated through a protective effect of low plasma CFHR1 concentrations, high plasma CFH or both. We examined the triangular relationships of CFH/CFHR3/CFHR1 genotype, plasma CFH or CFHR1 concentrations and AMD susceptibility in combined case–control (1256 cases, 1020 controls) and cross-sectional population (n = 1004) studies and carried out genome-wide association studies of plasma CFH and CFHR1 concentrations. A non-coding CFH SNP (rs6677604) and the CNP147 deletion were strongly correlated both with each other and with plasma CFH and CFHR1 concentrations. The plasma CFH-raising rs6677604 allele and raised plasma CFH concentration were each associated with AMD protection. In contrast, the protective association of the CNP147 deletion with AMD was not mediated by low plasma CFHR1, since AMD-free controls showed increased plasma CFHR1 compared with cases, but it may be mediated by the association of CNP147 with raised plasma CFH concentration. The results are most consistent with a regulatory locus within a 32 kb region of the CFH gene, with a major effect on plasma CFH concentration and AMD susceptibility.
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Affiliation(s)
- Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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Klein R, Myers CE, Meuer SM, Gangnon RE, Sivakumaran TA, Iyengar SK, Lee KE, Klein BEK. Risk alleles in CFH and ARMS2 and the long-term natural history of age-related macular degeneration: the Beaver Dam Eye Study. JAMA Ophthalmol 2013; 131:383-92. [PMID: 23494043 DOI: 10.1001/jamaophthalmol.2013.713] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To describe the relationships of risk alleles in complement factor H (CFH, rs1061170) and age-related maculopathy susceptibility 2 (ARMS2, rs10490924) to the incidence and progression of age-related macular degeneration (AMD) during a 20-year period. METHODS There were 4282 persons aged 43 to 86 years at the baseline examination in 1988-1990 enrolled in a population-based cohort study who participated in at least 1 examination spaced 5 years apart during a 20-year period and had gradable fundus photographs for AMD and genotype information on CFH and ARMS2. Low, intermediate, and high genetic risk for AMD was defined by the presence of 0 to 1, 2, or 3 to 4 risk alleles for CFH and ARMS2, respectively. Multistate models were used to estimate the progression of AMD throughout the entire age range. RESULTS There were 2820 (66%), 1129 (26%), and 333 persons (8%) with low, intermediate, and high genetic risk for AMD, respectively. The 5-year incidences of early and late AMD were 9.1% and 1.6%, respectively, and increased with age but did not differ significantly by sex. Using the multistate model, of persons aged 45 years with no AMD in the low, intermediate, and high AMD genetic risk groups, 33.0%, 39.9%, and 46.5%, respectively, were estimated to develop early AMD, and 1.4%, 5.2%, and 15.3% were estimated to develop late AMD by age 80 years. CONCLUSIONS These population-based data provide estimates of the long-term risk of the incidence and progression of AMD and its lesions by age and genetic risk alleles for CFH and ARMS2. They also show that when early AMD is present, knowing the phenotype contributes more to risk assessment than knowing the genetic risk based on these 2 AMD genes.
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Affiliation(s)
- Ronald Klein
- Departments of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.
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Determining the population frequency of the CFHR3/CFHR1 deletion at 1q32. PLoS One 2013; 8:e60352. [PMID: 23613724 PMCID: PMC3629053 DOI: 10.1371/journal.pone.0060352] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/25/2013] [Indexed: 01/04/2023] Open
Abstract
In this study we have used multiplex ligation-dependent probe amplification (MLPA) to measure the copy number of CFHR3 and CFHR1 in DNA samples from 238 individuals from the UK and 439 individuals from the HGDP-CEPH Human Genome Diversity Cell Line Panel. We have then calculated the allele frequency and frequency of homozygosity for the copy number polymorphism represented by the CFHR3/CFHR1 deletion. There was a highly significant difference between geographical locations in both the allele frequency (X2 = 127.7, DF = 11, P-value = 4.97x10-22) and frequency of homozygosity (X2 = 142.3, DF = 22, P-value = 1.33x10-19). The highest frequency for the deleted allele (54.7%) was seen in DNA samples from Nigeria and the lowest (0%) in samples from South America and Japan. The observed frequencies in conjunction with the known association of the deletion with AMD, SLE and IgA nephropathy is in keeping with differences in the prevalence of these diseases in African and European Americans. This emphasises the importance of identifying copy number polymorphism in disease.
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Kokkinopoulos I. 670 nm LED ameliorates inflammation in the CFH(-/-) mouse neural retina. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 122:24-31. [PMID: 23584451 DOI: 10.1016/j.jphotobiol.2013.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/12/2013] [Accepted: 03/17/2013] [Indexed: 12/27/2022]
Abstract
Para-inflammation in the neural retina is thought to contribute to the onset of some age-related retinal diseases. Continuous innate immune system activation, manifests in progressive chronic inflammation, macrophage invasion and cell loss, resulting in visual loss. We have previously shown that mitochondrial function is augmented following 670 nm LED exposure, leading to reduced retinal inflammation. Here, it was asked whether 670 nm LED regulates para-inflammation in an aged-related macular degeneration mouse model. Mutant CFH(-/-) mice were exposed to four 90 s exposures over 2 days for 1 week and 8 weeks. These regimes significantly reduced activated macrophage number, TNF-alpha and MIF protein expression levels. Immuno-reactivity to C3, C3b and calcitonin, all markers of inflammatory status were also altered. Finally, innate immune proteins, TLR 2 and 4, showed a marked decrease in protein expression. These findings support the notion that 670 nm LED regulates innate immunity, alleviating inflammation in the neural retina of an age-related macular degeneration mouse model.
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Affiliation(s)
- Ioannis Kokkinopoulos
- School of Biomedical and Health Sciences, Wolfson Centre for Age-Related Diseases, King's College London, UK.
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Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP, Buitendijk GHS, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JPA, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BEK, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJT, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HPN, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CCW, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JRW, Swaroop A, Weber BHF, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR. Seven new loci associated with age-related macular degeneration. Nat Genet 2013; 45:433-9, 439e1-2. [PMID: 23455636 PMCID: PMC3739472 DOI: 10.1038/ng.2578] [Citation(s) in RCA: 573] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 02/07/2012] [Indexed: 12/11/2022]
Abstract
Age-related macular degeneration (AMD) is a common cause of blindness in older individuals. To accelerate the understanding of AMD biology and help design new therapies, we executed a collaborative genome-wide association study, including >17,100 advanced AMD cases and >60,000 controls of European and Asian ancestry. We identified 19 loci associated at P < 5 × 10(-8). These loci show enrichment for genes involved in the regulation of complement activity, lipid metabolism, extracellular matrix remodeling and angiogenesis. Our results include seven loci with associations reaching P < 5 × 10(-8) for the first time, near the genes COL8A1-FILIP1L, IER3-DDR1, SLC16A8, TGFBR1, RAD51B, ADAMTS9 and B3GALTL. A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD.
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Affiliation(s)
- Lars G Fritsche
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
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Yuan D, Yang Q, Liu X, Yuan D, Yuan S, Xie P, Liu Q. Complement factor H Val62Ile variant and risk of age-related macular degeneration: a meta-analysis. Mol Vis 2013; 19:374-83. [PMID: 23441108 PMCID: PMC3580987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 02/11/2013] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To evaluate the precise association of complement factor H (CFH) Val62Ile polymorphism with age-related macular degeneration (AMD) susceptibility. METHODS We performed a meta-analysis using databases including PubMed, EMBASE, and Web of Science to find relevant studies. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using fixed-effect and random-effects models. The inconsistency index (I(2)) was used to assess heterogeneity. Funnel plots and Egger's test were used to evaluate publication bias. Sensitivity analysis was also performed. RESULTS Fourteen studies including 4,438 patients with AMD and 6,099 controls based on the search criteria were involved in the meta-analysis. In overall populations, the pooled OR(1) for genotype GA+GG versus homozygous genotype AA was 2.28 (95% confidence interval (CI): 1.48-3.52), the OR(2) of heterozygous genotype GA versus AA was 1.58 (95% CI: 1.13-2.19), the OR(3) of homozygous genotype GG versus AA was 2.90 (95% CI: 1.95-4.30), and the OR(4) of allele G versus A was 1.77 (95% CI: 1.43-2.21). In Asian populations, our results provided substantial evidence that the Val62Ile variant was significantly associated with AMD (OR(4) = 1.85, 95% CI: 1.63-2.09). However, in Caucasian populations, no significant association of Val62Ile with AMD was established in all circumstances. CONCLUSIONS Our analysis provides substantial evidence that the Val62Ile variant is significantly associated with AMD in Asian populations. However, our results have demonstrated no link between the Val62Ile polymorphism and AMD in Caucasian populations.
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Affiliation(s)
- Dongqing Yuan
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Qin Yang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Xiaoyi Liu
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Donglan Yuan
- Department of Nuclear Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Songtao Yuan
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Ping Xie
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Qinghuai Liu
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
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Klein R, Cruickshanks KJ, Myers CE, Sivakumaran TA, Iyengar SK, Meuer SM, Schubert CR, Gangnon RE, Klein BEK. The relationship of atherosclerosis to the 10-year cumulative incidence of age-related macular degeneration: the Beaver Dam studies. Ophthalmology 2013; 120:1012-9. [PMID: 23399375 DOI: 10.1016/j.ophtha.2012.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/30/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE To describe the relationships of intima-media thickness (IMT), plaque in the carotid artery, angina, myocardial infarction (MI), and stroke to the 10-year cumulative incidence of early and late age-related macular degeneration (AMD) and progression of AMD. DESIGN Cohort study. PARTICIPANTS A total of 1700 persons aged 53 to 96 years who participated in both the Epidemiology of Hearing Loss Study and the Beaver Dam Eye Study in 1998-2000, with photographs gradable for AMD at 5-year (2003-2005) and 10-year (2008-2010) follow-up examinations. METHODS The IMT and presence of plaque were assessed using B-mode ultrasonography of the carotid artery. Presence of angina, MI, and stroke were defined on the basis of a self-reported history of physician diagnosis. The presence and severity of AMD were determined by systematic grading of stereoscopic color fundus photographs. MAIN OUTCOME MEASURES Age-related macular degeneration. RESULTS The 10-year cumulative incidence of early AMD was 15.7%, and the 10-year cumulative incidence of late AMD was 4.0%. After adjusting for age, sex, body mass index, smoking status, age-related maculopathy susceptibility 2 (ARMS2) and complement factor H (CFH) genotypes, and other factors, mean IMT was associated with the 10-year incidence of early AMD (odds ratio [OR] per 0.1 mm IMT, 1.11; 95% confidence interval [CI], 1.00-1.21; P = 0.03) and late AMD (OR per 0.1 mm IMT, 1.27; CI, 1.10-1.47; P = 0.001). Mean IMT was associated with the 10-year incidence of pure geographic atrophy (OR per 0.1 mm IMT, 1.31; CI, 1.05-1.64; P = 0.02) but not exudative AMD (OR per 0.1 mm IMT, 1.14; CI, 0.97-1.34; P = 0.11). Similar associations were found for maximum IMT. The number of sites with plaque was related to the incidence of late AMD (OR per 0.1 mm IMT, 2.79 for 4-6 sites vs. none; CI, 1.06-7.37; P = 0.04) but not to early AMD. A history of angina, MI, or stroke was not related to any incident AMD outcome. CONCLUSIONS In these population-based data, carotid artery IMT and carotid plaques had a weak relationship to the incidence of late AMD that was independent of systemic and genetic risk factors. Angina, MI, and stroke were not related to AMD. It is unclear whether the carotid IMT is a risk indicator of processes affecting Bruch's membrane and the retinal pigment epithelium, or a measure of atherosclerosis affecting susceptibility to AMD. FINANCIAL DISCLOSURE(S) The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA.
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Liu MM, Chan CC, Tuo J. Genetic mechanisms and age-related macular degeneration: common variants, rare variants, copy number variations, epigenetics, and mitochondrial genetics. Hum Genomics 2012; 6:13. [PMID: 23244519 PMCID: PMC3500238 DOI: 10.1186/1479-7364-6-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/21/2012] [Indexed: 11/10/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex and multifaceted disease involving contributions from both genetic and environmental influences. Previous work exploring the genetic contributions of AMD has implicated numerous genomic regions and a variety of candidate genes as modulators of AMD susceptibility. Nevertheless, much of this work has revolved around single-nucleotide polymorphisms (SNPs), and it is apparent that a significant portion of the heritability of AMD cannot be explained through these mechanisms. In this review, we consider the role of common variants, rare variants, copy number variations, epigenetics, microRNAs, and mitochondrial genetics in AMD. Copy number variations in regulators of complement activation genes (CFHR1 and CFHR3) and glutathione S transferase genes (GSTM1 and GSTT1) have been associated with AMD, and several additional loci have been identified as regions of potential interest but require further evaluation. MicroRNA dysregulation has been linked to the retinal pigment epithelium degeneration in geographic atrophy, ocular neovascularization, and oxidative stress, all of which are hallmarks in the pathogenesis of AMD. Certain mitochondrial DNA haplogroups and SNPs in mitochondrially encoded NADH dehydrogenase genes have also been associated with AMD. The role of these additional mechanisms remains only partly understood, but the importance of their further investigation is clear to elucidate more completely the genetic basis of AMD.
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Affiliation(s)
- Melissa M Liu
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1857, USA
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Silva AS, Teixeira AG, Bavia L, Lin F, Velletri R, Belfort R, Isaac L. Plasma levels of complement proteins from the alternative pathway in patients with age-related macular degeneration are independent of Complement Factor H Tyr⁴⁰²His polymorphism. Mol Vis 2012; 18:2288-99. [PMID: 22969267 PMCID: PMC3436886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 08/28/2012] [Indexed: 11/06/2022] Open
Abstract
PURPOSE To investigate the influence of the Factor H (CFH) Tyr⁴⁰²His polymorphism on the plasma levels of the alternative pathway proteins CFH, C3, Factor B (FB), Factor D (FD), and Factor I (FI) and the inflammatory marker C-reactive protein (CRP) in 119 patients with age-related macular degeneration (AMD) and 152 unrelated control individuals. METHODS Patients with AMD and the control group were separated according to CFH polymorphism, age, and gender. Plasma complement proteins and CRP concentrations were determined with enzyme-linked immunosorbent assay, immunodiffusion, or nephelometry. RESULTS Significant differences in the concentrations of FD and FI were observed between the patients with AMD and the control individuals. We observed significantly reduced FD plasma levels in patients with AMD. We also identified a significant decrease in CFH plasma levels in female patients with AMD in relation to female controls. Plasma FI levels were significantly increased in patients with AMD compared to the control group. Regarding gender, a significant increase in FI plasma levels was observed in male patients. Finally, we found no significant correlation between the CFH Tyr(402)His polymorphism and the CFH, C3, FB, FD, FI, and CRP plasma levels. CONCLUSIONS Patients with AMD present altered levels of FD and FI in a manner independent of this CFH polymorphism, and gender apparently contributes to the plasma levels of these two proteins in patients with AMD and control individuals.
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Affiliation(s)
- Aldacilene Souza Silva
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Lorena Bavia
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fabio Lin
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Roberta Velletri
- Department of Ophthalmology, Federal University of São Paulo, São Paulo, Brazil
| | - Rubens Belfort
- Department of Ophthalmology, Federal University of São Paulo, São Paulo, Brazil
| | - Lourdes Isaac
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Cipriani V, Leung HT, Plagnol V, Bunce C, Khan JC, Shahid H, Moore AT, Harding SP, Bishop PN, Hayward C, Campbell S, Armbrecht AM, Dhillon B, Deary IJ, Campbell H, Dunlop M, Dominiczak AF, Mann SS, Jenkins SA, Webster AR, Bird AC, Lathrop M, Zelenika D, Souied EH, Sahel JA, Léveillard T, Cree AJ, Gibson J, Ennis S, Lotery AJ, Wright AF, Clayton DG, Yates JRW. Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3. Hum Mol Genet 2012; 21:4138-50. [PMID: 22694956 DOI: 10.1093/hmg/dds225] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of visual loss in Western populations. Susceptibility is influenced by age, environmental and genetic factors. Known genetic risk loci do not account for all the heritability. We therefore carried out a genome-wide association study of AMD in the UK population with 893 cases of advanced AMD and 2199 controls. This showed an association with the well-established AMD risk loci ARMS2 (age-related maculopathy susceptibility 2)-HTRA1 (HtrA serine peptidase 1) (P =2.7 × 10(-72)), CFH (complement factor H) (P =2.3 × 10(-47)), C2 (complement component 2)-CFB (complement factor B) (P =5.2 × 10(-9)), C3 (complement component 3) (P =2.2 × 10(-3)) and CFI (P =3.6 × 10(-3)) and with more recently reported risk loci at VEGFA (P =1.2 × 10(-3)) and LIPC (hepatic lipase) (P =0.04). Using a replication sample of 1411 advanced AMD cases and 1431 examined controls, we confirmed a novel association between AMD and single-nucleotide polymorphisms on chromosome 6p21.3 at TNXB (tenascin XB)-FKBPL (FK506 binding protein like) [rs12153855/rs9391734; discovery P =4.3 × 10(-7), replication P =3.0 × 10(-4), combined P =1.3 × 10(-9), odds ratio (OR) = 1.4, 95% confidence interval (CI) = 1.3-1.6] and the neighbouring gene NOTCH4 (Notch 4) (rs2071277; discovery P =3.2 × 10(-8), replication P =3.8 × 10(-5), combined P =2.0 × 10(-11), OR = 1.3, 95% CI = 1.2-1.4). These associations remained significant in conditional analyses which included the adjacent C2-CFB locus. TNXB, FKBPL and NOTCH4 are all plausible AMD susceptibility genes, but further research will be needed to identify the causal variants and determine whether any of these genes are involved in the pathogenesis of AMD.
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Affiliation(s)
- Valentina Cipriani
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK.
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Gold B, Sawitzke J, Im K, Kostiha B, Dean M. Author reply. Ophthalmology 2012. [DOI: 10.1016/j.ophtha.2012.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Mettu PS, Wielgus AR, Ong SS, Cousins SW. Retinal pigment epithelium response to oxidant injury in the pathogenesis of early age-related macular degeneration. Mol Aspects Med 2012; 33:376-98. [PMID: 22575354 DOI: 10.1016/j.mam.2012.04.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 04/14/2012] [Indexed: 01/06/2023]
Abstract
Age-related macular degeneration (AMD) represents the leading cause of vision loss in the elderly. Accumulation of lipid- and protein-rich deposits under the retinal pigment epithelium (RPE) heralds the onset of early AMD, but the pathogenesis of subretinal deposit formation is poorly understood. Numerous hypothetical models of deposit formation have been proposed, including hypotheses for a genetic basis, choroidal hypoperfusion, abnormal barrier formation, and lysosomal failure. This review explore the RPE injury hypothesis, characterized by three distinct stages (1) Initial RPE oxidant injury, caused by any number of endogenous or exogenous oxidants, results in extrusion of cell membrane "blebs," together with decreased activity of matrix metalloproteinases (MMPs), promoting bleb accumulation under the RPE as basal laminar deposits (BLD). (2) RPE cells are subsequently stimulated to increase synthesis of MMPs and other molecules responsible for extracellular matrix turnover (i.e., producing decreased collagen), affecting both RPE basement membrane and Bruchs membrane (BrM). This process leads to progression of BLD into basal linear deposits (BLinD) and drusen by admixture of blebs into BrM, followed by the formation of new basement membrane under the RPE to trap these deposits within BrM. We postulate that various hormones and other plasma-derived molecules related to systemic health cofactors are implicated in this second stage. (3) Finally, macrophages are recruited to sites of RPE injury and deposit formation. The recruitment of nonactivated or scavenging macrophages may remove deposits without further injury, while the recruitment of activated or reparative macrophages, through the release of inflammatory mediators, growth factors, or other substances, may promote complications and progression to the late forms of the disease.
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Affiliation(s)
- Priyatham S Mettu
- Duke Center for Macular Diseases, Duke Eye Center, Durham, NC 27710, USA
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Cantsilieris S, White SJ, Richardson AJ, Guymer RH, Baird PN. Comprehensive analysis of Copy Number Variation of genes at chromosome 1 and 10 loci associated with late age related macular degeneration. PLoS One 2012; 7:e35255. [PMID: 22558131 PMCID: PMC3338825 DOI: 10.1371/journal.pone.0035255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 03/14/2012] [Indexed: 11/18/2022] Open
Abstract
Copy Number Variants (CNVs) are now recognized as playing a significant role in complex disease etiology. Age-related macular degeneration (AMD) is the most common cause of irreversible vision loss in the western world. While a number of genes and environmental factors have been associated with both risk and protection in AMD, the role of CNVs has remained largely unexplored. We analyzed the two major AMD risk-associated regions on chromosome 1q32 and 10q26 for CNVs using Multiplex Ligation-dependant Probe Amplification. The analysis targeted nine genes in these two key regions, including the Complement Factor H (CFH) gene, the 5 CFH-related (CFHR) genes representing a known copy number "hotspot", the F13B gene as well as the ARMS2 and HTRA1 genes in 387 cases of late AMD and 327 controls. No copy number variation was detected at the ARMS2 and HTRA1 genes in the chromosome 10 region, nor for the CFH and F13B genes at the chromosome 1 region. However, significant association was identified for the CFHR3-1 deletion in AMD cases (p = 2.38 × 10(-12)) OR = 0.31, CI-0.95 (0.23-0.44), for both neovascular disease (nAMD) (p = 8.3 × 10(-9)) OR = 0.36 CI-0.95 (0.25-0.52) and geographic atrophy (GA) (p = 1.5 × 10(-6)) OR = 0.36 CI-0.95 (0.25-0.52) compared to controls. In addition, a significant association with deletion of CFHR1-4 was identified only in patients who presented with bilateral GA (p = 0.02) (OR = 7.6 CI-0.95 1.38-41.8). This is the first report of a phenotype specific association of a CNV for a major subtype of AMD and potentially allows for pre-diagnostic identification of individuals most likely to proceed to this end stage of disease.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Centre for Reproduction and Development, Monash Institute of Medical Research, Melbourne, Victoria, Australia
| | - Stefan J. White
- Centre for Reproduction and Development, Monash Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrea J. Richardson
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Robyn H. Guymer
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
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