Ocular genetics in the genomics age

Current genetic screening methods for inherited eye diseases are concentrated on the coding exons of known disease genes (gene panels, clinical exome). These tests have a variable and often limited diagnostic rate depending on the clinical presentation, size of the gene panel and our understanding of the inheritance of the disorder (with examples described in this issue). There are numerous possible explanations for the missing heritability of these cases including undetected variants within the relevant gene (intronic, up/down-stream and structural variants), variants harbored in genes outside the targeted panel, intergenic variants, variants undetectable by the applied technology, complex/non-Mendelian inheritance, and nongenetic phenocopies. In this article we further explore and review methods to investigate these sources of missing heritability.

Therapeutic advantage of pro-electrophilic drugs to activate the Nrf2/ARE pathway in Alzheimer's disease models

Alzheimer's disease (AD) is characterized by synaptic and neuronal loss, which occurs at least partially through oxidative stress induced by oligomeric amyloid-β (Aβ)-peptide. Carnosic acid (CA), a chemical found in rosemary and sage, is a pro-electrophilic compound that is converted to its active form by oxidative stress. The active form stimulates the Keap1/Nrf2 transcriptional pathway and thus production of phase 2 antioxidant enzymes. We used both in vitro and in vivo models. For in vitro studies, we evaluated protective effects of CA on primary neurons exposed to oligomeric Aβ. For in vivo studies, we used two transgenic mouse models of AD, human amyloid precursor protein (hAPP)-J20 mice and triple transgenic (3xTg AD) mice. We treated these mice trans-nasally with CA twice weekly for 3 months. Subsequently, we performed neurobehavioral tests and quantitative immunohistochemistry to assess effects on AD-related phenotypes, including learning and memory, and synaptic damage. In vitro, CA reduced dendritic spine loss in rat neurons exposed to oligomeric Aβ. In vivo, CA treatment of hAPP-J20 mice improved learning and memory in the Morris water maze test. Histologically, CA increased dendritic and synaptic markers, and decreased astrogliosis, Aβ plaque number, and phospho-tau staining in the hippocampus. We conclude that CA exhibits therapeutic benefits in rodent AD models and since the FDA has placed CA on the 'generally regarded as safe' (GRAS) list, thus obviating the need for safety studies, human clinical trials will be greatly expedited.

Protective effect of carnosic acid, a pro-electrophilic compound, in models of oxidative stress and light-induced retinal degeneration

PURPOSE

The herb rosemary has been reported to have antioxidant and anti-inflammatory activity. We have previously shown that carnosic acid (CA), present in rosemary extract, crosses the blood-brain barrier to exert neuroprotective effects by upregulating endogenous antioxidant enzymes via the Nrf2 transcriptional pathway. Here we investigated the antioxidant and neuroprotective activity of CA in retinal cell lines exposed to oxidative stress and in a rat model of light-induced retinal degeneration (LIRD).

METHODS

Retina-derived cell lines ARPE-19 and 661W treated with hydrogen peroxide were used as in vitro models for testing the protective activity of CA. For in vivo testing, dark-adapted rats were given intraperitoneal injections of CA prior to exposure to white light to assess protection of the photoreceptor cells. Retinal damage was assessed by measuring outer nuclear layer thickness and by electroretinogram (ERG).

RESULTS

In vitro, CA significantly protected retina-derived cell lines (ARPE-19 and 661W) against H(2)O(2)-induced toxicity. CA induced antioxidant phase 2 enzymes and reduced formation of hyperoxidized peroxiredoxin (Prx)2. Similarly, we found that CA protected retinas in vivo from LIRD, producing significant improvement in outer nuclear layer thickness and ERG activity.

CONCLUSIONS

These findings suggest that CA may potentially have clinical application to diseases affecting the outer retina, including age-related macular degeneration and retinitis pigmentosa, in which oxidative stress is thought to contribute to disease progression.

Dual neuroprotective pathways of a pro-electrophilic compound via HSF-1-activated heat-shock proteins and Nrf2-activated phase 2 antioxidant response enzymes

Activation of the Keap1/nuclear factor erythroid 2-related factor 2 (Nrf2) pathway and consequent induction of phase 2 antioxidant enzymes is known to afford neuroprotection. Here, we present a series of novel electrophilic compounds that protect neurons via this pathway. Natural products, such as carnosic acid (CA), are present in high amounts in the herbs rosemary and sage as ortho-dihydroquinones, and have attracted particular attention because they are converted by oxidative stress to their active form (ortho-quinone species) that stimulate the Keap1/Nrf2 transcriptional pathway. Once activated, this pathway leads to the production of a series of antioxidant phase 2 enzymes. Thus, such dihydroquinones function as redox-activated 'pro-electrophiles'. Here, we explored the concept that related para-dihydroquinones represent even more effective bioactive pro-electrophiles for the induction of phase 2 enzymes without producing toxic side effects. We synthesized several novel para-hydroquinone-type pro-electrophilic compounds (designated D1 and D2) to analyze their protective mechanism. DNA microarray, PCR, and western blot analyses showed that compound D1 induced expression of heat-shock proteins (HSPs), including HSP70, HSP27, and DnaJ, in addition to phase 2 enzymes such as hemeoxygenase-1 (HO-1), NADP(H) quinine-oxidoreductase1, and the Na(+)-independent cystine/glutamate exchanger (xCT). Treatment with D1 resulted in activation of Nrf2 and heat-shock transcription factor-1 (HSF-1) transcriptional elements, thus inducing phase 2 enzymes and HSPs, respectively. In this manner, D1 protected neuronal cells from both oxidative and endoplasmic reticulum (ER)-related stress. Additionally, D1 suppressed induction of 78 kDa glucose-regulated protein (GRP78), an ER chaperone protein, and inhibited hyperoxidation of peroxiredoxin 2 (PRX2), a molecule that is in its reduced state can protect from oxidative stress. These results suggest that D1 is a novel pro-electrophilic compound that activates both the Nrf2 and HSF-1 pathways, and may thus offer protection from oxidative and ER stress.

Genetic screening of leber congenital amaurosis in a large consanguineous Iranian family

The molecular defect of one large consanguineous Iranian kindred with Leber Congenital Amaurosis (LCA) is presented. The phenotype mapped to 17p13.1 (LCA1) and excluded from five other LCA loci. Sequence analysis of the GUCY2D gene identified a novel homozygous missense mutation (I816S) that segregated with the inherited disease-haplotype in six affected, eight parents, and two normal gene carriers. This mutation was absent in three other normal family members and 92 normal control subjects. In silico analysis predicted that alteration of the highly conserved isoleucine residue at position 816 to serine is deleterious by affecting secondary structure of the GUCY2D protein.

Evaluation of LOXL1 gene polymorphisms in exfoliation syndrome and exfoliation glaucoma

PURPOSE

To evaluate genetic susceptibility of lysyl oxidase-like 1 (LOXL1) gene polymorphisms to exfoliation syndrome (XFS) and exfoliation glaucoma (XFG) in a case-control cohort of American and European patients.

METHODS

DNA from a total of 620 individuals including 287 exfoliation patients and 333 healthy control subjects were extracted by standard methods. Three single nucleotide polymorphisms (SNPs) of rs1048661 (R141L), rs3825942 (G153D), and rs2165241 were genotyped in these individuals by SNaPshot Assay. The seven coding exons of the LOXL1 gene and their immediate flanking regions were directly sequenced in 95 affected patients. Data management and case-control association studies were performed with SNP-STAT and PLINK programs. The obtained DNA sequences were evaluated with the STADEN package.

RESULTS

The 287 unrelated exfoliation cases comprised of 171 American patients (mostly of European background) and 116 patients from 12 European countries. This phenotype was further divided into patients with exfoliation only and no glaucoma (XFO; n=95), exfoliation with glaucoma (XFG; n=133), and exfoliation unclassified (XFU; n=59). Genotypic data were analyzed separately for XFO, XFG, XFU, and XFS (all exfoliations; n=287) and for Americans and Europeans. The observed genotypic frequencies for each exfoliation phenotype or population were tabulated separately and tested for deviation from the Hardy-Weinberg equilibrium (HWE) using a standard Chi(2) test. There were no HWE deviations and no significant genotypic differences between these subcategories for the three studied SNPs. For the combined exfoliation cohort, homozygote genotypes of G/G (rs1048661), G/G (rs3825942), and T/T (rs2165241) were significantly overrepresented. Likewise, case-control allelic association for rs1048661 (p=7.74x10(-9)), rs3825942 (p=3.10x10(-17)), and rs2165241 (p=4.85x10(-24)) were highly significant. The corresponding two-locus haplotype frequencies of GG for rs1048661-rs3825942 (p=1.47x10(-27)), GT for rs1048661-rs2165241 (p=1.29x10(-24)), and GT for rs3825942-rs2165241 (p=2.02x10(-24)) were highly associated with exfoliation phenotypes. The combined effect of these three SNPs revealed that the GGT haplotype is overrepresented by 66% in exfoliation cases, and this deviation from controls is highly significant (p=1.93x10(-24)). This haplotype constituted a major risk factor for development of exfoliation in both XFS and XFG. By contrast, the GAC haplotype was significantly underrepresented (p=4.99x10(-18)) in exfoliation cases by 83% and may potentially have a protective effect for this condition with an estimated attributable risk percent reduction of 457%. The only other haplotype that was significantly different between cases and controls was TGC (p=5.82x10(-9)). No observation was made for the GAT haplotype. The combined three haplotypes of GGT, GAC, and TGC were associated with 91% of the exfoliation syndrome cases in the studied populations. Seven coding exons of LOXL1 were also sequenced in 95 affected cases. In addition to the three above-mentioned SNPs, 12 other variations were also observed in these patients (G240G, D292D, A320A, V385V, rs2304719, IVS3+23C>T, IVS3-155G>A, IVS3-101G>A, IVS4+49G>A, rs2304721, IVS5-121C>T, and rs2304722). None were considered a disease-causing mutation.

CONCLUSIONS

We confirmed a strong association with LOXL1 variants in our patients. For the LOXL1 gene, individual alleles of rs1048661 (G), rs3825942 (G), and rs2165241 (T) are highly associated with XFS and XFG in American and European populations. The GGT haplotype constitutes a major risk haplotype for exfoliation, and GAC may have a protective role. DNA sequencing of 95 affected patients did not show any mutations in this gene. The LOXL1 SNPs are located in the 15q24.1 band and within a genetic locus (GLC1N) that is associated with primary open-angle glaucoma (POAG). However, the LOXL1 genetic predisposition is only limited to exfoliation with or without glaucoma and does not include the POAG phenotype.

Embryonic expression of the optineurin (glaucoma) gene in different stages of mouse development

PURPOSE

To analyze optineurin (Optn) gene expression in various embryonic stages of mouse development by whole mount in situ hybridization.

METHODS

FVB/NcrlBR mouse embryos (10.5 and 13.5 dpc) were collected by timed breeding experiments. A 712 bp Optn cDNA fragment was amplified by PCR and cloned into a transcription vector pCRII-TOPO. Digoxigenin labeled sense and antisense RNA probes were generated by in vitro transcription. The labeled RNA probe was localized using an anti-digoxigenin antibody conjugated with alkaline phosphatase. Colorimetric detection was performed with substrate solution containing, 4-nitro-blue tetrazolium chloride (NBT) and 5-bromo-4-chloro-3-indolyl phosphate (BCIP).

RESULTS

This study revealed that the developing eye represents a major expression site for Optn. At both 10.5 and 13.5 dpc a strong specific expression was detected in the outer layer of the optic cup (future pigment layer of the retina). This is in contrast to the expression of another glaucoma gene, Cyp1b1, the expression of which at this state is only limited to the inner (neural) layer of the optic cup (future nervous layer of the retina). Inspection of sections from the cephalic region of whole mounts also revealed limited Optn staining in the lens as well as in the optic nerve. A second Optn expression domain was detected at the base of the developing forelimb. The biological significance of this observation is not clear and remains to be determined.

CONCLUSIONS

Eye and forelimb were identified as two major sites for expression of the Optn gene. These findings suggest that Optn expression is triggered during early stages of eye development. Expression of the Optn gene in ocular tissues during mouse embryogenesis correlates with the presence and distribution of the optineurin protein, as previously reported in adult ocular tissues. These findings are also in agreement with the predicted function of Optn protein in the eye and the role of its ortholog in human glaucoma. Further investigations are required to determine the molecular mechanisms of Optn in the developing murine forelimb.

Analysis of rare variants and common haplotypes in the optineurin gene in Swedish glaucoma cases

OBJECTIVE

Glaucoma, a leading cause of blindness in the world, is characterized by neuropathy of the retinal ganglion cells and the optic nerve. Recently, sequence alterations in the optineurin gene were shown to be associated with the disease in families with primarily normal tension glaucoma.

METHODS

In the present study, 200 patients with primary open-angle glaucoma, 200 patients with exfoliative glaucoma, and 200 matched controls were tested for alterations in the coding sequences using denaturing high-performance liquid chromatography and sequencing. In addition, single nucleotide polymorphisms distributed throughout the gene were typed and haplotypes were constructed.

RESULTS

No disease-causing alterations were found in either of the patient cohorts. The risk-associated allele M98K was found in equal amounts in both patients and controls. Analysis of haplotype frequencies and distribution revealed high haplotype diversity but no differences between patients and controls.

CONCLUSION

These experiments show no association between optineurin and our Swedish cohorts of high-pressure glaucoma cases, either in coding sequence or in haplotype frequency and distribution.

Molecular cloning and expression profiling of optineurin in the rhesus monkey

PURPOSE

It has been shown that mutations in the optineurin (OPTN) gene are involved in the etiology of adult-onset primary open-angle glaucoma (POAG). In view of close similarities between human and nonhuman primate ocular development and function, the rhesus monkey is considered a suitable model for human visual system research. Therefore, this study was conducted to clone the orthologue of the human OPTN gene in the rhesus monkey (Rh-OPTN) and to determine its genomic organization. A further purpose was to establish Rh-OPTN protein expression profiles and tissue distribution in the rhesus anterior segment, retina, and optic nerve.

METHODS

The Rh-OPTN gene was cloned and its genomic structure determined. The mRNA expression pattern was examined by Northern blot analysis. The protein's cellular localization, ocular expression, and tissue distribution were established by immunolabeling.

RESULTS

The Rh-OPTN gene has 13 exons and encodes for a 571-amino-acid protein. Both cDNA and amino acid sequences are 96% identical with the human OPTN. Northern blot analysis revealed prominent expression of two different transcripts in heart, brain, kidney, lung, spleen, skeletal muscle, and small intestine. Cellular and tissue distribution of Rh-OPTN protein were highly similar to its human and mouse homologous proteins.

CONCLUSIONS

The optineurin gene and protein are evolutionary conserved between humans and the rhesus monkey. High similarity of ocular expression and tissue distribution between the two optineurin proteins suggests that this nonhuman primate is a suitable model for the pathophysiology and treatment of human glaucomatous optic neuropathy.

Clinical Features and Course of Patients with Glaucoma with the E50K Mutation in the Optineurin Gene

PURPOSE

To investigate the clinical features of subjects with glaucoma with the E50K mutation in the optineurin (OPTN) gene and to compare the onset, severity, and clinical course of these patients with a control group of subjects with glaucoma without this mutation.

METHODS

The phenotype of well-characterized subjects from Moorfields Eye Hospital, London, who had been identified as carrying the OPTN E50K mutation was examined. A wide range of structural, psychophysical, and demographic factors were then compared with those in a control group of subjects with glaucoma without this mutation.

RESULTS

Eleven subjects with glaucoma with the E50K mutation (nine in two families and two sporadic cases) were studied. All 11 subjects had normal tension glaucoma (NTG), with presenting and highest IOP of 15.3 +/- 3.0 and 16.5 +/- 2.5 mm Hg (+/-SD) on diurnal testing. Compared with 87 NTG control subjects who did not have this mutation, subjects with E50K presented at a younger age (40.8 +/- 15 years, P = 0.0001) and had more advanced optic disc cupping (mean cup-disc ratio +/- SD 0.86 +/- 0.1, P = 0.001) and smaller neuroretinal rim area (+/-SD; 0.5 +/- 0.28 mm2, P = 0.001) at diagnosis. The rate of filtration surgery performed for progressive visual field loss in those with and without the E50K mutation was 72.7% and 25.3%, respectively (P = 0.003), and all subjects with E50K were found to have progressing visual fields. In addition, seven E50K mutation-carrying individuals in two families (age range, 23-58 years) presented with normal optic discs and visual fields and, as yet, no signs of glaucoma.

CONCLUSIONS

In this study, subjects with glaucoma who had the OPTN E50K mutation were found to have NTG that appeared to be more severe than that in a control group of subjects with NTG without this mutation. The findings emphasize the importance of early detection and treatment of glaucoma in such individuals, to minimize visual loss.

Molecular cloning, genomic structure, and protein characterization of mouse optineurin☆

We recently identified optineurin (OPTN) as a novel gene for glaucoma and determined its mRNA and protein expression patterns in different human tissues. Herein, we describe the cloning, mapping, genomic organization, and mRNA and protein expression patterns for murine optineurin (Optn). We mapped Optn to chromosome 2, within a region that is syntenic to human 10p14. Optn has 13 coding exons and its exon-intron boundaries are evolutionarily conserved with human. Optn encodes an 884-amino-acid protein and shows 78% identity to OPTN. Northern blot analysis revealed three mRNA transcripts with highest expression in adult liver, heart, and testis and with earliest detectable message in 7-day-old embryos. In situ hybridization showed prominent ocular expression during mouse embryonic development. Optn colocalizes with vesicular structures near the nucleus and is expressed in anterior segment, retina, and optic nerve blood vessels. Gene and protein ocular profiling of Optn is a prerequisite for developing a mouse model for glaucoma.

Expression of cytochrome P4501b1 (Cyp1b1) during early murine development

PURPOSE

To examine the embryonic expression of cytochrome P4501b1 (Cyp1b1) gene by whole mount in situ hybridization.

METHODS

FVB/NcrlBR mouse embryos staged at 9.5, 10.5, and 11.5 dpc were obtained by timed breeding experiments. Antisense and sense RNA probes labeled with digoxigenin UTP were generated by in vitro transcription of an 848 bp Cyp1b1 cDNA fragment that was subcloned into transcription vector pCRII-TOPO. The digoxigenin labeled RNA was localized using an alkaline phosphatase conjugated anti-digoxigenin Fab fragment. Colorimetric detection of the digoxigenin labeled probe was performed with substrate solution containing 4-nitro-blue tetrazolium chloride (NBT) and 5-bromo-4-chloro-3-indolyl phosphate (BCIP).

RESULTS

During early stages of murine development Cyp1b1 mRNA was detected in the developing eye, hindbrain, branchial arches, forelimb bud, ligaments supporting the liver primordium and developing kidney. In the eye and forelimb bud Cyp1b1 displayed restricted expression along the axes of development. In the developing eye Cyp1b1 exhibited dorsal expression with respect to the dorso-distal/proximo-ventral axis and anterior expression with respect to the anterior-nasal/posterior-temporal axis. In the forelimb bud Cyp1b1 expression was localized posteriorly. The polarity of Cyp1b1 expression was lost at 11.5 dpc, at which time expression was additionally seen in ventral (eye) and anterior (forelimb bud) areas.

CONCLUSIONS

The spatio-temporal expression patterns observed in this study suggest that during early stages of murine development, Cyp1b1 participates in establishment and/or maintenance of polarity along the axes of embryonic development. Expression of Cyp1b1 in the dorso-distal end of the optic cup, from which the ciliary body and iris are derived, correlates with the expression patterns seen in adult tissues and the abnormal development of these structures as part of the glaucoma phenotypes resulting from Cyp1b1 mutations.

Optineurin in primary open angle glaucoma

The authors' initial estimate indicated that mutations in Optineurin are responsible for a significant proportion of LPG/POAG families. Currently, there are up to 1.2 million persons with LPG and up to 2.47 million persons with POAG in the United States alone. Perhaps twice as many individuals are already affected with this condition without any identifiable clinical signs or symptoms. Investigators are eagerly awaiting confirmation of OPTN mutations in other glaucoma populations. Although additional mutations have already been identified in the sporadic cases of LPG, the significance of this gene in high-pressure POAG requires more intensive investigation. Limited data on partial screening of this gene indicate that OPTN mutations are responsible for a limited number of cases of high-pressure POAG. If the reported mutation rates of OPTN in the LPG group can be confirmed in other LPG or POAG patients, then this gene would be useful in diagnosing presymptomatic persons many decades before they develop this silent and blinding eye condition. Early identification of such at-risk patients would provide an opportunity for immediate targeted medical treatments and specific glaucoma therapy that might significantly delay or completely stop the gradual progression of this condition. Therefore, identification of glaucoma-causing genes such as Myocilin, Optineurin, and others could provide molecular diagnostic tools for this category of optic neuropathy. Although patients with advanced glaucoma will not directly benefit from the use of such molecular diagnostic tools, their immediate family members could certainly benefit from the identification of the cause of the glaucoma decades before the first manifestation of the disease. In summary, a series of mutations in the Optineurin gene have been shown to be the principal cause of adult-onset LPG/POAG phenotype in certain pedigrees. The exact mechanisms through which these mutations lead to the development of glaucoma require additional functional study. The existing evidence suggests that direct interaction of Optineurin with E3-14.7K protein probably utilizes TNF-alpha or Fas-ligand pathways to mediate apoptosis, inflammation, or vasoconstriction. Optineurin also functions through its interactions with other proteins in cellular morphogenesis and membrane trafficking (RAB8), vesicle trafficking (Huntingtin), transcription activation (TFIIIA), and assembly or activity of two unknown kinases. Identification of Optineurin as an adult-onset glaucoma gene and its known interaction with a group of proteins provides the first opportunity to study biochemical pathways that are thought to be involved in causation of this group of eye disorders. Furthermore, identification of this gene as a contributing factor to the development of glaucoma gives a useful tool for screening of this disorder in the elderly population and other high-risk individuals. The exact impact of OPTN in the development of all glaucoma phenotypes requires future study.

Adult-onset primary open-angle glaucoma caused by mutations in optineurin

Primary open-angle glaucoma (POAG) affects 33 million individuals worldwide and is a leading cause of blindness. In a study of 54 families with autosomal dominantly inherited adult-onset POAG, we identified the causative gene on chromosome 10p14 and designated it OPTN (for "optineurin"). Sequence alterations in OPTN were found in 16.7% of families with hereditary POAG, including individuals with normal intraocular pressure. The OPTN gene codes for a conserved 66-kilodalton protein of unknown function that has been implicated in the tumor necrosis factor-alpha signaling pathway and that interacts with diverse proteins including Huntingtin, Ras-associated protein RAB8, and transcription factor IIIA. Optineurin is expressed in trabecular meshwork, nonpigmented ciliary epithelium, retina, and brain, and we speculate that it plays a neuroprotective role.