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Cevik S, Biswas SB, Biswas-Fiss EE. Structural and Pathogenic Impacts of ABCA4 Variants in Retinal Degenerations-An In-Silico Study. Int J Mol Sci 2023; 24:ijms24087280. [PMID: 37108442 PMCID: PMC10138569 DOI: 10.3390/ijms24087280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The retina-specific ATP-binding cassette transporter protein ABCA4 is responsible for properly continuing the visual cycle by removing toxic retinoid byproducts of phototransduction. Functional impairment caused by ABCA4 sequence variations is the leading cause of autosomal recessive inherited retinal disorders, including Stargardt disease, retinitis pigmentosa, and cone-rod dystrophy. To date, more than 3000 ABCA4 genetic variants have been identified, approximately 40 percent of which have not been able to be classified for pathogenicity assessments. This study examined 30 missense ABCA4 variants using AlphaFold2 protein modeling and computational structure analysis for pathogenicity prediction. All variants classified as pathogenic (n = 10) were found to have deleterious structural consequences. Eight of the ten benign variants were structurally neutral, while the remaining two resulted in mild structural changes. This study's results provided multiple lines of computational pathogenicity evidence for eight ABCA4 variants of uncertain clinical significance. Overall, in silico analyses of ABCA4 can provide a valuable tool for understanding the molecular mechanisms of retinal degeneration and their pathogenic impact.
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Affiliation(s)
- Senem Cevik
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Esther E Biswas-Fiss
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
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May A, Su F, Dinh B, Ehlen R, Tran C, Adivikolanu H, Shaw PX. Ongoing controversies and recent insights of the ARMS2-HTRA1 locus in age-related macular degeneration. Exp Eye Res 2021; 210:108605. [PMID: 33930395 DOI: 10.1016/j.exer.2021.108605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/10/2021] [Accepted: 04/21/2021] [Indexed: 01/17/2023]
Abstract
Age-related macular degeneration (AMD) is the most common cause of central vision loss among elderly populations in industrialized countries. Genome-wide association studies have consistently associated two genomic loci with progression to late-stage AMD: the complement factor H (CFH) locus on chromosome 1q31 and the age-related maculopathy susceptibility 2-HtrA serine peptidase 1 (ARMS2-HTRA1) locus on chromosome 10q26. While the CFH risk variant has been shown to alter complement activity, the ARMS2-HTRA1 risk haplotype remains enigmatic due to high linkage disequilibrium and inconsistent functional findings spanning two genes that are plausibly causative for AMD risk. In this review, we detail the genetic and functional evidence used to support either ARMS2 or HTRA1 as the causal gene for AMD risk, emphasizing both the historical development and the current understanding of the ARMS2-HTRA1 locus in AMD pathogenesis. We conclude by summarizing the evidence in favor of HTRA1 and present our hypothesis whereby HTRA1-derived ECM fragments mediate AMD pathogenesis.
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Affiliation(s)
- Adam May
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Fei Su
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Brian Dinh
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Rachael Ehlen
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Christina Tran
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Harini Adivikolanu
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
| | - Peter X Shaw
- Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, 9415 Campus Point Drive, La Jolla, CA 92093-0946, USA; Altman Clinical and Translational Research Institute, University of California, San Diego, 9452 Medical Center Drive, La Jolla, CA 92093-0990, USA.
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Age-related macular degeneration associated polymorphism rs10490924 in ARMS2 results in deficiency of a complement activator. J Neuroinflammation 2017; 14:4. [PMID: 28086806 PMCID: PMC5234120 DOI: 10.1186/s12974-016-0776-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/09/2016] [Indexed: 12/02/2022] Open
Abstract
Background Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. The polymorphism rs10490924 in the ARMS2 gene is highly associated with AMD and linked to an indel mutation (del443ins54), the latter inducing mRNA instability. At present, the function of the ARMS2 protein, the exact cellular sources in the retina and the biological consequences of the rs10490924 polymorphism are unclear. Methods Recombinant ARMS2 was expressed in Pichia pastoris, and protein functions were studied regarding cell surface binding and complement activation in human serum using fluoresence-activated cell sorting (FACS) as well as laser scanning microscopy (LSM). Biolayer interferometry defined protein interactions. Furthermore, endogenous ARMS2 gene expression was studied in human blood derived monocytes and in human induced pluripotent stem cell-derived microglia (iPSdM) by PCR and LSM. The ARMS2 protein was localized in human genotyped retinal sections and in purified monocytes derived from AMD patients without the ARMS2 risk variant by LSM. ARMS2 expression in monocytes under oxidative stress was determined by Western blot analysis. Results Here, we demonstrate for the first time that ARMS2 functions as surface complement regulator. Recombinant ARMS2 binds to human apoptotic and necrotic cells and initiates complement activation by recruiting the complement activator properdin. ARMS2-properdin complexes augment C3b surface opsonization for phagocytosis. We also demonstrate for the first time expression of ARMS2 in human monocytes especially under oxidative stress and in microglia cells of the human retina. The ARMS2 protein is absent in monocytes and also in microglia cells, derived from patients homozygous for the ARMS2 AMD risk variant (rs10490924). Conclusions ARMS2 is likely involved in complement-mediated clearance of cellular debris. As AMD patients present with accumulated proteins and lipids on Bruch’s membrane, ARMS2 protein deficiency due to the genetic risk variant might be involved in drusen formation. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0776-3) contains supplementary material, which is available to authorized users.
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Kozyra M, Ingelman-Sundberg M, Lauschke VM. Rare genetic variants in cellular transporters, metabolic enzymes, and nuclear receptors can be important determinants of interindividual differences in drug response. Genet Med 2016; 19:20-29. [DOI: 10.1038/gim.2016.33] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 12/17/2022] Open
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Kortvely E, Ueffing M. Gene Structure of the 10q26 Locus: A Clue to Cracking the ARMS2/HTRA1 Riddle? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:23-9. [PMID: 26427389 DOI: 10.1007/978-3-319-17121-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Age-related macular degeneration (AMD) is a sight-threatening disorder of the central retina. Being the leading cause of visual impairment in senior citizens, it represents a major public health issue in developed countries. Genetic studies of AMD identified two major susceptibility loci on chromosomes 1 and 10. The high-risk allele of the 10q26 locus encompasses three genes, PLEKHA1, ARMS2, and HTRA1 with high linkage disequilibrium and the individual contribution of the encoded proteins to disease etiology remains controversial. While PLEKHA1 and HTRA1 are highly conserved proteins, ARMS2 is only present in primates and can be detected by using RT-PCR. On the other hand, there is no unequivocal evidence for the existence of the encoded protein. However, it has been reported that risk haplotypes only affect the expression of ARMS2 (but not of HTRA1), making ARMS2 the best candidate for being the genuine AMD gene within this locus. Yet, homozygous carriers of a common haplotype carry a premature stop codon in the ARMS2 gene (R38X) and therefore lack ARMS2, but this variant is not associated with AMD. In this work we aimed at characterizing the diversity of transcripts originating from this locus, in order to find new hints on how to resolve this perplexing paradox. We found chimeric transcripts originating from the PLEKHA1 gene but ending in ARMS2. This finding may give a new explanation as to how variants in this locus contribute to AMD.
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Affiliation(s)
- Elod Kortvely
- Division of Experimental Ophthalmology, University of Tuebingen, Roentgenweg 11, 72076, Tuebingen, Germany.
| | - Marius Ueffing
- Division of Experimental Ophthalmology, University of Tuebingen, Roentgenweg 11, 72076, Tuebingen, Germany.
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Yang J, Li Y, Chan L, Tsai YT, Wu WH, Nguyen HV, Hsu CW, Li X, Brown LM, Egli D, Sparrow JR, Tsang SH. Validation of genome-wide association study (GWAS)-identified disease risk alleles with patient-specific stem cell lines. Hum Mol Genet 2014; 23:3445-55. [PMID: 24497574 DOI: 10.1093/hmg/ddu053] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While the past decade has seen great progress in mapping loci for common diseases, studying how these risk alleles lead to pathology remains a challenge. Age-related macular degeneration (AMD) affects 9 million older Americans, and is characterized by the loss of the retinal pigment epithelium (RPE). Although the closely linked genome-wide association studies ARMS2/HTRA1 genes, located at the chromosome 10q26 locus, are strongly associated with the risk of AMD, their downstream targets are unknown. Low population frequencies of risk alleles in tissue banks make it impractical to study their function in cells derived from autopsied tissue. Moreover, autopsy eyes from end-stage AMD patients, where age-related RPE atrophy and fibrosis are already present, cannot be used to determine how abnormal ARMS2/HTRA1 expression can initiate RPE pathology. Instead, induced pluripotent stem (iPS) cell-derived RPE from patients provides us with earlier stage AMD patient-specific cells and allows us to analyze the underlying mechanisms at this critical time point. An unbiased proteome screen of A2E-aged patient-specific iPS-derived RPE cell lines identified superoxide dismutase 2 (SOD2)-mediated antioxidative defense in the genetic allele's susceptibility of AMD. The AMD-associated risk haplotype (T-in/del-A) impairs the ability of the RPE to defend against aging-related oxidative stress. SOD2 defense is impaired in RPE homozygous for the risk haplotype (T-in/del-A; T-in/del-A), while the effect was less pronounced in RPE homozygous for the protective haplotype (G-Wt-G; G-Wt-G). ARMS2/HTRA1 risk alleles decrease SOD2 defense, making RPE more susceptible to oxidative damage and thereby contributing to AMD pathogenesis.
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Affiliation(s)
- Jin Yang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA, Tianjin Medical University Eye Hospital, Tianjin 300384, China
| | - Yao Li
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Lawrence Chan
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Yi-Ting Tsai
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Wen-Hsuan Wu
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Huy V Nguyen
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Chun-Wei Hsu
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Xiaorong Li
- Tianjin Medical University Eye Hospital, Tianjin 300384, China
| | - Lewis M Brown
- Quantitative Proteomics Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dieter Egli
- The New York Stem Cell Foundation Laboratory, New York, NY 10032, USA and
| | - Janet R Sparrow
- Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine, Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA, Edward S. Harkness Eye Institute, Columbia University, New York, NY 10032, USA, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY 10032, USA
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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: 73] [Impact Index Per Article: 6.6] [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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Teper SJ, Nowińska A, Wylęgała E. A69S and R38X ARMS2 and Y402H CFH gene polymorphisms as risk factors for neovascular age-related macular degeneration in Poland - a brief report. Med Sci Monit 2012; 18:PR1-3. [PMID: 22293892 PMCID: PMC3560583 DOI: 10.12659/msm.882447] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The wet form of age-related macular degeneration (ARMD) is a leading cause of irreversible blindness in Caucasians. Our purpose was to assess influence of gene polymorphisms A69S (rs10490924) and R38X (rs2736911) ARMS2 and Y402 (rs1061170) CFH on wet ARMD risk in a Polish population. MATERIAL/METHODS 130 unrelated patients (90 with wet ARMD and 40 controls) took part in the study. Dry blood was used for DNA isolation. PCR amplification and gene sequencing were performed. In subjects with R38X and A69S, SNP gene cloning was used to exclude the possible combined variant. RESULTS Homozygous Y402H and A69S conferred a significance risk of wet ARMD in Poland: Y402H odds ratio (OR) was 5.57 (95% confidence interval: 1.58-19.6), p=0.002; and A69S OR was 7.72 (95% confidence interval: 1.73-34.36), p=0.001. R38X is probably more common in healthy subjects: OR was 0.45 (95% confidence interval: 0.19-1.05), p=0.053. CONCLUSIONS The etiologic role in ARMD of A69S ARMS2 and Y402H CFH gene variants were confirmed in a Polish population for the first time. R38X variant of ARMS2 seems to be protective from wet ARMD.
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Capoluongo E, Concolino P, Piccardi M, Marangoni D, Mello E, Minnella AM, Savastano C, Fadda A, Zuppi C, Bisti S, Falsini B. Retinal function and CFH-ARMS2 polymorphisms analysis: a pilot study in Italian AMD patients. Neurobiol Aging 2012; 33:1852.e5-12. [PMID: 22552255 DOI: 10.1016/j.neurobiolaging.2012.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/09/2012] [Accepted: 03/15/2012] [Indexed: 11/16/2022]
Abstract
Two major susceptibility genes, complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2), have been implicated in age-related macular degeneration (AMD) pathogenesis. We analyzed the association between CFH rs1061170 and/or ARMS2 rs10490924 polymorphisms with central retinal function properties, as evaluated by focal electroretinogram (fERG). Forty early AMD patients, with preserved visual acuity and typical macular lesions, underwent fERG recording (in response to 41 Hz flicker stimuli presented to the central 18 degrees) and CFH/ARMS2 genotyping. Mean fERG amplitude and sensitivity decreased in patients carrying CFH rs1061170 polymorphism (p < 0.01), compared with wild type ones, although visual acuity and funduscopic features were similar across the 2 groups. No significant fERG phase changes were observed. No association was detected between ARMS2 (rs10490924) polymorphism and fERG parameters. Our findings indicate that CFH (rs1061170) polymorphism impacts significantly on retinal function in early AMD patients, and support the hypothesis that dysfunctional CFH might result in early retinal function loss due to a reduction in the immune antioxidant defense mechanism.
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Affiliation(s)
- Ettore Capoluongo
- Istituto di Biochimica Clinica, Università Cattolica del S Cuore, Rome, Italy
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Colak E, Majkic-Singh N, Zoric L, Radosavljevic A, Kosanovic-Jakovic N. The role of CRP and inflammation in the pathogenesis of age-related macular degeneration. Biochem Med (Zagreb) 2012; 22:39-48. [PMID: 22384518 PMCID: PMC4062327 DOI: 10.11613/bm.2012.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex, degenerative and progressive disease involving the multiple genetic and environmental factors that can result in severe visual loss. The etiology of AMD is not well understood. Many theories exist and feature mechanisms of oxidative stress, atherosclerotic-like changes, genetic predisposition and inflammation. The most recent clinical studies appointed to a great role of inflammation and C-reactive protein (CRP) in the pathogenesis of AMD. There is a large body of evidence indicating the association of CRP with endothelial dysfunction, oxidative stress and production of reactive oxygen species (ROS), as well as with lipid status disorder in AMD patients. According to recent studies, CRP is definitely not only the inflammatory marker but also a mediator of development of the vascular disorders in the retinal circulation. The results obtained from the present studies may help our understanding the pathogenesis of the retinal vascular disease associated with high levels of CRP.
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Affiliation(s)
- Emina Colak
- Institute of Medical Biochemistry, Clinical Center of Serbia and Farmaceutical Faculty, University of Belgrade, Belgrade, Serbia.
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Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration. Hum Genomics 2012; 5:420-40. [PMID: 21807600 PMCID: PMC3525964 DOI: 10.1186/1479-7364-5-5-420] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Predictive tests for estimating the risk of developing late-stage neovascular age-related macular degeneration (AMD) are subject to unique challenges. AMD prevalence increases with age, clinical phenotypes are heterogeneous and control collections are prone to high false-negative rates, as many control subjects are likely to develop disease with advancing age. Risk prediction tests have been presented previously, using up to ten genetic markers and a range of self-reported non-genetic variables such as body mass index (BMI) and smoking history. In order to maximise the accuracy of prediction for mainstream genetic testing, we sought to derive a test comparable in performance to earlier testing models but based purely on genetic markers, which are static through life and not subject to misreporting. We report a multicentre assessment of a larger panel of single nucleotide polymorphisms (SNPs) than previously analysed, to improve further the classification performance of a predictive test to estimate the risk of developing choroidal neovascular (CNV) disease. We developed a predictive model based solely on genetic markers and avoided inclusion of self-reported variables (eg smoking history) or non-static factors (BMI, education status) that might otherwise introduce inaccuracies in calculating individual risk estimates. We describe the performance of a test panel comprising 13 SNPs genotyped across a consolidated collection of four patient cohorts obtained from academic centres deemed appropriate for pooling. We report on predictive effect sizes and their classification performance. By incorporating multiple cohorts of homogeneous ethnic origin, we obtained >80 per cent power to detect differences in genetic variants observed between cases and controls. We focused our study on CNV, a subtype of advanced AMD associated with a severe and potentially treatable form of the disease. Lastly, we followed a two-stage strategy involving both test model development and test model validation to present estimates of classification performance anticipated in the larger clinical setting. The model contained nine SNPs tagging variants in the regulators of complement activation (RCA) locus spanning the complement factor H (CFH), complement factor H-related 4 (CFHR4), complement factor H-related 5 (CFHR5) and coagulation factor XIII B subunit (F13B) genes; the four remaining SNPs targeted polymorphisms in the complement component 2 (C2), complement factor B (CFB), complement component 3 (C3) and age-related maculopathy susceptibility protein 2 (ARMS2) genes. The pooled sample size (1,132 CNV cases, 822 controls) allowed for both model development and model validation to confirm the accuracy of risk prediction. At the validation stage, our test model yielded 82 per cent sensitivity and 63 per cent specificity, comparable with metrics reported with earlier testing models that included environmental risk factors. Our test had an area under the curve of 0.80, reflecting a modest improvement compared with tests reported with fewer SNPs.
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Stanton CM, Chalmers KJ, Wright AF. The chromosome 10q26 susceptibility locus in age-related macular degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:365-70. [PMID: 22183354 DOI: 10.1007/978-1-4614-0631-0_47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
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Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes. BMC Genomics 2011; 12:229. [PMID: 21569303 PMCID: PMC3110572 DOI: 10.1186/1471-2164-12-229] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 05/11/2011] [Indexed: 01/21/2023] Open
Abstract
Background Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. Results We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies. We identified 324 genes with significant genome-wide dosage effects, including well investigated genes like SOD1, APP, RUNX1 and DYRK1A as well as a large proportion of novel genes (N = 62). Furthermore, we characterized these genes using gene ontology, molecular interactions and promoter sequence analysis. In order to judge relevance of the 324 genes for more general cerebral pathologies we used independent publicly available microarry data from brain studies not related with DS and identified a subset of 79 genes with potential impact for neurocognitive processes. All results have been made available through a web server under http://ds-geneminer.molgen.mpg.de/. Conclusions Our study represents a comprehensive integrative analysis of heterogeneous data including genome-wide transcript levels in the domain of trisomy 21. The detected dosage effects build a resource for further studies of DS pathology and the development of new therapies.
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Friedrich U, Myers CA, Fritsche LG, Milenkovich A, Wolf A, Corbo JC, Weber BH. Risk- and non-risk-associated variants at the 10q26 AMD locus influence ARMS2 mRNA expression but exclude pathogenic effects due to protein deficiency. Hum Mol Genet 2011; 20:1387-99. [PMID: 21252205 PMCID: PMC3049360 DOI: 10.1093/hmg/ddr020] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 01/13/2011] [Indexed: 01/11/2023] Open
Abstract
Fifteen variants in 10q26 are in strong linkage disequilibrium and are associated with an increased risk for age-related macular degeneration (AMD), a frequent cause of blindness in developed countries. These variants tag a single-risk haplotype encompassing the genes ARMS2 (age-related maculopathy susceptibility 2) and part of HTRA1 (HtrA serine peptidase 1). To define the true AMD susceptibility gene in 10q26, several studies have focused on the influence of risk alleles on the expression of ARMS2 and/or HTRA1, but the results have been inconsistent. By heterologous expression of genomic ARMS2 variants, we now show that ARMS2 mRNA levels transcribed from the risk haplotype are significantly reduced compared with non-risk mRNA isoforms. Analyzing variant ARMS2 constructs, this effect could specifically be assigned to the known insertion/deletion polymorphism (c.(*)372_815del443ins54) in the 3'-untranslated region of ARMS2. Reporter gene assays with HTRA1 promoter sequences demonstrated the presence of a Müller glia-specific cis-regulatory region further upstream of the transcription start site. However, AMD risk alleles had little or no effect on HTRA1 promoter activity in the retina. Analysis of a large series of human post-mortem retina/retinal pigment epithelial samples heterozygous for the risk haplotype confirmed the in vitro/ex vivo results and demonstrated that the risk haplotype affects ARMS2 but not HTRA1 mRNA expression. Furthermore, we provide in vivo evidence that a common non-risk-associated non-synonymous variant (rs2736911) also leads to decreased ARMS2 transcript levels. Consequently, our data suggest that pathogenic effects due to ARMS2 protein deficiency are unlikely to account for AMD pathology.
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Affiliation(s)
- Ulrike Friedrich
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Connie A. Myers
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA and
| | - Lars G. Fritsche
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Andrea Milenkovich
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Armin Wolf
- Department of Ophthalmology, Ludwig-Maximilians University, Mathildenstrasse 8, 80336 Munich, Germany
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA and
| | - Bernhard H.F. Weber
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
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Progression of geographic atrophy and genotype in age-related macular degeneration. Ophthalmology 2010; 117:1554-9, 1559.e1. [PMID: 20381870 DOI: 10.1016/j.ophtha.2009.12.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 12/08/2009] [Accepted: 12/08/2009] [Indexed: 12/22/2022] Open
Abstract
PURPOSE We sought to determine whether genotype is associated with rate of growth of geographic atrophy (GA) in eyes with age-related macular degeneration (AMD). DESIGN Prospective analysis of participants in a randomized controlled clinical trial. PARTICIPANTS We included 114 eyes of 114 participants in the Age-Related Eye Disease Study (AREDS). METHODS Fundus photographs from AREDS participants with GA from whom a DNA specimen had been obtained and serial photographs had been taken over a minimum of 2 years were evaluated for progression as determined by change in cumulative area of GA. All fundus photographs were scanned, digitized, and centrally graded longitudinally for area of GA. The relationship of GA progression with previously identified genetic variants associated with AMD was assessed. MAIN OUTCOME MEASURES Genotype frequencies and change in cumulative area of GA. RESULTS The mean growth rate of GA for the 114 eyes was 1.79 mm(2)/year (range, 0.17-4.76). No association between growth rate and genotype was present for variants in the CFH, C2, C3, APOE, and TLR3 genes. For the single nucleotide polymorphism rs10490924 in LOC387715/ARMS2, there was a significant association of GA growth rate, both adjusted and unadjusted for initial lesion size, with the homozygous risk genotype as compared with the homozygous nonrisk genotype (unadjusted P = 0.002; Bonferroni-corrected P = 0.014) and for allelic association (Bonferroni-corrected P value = 0.011). Analyses of other measures of GA progression (progression to central GA from extrafoveal GA and development of bilateral GA in those initially with unilateral GA) showed no statistically significant association between progression and the LOC387715/ARMS2/HTRA1 genotype. CONCLUSIONS Growth rates of GA calculated from digitized serial fundus photographs showed no association with variants in the CFH, C2, C3, APOE, or TLR3 genes. There was a nominally significant association with the LOC387715/ARMS2/HTRA1 genotype, although this finding was not supported by analyses of secondary measures of GA progression. Replication in other populations is needed to establish the existence of an association.
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Hu J, Bok D. Culture of highly differentiated human retinal pigment epithelium for analysis of the polarized uptake, processing, and secretion of retinoids. Methods Mol Biol 2010; 652:55-73. [PMID: 20552421 DOI: 10.1007/978-1-60327-325-1_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The retinal pigment epithelium (RPE) occupies a strategic position within the eye, given its location between the neurosensory retina and the vascular bed (choroid) that nourishes the photoreceptor cells (rods and cones). Among the many attributes of this versatile monolayer of cells is its unique ability to convert vitamin A (retinol) into the prosthetic group (11-cis-retinal) for the rod and cone opsins, the photopigments essential for vision. It does so by absorbing retinol via a receptor-mediated process that involves the interaction of a carrier protein secreted by the liver, retinol-binding protein (RBP), and a receptor/channel that is the gene product of STRA6 (stimulated by retinoic acid 6). Following its uptake through the basolateral plasma membrane of the RPE, retinol encounters a brigade of binding proteins, membrane-bound receptors, and enzymes that mediate its multi-step conversion to 11-cis-retinal and the transport of this visual chromophore to the light-sensitive photoreceptor cell outer segment, the portion of the cell that houses the phototransduction cascade. This process is iterative, repeating itself via the retinoid visual cycle. Most of the human genes that code for this cohort of proteins carry disease-causing mutations in humans. The consequences of these mutations range in severity from relatively mild dysfunction such as congenital stationary night blindness to total blindness. The RPE, although post-mitotic in situ, is capable of proliferation when removed from its native milieu. This offers one the opportunity to study the retinoid visual cycle in modular form, providing insights into this intriguing process in health and disease. This chapter describes a cell culture method whereby the entire visual cycle can be created in vitro.
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Affiliation(s)
- Jane Hu
- Jules Stein Eye Institute and Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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17
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Bergeron-Sawitzke J, Gold B, Olsh A, Schlotterbeck S, Lemon K, Visvanathan K, Allikmets R, Dean M. Multilocus analysis of age-related macular degeneration. Eur J Hum Genet 2009; 17:1190-9. [PMID: 19259132 PMCID: PMC2729805 DOI: 10.1038/ejhg.2009.23] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 11/10/2008] [Accepted: 12/18/2008] [Indexed: 11/08/2022] Open
Abstract
Age-related macular degeneration (AMD) is a late onset vision disorder. Recent studies demonstrate that alterations in complement cascade genes are associated with AMD. Of the three identified complement loci, variants in complement factor H (CFH) have the highest impact as does an independent locus at 10q26. Our matched case-control study using the Age-Related Eye Disease Study (AREDS) cohort confirms and extends the associations in these loci. Subjects were genotyped for single nucleotide polymorphisms (SNPs) from CFH, complement component 2 (C2), complement component 3 (C3), complement factor B (CFB), age-related maculopathy susceptibility (ARMS2), HtrA serine peptidase 1 (HTRA1), and apolipoprotein E (APOE). Individual SNPs, and haplotypes showed risk trends consistent with those seen in other population studies for CFH, C3, C2, and CFB. SNP rs10490924 on chromosome 10 in exon 1 of the ARMS2 gene showed a highly significant association with an odds ratio (OR) of 3.2 (95% CI 2.4-4.2) for the risk allele and rs11200638 located in the proximal promoter region of HTRA1 showed a higher significant association with an OR of 3.4 (95% CI 2.5-4.6) with our AMD cases. We found that APOE haplotypes were not significantly associated with disease status. Adjustments for other risk factors did not significantly alter the observed associations. This study validates the complement pathway's involvement in AMD and suggests that allelic variants in complement genes have a direct role in disease. These results also support previous findings that variants in the region of 10q26 exert an independent risk for AMD.
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Affiliation(s)
| | - Bert Gold
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Adam Olsh
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Sarah Schlotterbeck
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Kendal Lemon
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, USA
- Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Michael Dean
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
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Abstract
Technological and analytical advances have led to an unprecedented catalog of genomic regions associated with a broad range of clinically relevant phenotypes in humans. However, some examples notwithstanding, the causes of the overwhelming majority of genetic diseases remain obscure. More importantly, an emerging lesson from genome-wide association studies is that, in most instances, the resolution necessary for identifying actual genes that underlie the phenotype is limited, as is our ability to develop mechanistic, testable disease models from such studies. These new realities will probably necessitate a paradigm shift in our approach to complex traits, for which the combinatorial application of genomic and functional studies will be necessary to understand the mechanism and pathology of genetic disease. Here I will discuss these issues and highlight how additional sequencing and genotyping of ever-increasing cohort sizes without functional interpretation is unlikely to improve our ability to dissect the genetic basis of complex traits.
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Affiliation(s)
- Nicholas Katsanis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Abstract
Age-related macular degeneration is the leading cause of blindness in elderly populations of European descent. The most consistent risk factors associated with this ocular condition are increasing age and cigarette smoking. Genetic investigations have shown that complement factor H, a regulator of the alternative complement pathway, and LOC387715/HtrA1 are the most consistent genetic risk factors for age-related macular degeneration. Although the pathogenesis of this disease is unknown, oxidative stress might have an important role. Treatment with antioxidant vitamins and zinc can reduce the risk of developing advanced age-related macular degeneration by about a quarter in those at least at moderate risk. Intravitreal injections of ranibizumab, a monoclonal antibody that inhibits all forms of vascular endothelial growth factor, have been shown to stabilise loss of vision and, in some cases, improve vision in individuals with neovascular age-related macular degeneration. These findings, combined with assessments of possible environmental and genetic interactions and new approaches to modulate inflammatory pathways, will hopefully further expand our ability to understand and treat age-related macular degeneration.
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Affiliation(s)
- Hanna R Coleman
- Division of Epidemiology and Clinical Research, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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Abstract
Recent years have seen great advances in generating and analyzing data to identify the genetic architecture of biological traits. Human disease has understandably received intense research focus, and the genes responsible for most Mendelian diseases have successfully been identified. However, the same advances have shown a consistent if less satisfying pattern, in which complex traits are affected by variation in large numbers of genes, most of which have individually minor or statistically elusive effects, leaving the bulk of genetic etiology unaccounted for. This pattern applies to diverse and unrelated traits, not just disease, in basically all species, and is consistent with evolutionary expectations, raising challenging questions about the best way to approach and understand biological complexity.
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Affiliation(s)
- Kenneth M Weiss
- Department of Anthropology and Integrated Biosciences Genetics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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