1000 Genomes Project Our AMD genomics dataset were part of the 1000 Genomes Project that reconstructed the genomes of 2,504 individuals from 26 populations and characterized over 88 million variants, all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries (5). AMD and maculopathies Our laboratory has been involved in AMD genetic studies for years, performed one of the first two large genome-wide association studies (GWAS) and were co-leaders in the meta-analysis consortium that led to the identification of 19 associated loci explaining up to half of AMD heritability. Recent studies are as follows: 1) A a large exome-chip consortium that has identified 52 independently associated common and rare variants spread across 34 AMD loci. Sixteen new loci reached genome-wide significance for the first time. Accumulated rare coding variants in CFH, CFI, and TIMP3 and a loss-of-function variant in SLC16A8 implicate specific genes in disease biology. One signal, near MMP9, was specific to wet AMD, although in general, wet and dry AMD subtypes exhibit predominantly shared genetics (4). 2) We identified a rare variant in Fibrillin 2 (FBN2) in a family with inherited maculopathy. FBN2 is localized to Bruch's membrane and is reduced in aging and AMD eyes. We independently detected a suggestive association of a common FBN2 non-synonymous variant with AMD in 10,337 cases and 11,174 controls. Thus, rare and common variants in the single FBN2 gene can contribute to Mendelian and complex forms of macular degeneration. This study provides genetic evidence for a key role of Bruch's membrane in maintaining blood-retina homeostasis and establishes the importance of studying orphan diseases for understanding common clinical phenotypes (13). 3) In a collaborative study, the analysis of the largest dataset on geographic atrophy (GA) lesion growth (N = 388) revealed a significant and independent contribution of three factors; two genetic factors (ARMS2_rs10490924 and C3_rs2230199) and one clinical component (presence of GA in the fellow eye). These correlations jointly explain up to 7.2% of the observed inter-individual variance in GA lesion progression and should be considered in strategy planning of interventional clinical trials. (6); 4) In collaboration with S. Merbs, we investigated the contribution of epigenetics to AMD. Although genome-wide DNA methylation profiling of blood from AMD patients and controls showed no differential methylation site reaching significance, we found small but significant DNA methylation differences in neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924. We further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to epigenetic control and contribute to AMD development and progression (11). 5) We collaborated with E. Chew (NEI) and others in the retrospective evaluation of a clinical trial of vitamins and minerals in AMD to test if genetic variants in CFH and ARMS2 could predict the response to antioxidant and zinc supplement. No clinically significant association was observed between CFH and ARMS2 genotypes and response to nutritional supplements. Thus, genetic testing at only two loci provides no benefit in managing nutritional supplementation for patients at risk of late AMD. (3) 6) To elucidate the function of the aryl hydrocarbon receptor (AHR), that is involved in cellular response to environmental signals, we analyzed Ahr-/- mouse retina. We detected subretinal accumulation of microglia and focal RPE atrophy, characteristics observed in AMD, and reduced ERG c-wave amplitudes. Altered function of AHR may contribute to AMD progression and provide a target for pharmacological intervention (7). Retinal dystrophies In collaborative studies with Israeli scientists, we identified through whole exome sequencing (WES) mutations in known retinal disease genes in 33 out of 68 Israeli families with inherited retinopathies (1). Cone dystrophy (CD) and cone-rod dystrophy (CRD) are heterogeneous diseases in which cone photoreceptor dysfunction or loss precedes/accompanies rod degeneration. Known gene mutations account for less than 25% of the cases. We identified two novel disease-causing variants (p.E841K and p.K846N) in the GUCY2D gene in CD/CRD families. Additional studies revealed GUCY2D as a major cause of autosomal dominant CD and COD in Israel (9). We further detected a nonsense mutation, p.R270*, in ALMS1 and two novel potentially disease-causing missense variants, p.R1581C and p.Y2070C, in DYSF by homozygosity mapping followed by WES in a consanguineous Israeli family with early onset CRD and muscular dystrophy. ALMS1 and DYSF are genetically and physically linked on chromosome 2 in a region associated with Alstrm syndrome (which includes CRD) and with limb girdle muscular dystrophy, respectively. Affected family members lack additional systemic manifestations of Alstrm syndrome but exhibit mild muscular dystrophy. Our study thus implicates ALMS1 as a nonsyndromic retinal disease gene (8). Mutations in the CEP290 gene cause vision loss in almost 25% of LCA in addition to more severe syndromic phenotypes. We have generated and characterized several mouse models of Cep290 disease (2). The hypomorphic rd16 mouse is a model of CEP290-LCA, whereas Cep290-/- mice exhibit a severe phenotype and die around weaning from hydrocephalus. The Cep290-/- mice develop rapid retinal degeneration starting at postnatal day (P)12, with dramatic disruption of outer segment morphogenesis. Even more dramatic is the phenotype of the Cep290gt/gt mice that die at mid-gestation. Rare Cep290gt/gt mice that are born and survive for 2-3 weeks display hydrocephalus and severely cystic kindneys. Partial loss of CEP290-interacting ciliopathy protein MKKS mitigates lethality and renal pathology in Cep290(gt/gt) mice. Our studies set the stage for elucidating mechanisms of CEP290-LCA and syndromic ciliopathies such as Jourbert and Meckel Gruber syndrome (12). Reprogramming of somatic cells to pluripotency allows de novo differentiation to photoreceptors and modeling of retinal disease in a dish using the patients' own cells to study pathogenesis and discover new molecules for therapy. We have generated and are characterizing induced pluripotent stem cells (iPSCs) from patients with mutations in CEP290 and NPHP5 that present LCA and other ciliopathy phenotypes. We have also generated iPSCs from the rd16 mouse, a model of Cep290-LCA, to complement human studies (EY000474). Coloboma Ocular coloboma results from a defect in fusion of the optic fissure. In a collaborative effort, we identified a heterozygous frameshift mutation in the WNT receptor FZD5 (p.Ala219Glufs*49), segregating in a family with dominant ocular coloboma. The mutant protein is secreted and behaves as a dominant-negative FZD5 receptor to antagonize WNT signaling. Expression of the mutant protein causes microphthalmia and coloboma in zebrafish and disruption of apical junction of the retinal neural epithelium in mouse. Our studies directly show the involvement of WNT-FZD pathway in human coloboma (Liu et al. submitted). Robinow syndrome In collaboration with T. Li, we implicated Prickle1 as a key component of the Wnt-signaling pathway. Our studies suggest that Prickle1 may mediate some of the WNT5A-associated genetic defects in Robinow syndrome (10).

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Keenan, Tiarnan D; Agrón, Elvira; Domalpally, Amitha et al. (2018) Progression of Geographic Atrophy in Age-related Macular Degeneration: AREDS2 Report Number 16. Ophthalmology 125:1913-1928
Yan, Qi; Ding, Ying; Liu, Yi et al. (2018) Genome-wide analysis of disease progression in age-related macular degeneration. Hum Mol Genet 27:929-940
Zelinger, Lina; Swaroop, Anand (2018) RNA Biology in Retinal Development and Disease. Trends Genet 34:341-351
Adlakha, Yogita K; Swaroop, Anand (2018) Determination of Mitochondrial Oxygen Consumption in the Retina Ex Vivo: Applications for Retinal Disease. Methods Mol Biol 1753:167-177
Corso-Díaz, Ximena; Jaeger, Catherine; Chaitankar, Vijender et al. (2018) Epigenetic control of gene regulation during development and disease: A view from the retina. Prog Retin Eye Res 65:1-27
Pietraszkiewicz, Alexandra; van Asten, Freekje; Kwong, Alan et al. (2018) Association of Rare Predicted Loss-of-Function Variants in Cellular Pathways with Sub-Phenotypes in Age-Related Macular Degeneration. Ophthalmology 125:398-406
Swaroop, Manju; Brooks, Matthew J; Gieser, Linn et al. (2018) Patient iPSC-derived neural stem cells exhibit phenotypes in concordance with the clinical severity of Mucopolysaccharidosis I. Hum Mol Genet :
DiStefano, Tyler; Chen, Holly Yu; Panebianco, Christopher et al. (2018) Accelerated and Improved Differentiation of Retinal Organoids from Pluripotent Stem Cells in Rotating-Wall Vessel Bioreactors. Stem Cell Reports 10:300-313
van Asten, Freekje; Simmons, Michael; Singhal, Ayush et al. (2018) A Deep Phenotype Association Study Reveals Specific Phenotype Associations with Genetic Variants in Age-related Macular Degeneration: Age-Related Eye Disease Study 2 (AREDS2) Report No. 14. Ophthalmology 125:559-568
Veleri, Shobi; Nellissery, Jacob; Mishra, Bibhudatta et al. (2017) REEP6 mediates trafficking of a subset of Clathrin-coated vesicles and is critical for rod photoreceptor function and survival. Hum Mol Genet 26:2218-2230

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