Genome-wide association studies in the hunt for genes causing primary open-angle glaucoma: a review

Laser Capture Microdissection of Highly Pure Trabecular Meshwork from Mouse Eyes for Gene Expression Analysis

Laser capture microdissection (LCM) has allowed gene expression analysis of single cells and enriched cell populations in tissue sections. LCM is a great tool for the study of the molecular mechanisms underlying cell differentiation and the development and progression of various diseases, including glaucoma. Glaucoma, which comprises a family of progressive optic neuropathies, is the most common cause of irreversible blindness worldwide. Structural changes and damage within the trabecular meshwork (TM) can result in increased intraocular pressure (IOP), which is a major risk factor for developing glaucoma. However, the precise molecular mechanisms involved are still poorly understood. The ability to perform gene expression analysis will be crucial in obtaining further insights into the function of these cells and its role in the regulation of IOP and glaucoma development. To achieve this, a reproducible method for isolating highly enriched TM from frozen sections of mouse eyes and a method for downstream gene expression analysis, such as RT-qPCR and RNA-Seq is needed. The method described herein is developed to isolate highly pure TM from mouse eyes for downstream digital PCR and microarray analysis. In addition, this technique can be easily adapted for the isolation of other highly enriched ocular cells and cell compartments that have been difficult to isolate from mouse eyes. The combination of LCM and RNA analysis can contribute to a more comprehensive understanding of the cellular events underlying glaucoma.

Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium

Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects of variants across the genome, it is believed that gene-gene interactions can help elucidate part of the missing heritability by allowing for the test of interactions between genetic variants to mimic the complex nature of biology. To explain the etiology of glaucoma, we first performed a genome-wide association study (GWAS) on glaucoma case-control samples obtained from electronic medical records (EMR) to establish the utility of EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype. Our findings from GWAS suggest consistent evidence of several known associations in POAG. We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical Records and GEnomics Network (eMERGE) network dataset. Genes from the top epistatic interactions from eMERGE data (Likelihood Ratio Test i.e. LRT p-value <1e-05) were then tested for replication in the NEIGHBOR consortium dataset. To replicate our findings, we performed a gene-based SNP-SNP interaction analysis in NEIGHBOR and observed significant gene-gene interactions (p-value <0.001) among the top 17 gene-gene models identified in the discovery phase. Variants from gene-gene interaction analysis that we found to be associated with POAG explain 3.5% of additional genetic variance in eMERGE dataset above what is explained by the SNPs in genes that are replicated from previous GWAS studies (which was only 2.1% variance explained in eMERGE dataset); in the NEIGHBOR dataset, adding replicated SNPs from gene-gene interaction analysis explain 3.4% of total variance whereas GWAS SNPs alone explain only 2.8% of variance. Exploring gene-gene interactions may provide additional insights into many complex traits when explored in properly designed and powered association studies.

The complex nature of primary-open angle glaucoma (POAG) has left researchers exploring the genetic architecture and searching for the missing heritability using a number of different study designs. Over the past decade, many studies have been conducted to explain the etiology of POAG; however, a high proportion of estimated heritability still remains unexplained. GWA studies for POAG have identified significant associations but these associations have only explained a small proportion of the genetic risk (odds ratios range between 1–3). In this paper, we sought to confirm the primary genome-wide significant associations that have been discovered so far for glaucoma in phenotypes developed from EMR data in an effort to show that EMR data can be a powerful resource for finding genetic variants influencing POAG susceptibility. Next, we tested for statistical interactions, which can be presented as an important tool in an attempt to explain POAG heritability. We used a reduced list of variants filtered by marginal main effect analysis to look for epistatic interactions. We present our results from replication of gene-based interaction analyses performed in eMERGE and the NEIGHBOR consortium data. Using expression data and annotations from various publicly available databases, the most significant genes that replicated in our analyses show expression in the eye and trabecular meshwork. Analysis for estimation of genetic variance explained by significant associations from previous GWAS and replicated variants from gene-based interactions suggest that these explain 5.6% of variance in eMERGE dataset and also explain 3.4% variance in NEIGHBOR dataset.

Associations of vitamin D deficiency and vitamin D receptor (Cdx-2, Fok I, Bsm I and Taq I) polymorphisms with the risk of primary open-angle glaucoma

BACKGROUND

Vitamin D deficiency and vitamin D receptor gene polymorphisms are known to be significantly associated with high myopia. Whether this genetic variant may impact primary open-angle glaucoma is largely unknown. This study investigated whether vitamin D receptor gene polymorphisms are altered in primary open-angle glaucoma subjects carrying the risk allele, and whether vitamin D deficiency is an important factor in the development of glaucoma.

METHODS

Seventy-three POAG patients and 71 age-matched controls from the Han population were enrolled. Serum levels of 1a, 25-Dihydroxyvitamin D3 were measured by enzyme-linked immunoabsorbent assay. Vitamin D receptor polymorphisms (Cdx-2, Fok I, Bsm I and Taq I) were analyzed using real-time polymerase-chain reaction high resolution melting analysis.

RESULTS

Serum levels of 1a, 25-Dihydroxyvitamin in primary open-angle glaucoma patients were lower than in age-matched controls. Statistical analysis revealed a significant difference in the allelic frequencies of the BsmI and TaqI genotypes between primary open-angle glaucoma patients and age-matched controls, while other polymorphisms did not show any significant differences.

CONCLUSIONS

Vitamin D deficiency and the presence of the BsmI 'B' allele and the TaqI 't' allele are relevant risk factors in the development of glaucoma.

TRIAL REGISTRATION

Clinical Trials.gov: NCT02539745 . The study was registered retrospectively on August 3rd, 2015. The first participant was enrolled on July 4th, 2013.

Mice Homozygous for a Deletion in the Glaucoma Susceptibility Locus INK4 Show Increased Vulnerability of Retinal Ganglion Cells to Elevated Intraocular Pressure

A genomic region located on chromosome 9p21 is associated with primary open-angle glaucoma and normal tension glaucoma in genome-wide association studies. The genomic region contains the gene for a long noncoding RNA called CDKN2B-AS, two genes that code for cyclin-dependent kinase inhibitors 2A and 2B (CDKN2A/p16(INK4A) and CDKN2B/p15(INK4B)) and an additional protein (p14(ARF)). We used a transgenic mouse model in which 70 kb of murine chromosome 4, syntenic to human chromosome 9p21, are deleted to study whether this deletion leads to a discernible phenotype in ocular structures implicated in glaucoma. Homozygous mice of this strain were previously reported to show persistent hyperplastic primary vitreous. Fundus photography and optical coherence tomography confirmed that finding but showed no abnormalities for heterozygous mice. Optokinetic response, eletroretinogram, and histology indicated that the heterozygous and mutant retinas were normal functionally and morphologically, whereas glial cells were activated in the retina and optic nerve head of mutant eyes. In quantitative PCR, CDKN2B expression was reduced by approximately 50% in the heterozygous mice and by 90% in the homozygous mice, which suggested that the CDKN2B knock down had no deleterious consequences for the retina under normal conditions. However, compared with wild-type and heterozygous animals, the homozygous mice are more vulnerable to retinal ganglion cell loss in response to elevated intraocular pressure.

SLC1A1 Gene Variants and Normal Tension Glaucoma: An Association Study

BACKGROUND

It has been hypothesized that dysfunction of the solute carrier family 1, member1 gene (SLC1A1), which encodes the glutamate aspartate transporter, may play a role in normal tension glaucoma. In this study we investigate whether SLC1A1 is associated with normal tension glaucoma in Japanese patients.

METHODS

A total of 292 Japanese patients with normal tension glaucoma and 500 healthy control subjects were recruited. We genotyped 12 single-nucleotide polymorphisms in SLC1A1. We also performed an imputation analysis to evaluate the potential association of un-genotyped SLC1A1 single-nucleotide polymorphisms, and 165 single-nucleotide polymorphisms were imputed.

RESULTS

We observed an increased frequency of the G allele of rs10739062 in patients compared to controls (p = 0.043, OR = 1.25). The rs10739062 polymorphism exhibited a dominant effect: individuals with genotype GG and GC showed a 1.91-fold increase in risk compared to genotype CC (p = 0.0082). However, the statistical significance disappeared after Bonferroni correction for multiple testing (pc > 0.05). We did not find any significant association between any of the remaining 176 single-nucleotide polymorphisms and disease risk.

CONCLUSIONS

Our study showed a lack of association between SLC1A1 variants and normal tension glaucoma in Japanese patients, suggesting that the SLC1A1 gene does not play a critical role in the development of the disorder in this patient population. However, further genetic studies with larger sample sizes are needed to clarify whether SLC1A1 may make some contribution that affects the risk of developing normal tension glaucoma.

The primary open-angle african american glaucoma genetics study: baseline demographics

PURPOSE

To describe the baseline characteristics of the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study cohort, the largest African American population with primary open-angle glaucoma (POAG) recruited at a single institution (University of Pennsylvania [UPenn], Department of Ophthalmology, Scheie Eye Institute) to date.

DESIGN

Population-based, cross-sectional, case-control study.

PARTICIPANTS

A total of 2520 African American subjects aged 35 years or more who were recruited from the greater Philadelphia, Pennsylvania area.

METHODS

Each subject underwent a detailed interview and eye examination. The interview assessed demographic, behavioral, medical, and ocular risk factors. Current ZIP codes surrounding UPenn were recorded and US census data were queried to infer socioeconomic status. The eye examination included measurement of visual acuity (VA) and intraocular pressure, and a detailed anterior and posterior segment examination, including gonioscopy, dilated fundus and optic disc examination, visual fields, stereo disc photography, optical coherence tomography, and measurement of central corneal thickness.

MAIN OUTCOME MEASURES

The baseline characteristics of gender, age, and glaucoma diagnosis were collected. Body mass index (BMI), hypertension, diabetes, alcohol and tobacco use, ocular conditions (including blindness, cataract, nonproliferative diabetic retinopathy, and age-related macular degeneration), and use of ocular medication and surgery were examined. Median population density, income, education level, and other socioeconomic measures were determined for the study cohort.

RESULTS

Of the 2520 African Americans recruited to the POAAGG study to date, 2067 (82.0%), including 807 controls and 1260 POAG cases, met all inclusion criteria and completed the detailed clinical ocular examination. Cases were more likely to have a lower BMI (P < 0.01) and report a history of blindness (VA of ≤20/200; P < 0.001), whereas controls were more likely to have diabetes (P < 0.001), have nonproliferative diabetic retinopathy (P = 0.02), and be female (P < 0.001). Study participants were drawn largely from predominantly African American neighborhoods of low income, high unemployment, and lower education surrounding UPenn.

CONCLUSIONS

The POAAGG study has currently recruited more than 2000 African Americans eligible for a POAG genetics study. Blindness and low BMI were significantly associated with POAG. This population was predominantly recruited from neighborhoods whose population income exists at or near the federal poverty level.

Discovery and functional annotation of SIX6 variants in primary open-angle glaucoma

Glaucoma is a leading cause of blindness worldwide. Primary open-angle glaucoma (POAG) is the most common subtype and is a complex trait with multigenic inheritance. Genome-wide association studies have previously identified a significant association between POAG and the SIX6 locus (rs10483727, odds ratio (OR) = 1.32, p = 3.87×10⁻¹¹). SIX6 plays a role in ocular development and has been associated with the morphology of the optic nerve. We sequenced the SIX6 coding and regulatory regions in 262 POAG cases and 256 controls and identified six nonsynonymous coding variants, including five rare and one common variant, Asn141His (rs33912345), which was associated significantly with POAG (OR = 1.27, p = 4.2×10⁻¹⁰) in the NEIGHBOR/GLAUGEN datasets. These variants were tested in an in vivo Danio rerio (zebrafish) complementation assay to evaluate ocular metrics such as eye size and optic nerve structure. Five variants, found primarily in POAG cases, were hypomorphic or null, while the sixth variant, found only in controls, was benign. One variant in the SIX6 enhancer increased expression of SIX6 and disrupted its regulation. Finally, to our knowledge for the first time, we have identified a clinical feature in POAG patients that appears to be dependent upon SIX6 genotype: patients who are homozygous for the SIX6 risk allele (His141) have a statistically thinner retinal nerve fiber layer than patients homozygous for the SIX6 non-risk allele (Asn141). Our results, in combination with previous SIX6 work, lead us to hypothesize that SIX6 risk variants disrupt the development of the neural retina, leading to a reduced number of retinal ganglion cells, thereby increasing the risk of glaucoma-associated vision loss.

Primary open angle glaucoma is a blinding disease for which there is currently no cure, only treatments that may slow its progress. To help understand the mechanisms of this disease and to design more effective treatments, we identified previously a locus, SIX6, that increases the risk of glaucoma. This gene is involved in early eye development and helps to form the retina. In this paper, we test specific sequence variants in SIX6 that are found in glaucoma patients. We show that these variants have a reduced function that interferes with their ability to direct proper formation of the retina. One variant in particular is common, and may be the main reason that this gene is important in the glaucoma disease process. Patients who have two copies of this sequence variant show a change in the structure of their eye consistent with fewer neurons that carry the visual signal to the brain. These neurons typically die as people age, and people who begin life with fewer visual neurons may have an increased risk of glaucoma. Additional research in this topic may lead to new treatments that preserve sight.

Corneal biomechanical properties and glaucoma-related quantitative traits in the EPIC-Norfolk Eye Study

PURPOSE

We examined the association of corneal hysteresis (CH) with Heidelberg retina tomograph (HRT)- and Glaucoma Detection with Variable Corneal Compensation scanning laser polarimeter (GDxVCC)-derived measures in a British population.

METHODS

The EPIC-Norfolk Eye Study is nested within a multicenter cohort study--the European Prospective Investigation of Cancer. Ocular response analyzer (ORA), HRT3, and GDxVCC measurements were taken at the research clinic. Three ORA measurements were taken per eye, and the single best value used. Participants meeting predefined criteria were referred for a second examination, including Goldmann applanation tonometry (GAT) and central corneal thickness (CCT) measurement. Generalized estimating equation models were used to examine the associations of CH with HRT and GDxVCC parameters, adjusted for disc area. The GDxVCC analyses were adjusted further for typical scan score to handle atypical retardation.

RESULTS

There were complete research clinic data from 5134 participants. Corneal hysteresis was associated positively with HRT rim area (P < 0.001), and GDxVCC retinal nerve fiber layer (RNFL) average thickness (P = 0.006) and modulation (P = 0.003), and associated negatively with HRT linear cup-to-disc ratio (LCDR, P < 0.001), after adjustment for Goldmann-correlated IOP and other possible confounders. In the 602 participants undergoing the second examination, CH was associated negatively with LCDR (P = 0.008) after adjustment for GAT, CCT, and other possible confounders.

CONCLUSIONS

Lower CH was associated with HRT and GDxVCC parameters in a direction that is seen in glaucoma and with ageing. Further research is required to establish if this is a causal relationship, or due to residual confounding by age, IOP, or CCT.

Laser scanning tomography in the EPIC-Norfolk Eye Study: principal components and associations

PURPOSE

To describe Heidelberg Retina Tomograph (HRT) measures, their principal components, and their associations in a British population.

METHODS

The European Prospective Investigation of Cancer (EPIC)-Norfolk Eye Study is nested within a multicenter cohort study. Measurements were taken with the HRT-2 and the software subsequently updated to yield HRT-3 parameters. Principal components analysis (PCA) was used to identify distinct components of the HRT variables. Generalized estimating equation models were used to examine associations of these components with age, sex, height, body mass index (BMI), blood pressure, social class, education, alcohol intake, smoking status, axial length, IOP, and lens status.

RESULTS

Complete data were available from 10,859 eyes of 6430 participants with a mean age of 68 years. Principal components analysis identified three components with an eigenvalue greater than 1, explaining 79.9% of the variance of all the HRT measures. These were named cup, retinal nerve fiber layer (RNFL), and rim based on the factor loadings they were most correlated with. Older age was significantly associated with a greater cup (P = 0.003), smaller RNFL (P < 0.001), and smaller rim (P < 0.001). Female sex (P = 0.001), higher education (P < 0.001), and shorter axial length (P < 0.001) were associated with a greater RNFL. Lower BMI and higher IOP were associated with a greater cup (both, P < 0.001) and a smaller rim (BMI, P = 0.001; IOP, P < 0.001).

CONCLUSIONS

Heidelberg Retina Tomograph measures in this cohort were largely explained by three principal components related to optic disc cup, RNFL, and rim. Associations with cup and rim were distinct to associations with RNFL, suggesting different underlying determinants.

Lack of association of apolipoprotein E (Apo E) ε2/ε3/ε4 polymorphisms with primary open-angle glaucoma: a meta-analysis from 1916 cases and 1756 controls

Background

A number of case-control studies were conducted to investigate the association of apolipoprotein E (Apo E) polymorphisms with primary open angle glaucoma (POAG). But the results remain controversial. This meta-analysis aims to comprehensively evaluate the relationship between a common ε2/ε3/ε4 polymorphism in Apo E gene on the risk of POAG.

Method

A comprehensive literature search for studies published up to April 2013 was performed. Summary odds ratios (ORs) and 95% confidence intervals (CI) were calculated employing random-effects models irrespective of between-study heterogeneity. Publication bias of literatures was evaluated using funnel plots and Egger's test.

Results

A total of 12 studies including 1916 cases and 1756 controls meeting the predefined criteria were involved in this meta-analysis. Overall, the Apo E ε2 allele and ε4 allele were not associated with POAG, compared with those carrying ε3 allele, with ORs of 0.98 (95% CI, 0.79 to 1.23; P = 0.872) and 1.05 (95% CI, 0.78 to 1.41; P = 0.743), respectively. Genotypic analysis also found no significant association between the ε4 carriers (ε3/ε4+ε4/ε4), ε2 carriers (ε2/ε3+ε2/ε2) and POAG, compared with participants with Apo E ε3/3, with ORs of 0.91 (95% CI, 0.66 to 1.25; P = 0.543) and 1.08 (95% CI, 0.74 to 1.57; P = 0.694), respectively. In the subgroup analysis by ethnicity, source of controls, genotyping methods, Hardy-Weinberg equilibrium or not, or type of the POAG, still no obvious associations were found.

Conclusions

This meta-analysis suggests that Apo E ε2/ε3/ε4 polymorphisms may not be associated with the risk of POAG. However, well-designed studies with larger sample size and more ethnic groups are required to further validate the results.

Associations with retinal nerve fiber layer measures in the EPIC-Norfolk Eye Study

PURPOSE

To describe GDxVCC retinal nerve fiber layer (RNFL) measures and associations in a predominantly white British population.

METHODS

The EPIC-Norfolk Eye Study is nested within a large multicenter cohort study, the European Prospective Investigation of Cancer. RNFL measurements were taken using the GDxVCC. Generalized estimating equation models were used to assess associations of RNFL measures with age, sex, body mass index (BMI), height, blood pressure, social class, education level, alcohol intake, smoking status, axial length, intraocular pressure, and lens status. Models were linearly adjusted for typical scan score to handle scans with atypical retardation.

RESULTS

There were complete data from 11,030 eyes of 6309 participants with mean age 68 years (48-90 years). Older age (-1.53 μm/decade [95% confidence interval {CI} -1.73, -1.33], P < 0.001), male sex (-0.44 μm [95% CI -0.04, -0.84], P = 0.031), shorter axial length (-0.15 μm/mm [95% CI -0.02, -0.28], P = 0.024), and pseudophakia (-0.49 μm [95% CI -0.94, -0.04], P = 0.033) were associated with thinner RNFL after adjustment for possible confounders. Higher BMI was associated with a thinner RNFL in men only (-0.30 μm/5 kg/m(2) [95% CI -0.58, -0.02], P = 0.039).

CONCLUSIONS

This analysis of associations with RNFL thickness in a largely healthy population may provide insight into the determinants of glaucoma, suggesting higher risk in those who are older, in men, and in men with a higher BMI.

The potential of stem cell research for the treatment of neuronal damage in glaucoma

Stem cell research offers a wide variety of approaches for the advancement of our understanding of basic mechanisms of neurodegeneration and tissue regeneration and for the discovery and development of new therapeutic strategies to prevent and restore neuronal cell loss. Similar to most other regions of our central nervous system, degenerative diseases of the retina lead to the loss of neurons, which are not replaced. Recent work in animals has provided proof-of-concept evidence for the restoration of photoreceptor cells by cell transplantation and neuronal cell replacement by regeneration from endogenous cell sources. However, efficient therapeutic prevention of neuronal cell loss has not been achieved. Moreover, successful cell replacement of retinal neurons in humans, including that of ganglion cells, remains a major challenge. Future successes in the discovery and translation of neuroprotective drug and gene therapies and of cell-based regenerative therapies will depend on a better understanding of the underlying disease pathomechanisms. Existing stem cell and cell-reprogramming technologies offer the potential to generate human retina cells, to develop specific human-cell-based retina disease models, and to open up novel therapeutic strategies. Further, we might glean substantial knowledge from species that can or cannot regenerate their neuronal retina, in the search for new therapeutic approaches. Thus, stem cell research will pave the way toward clinical translation. In this review, I address some of the major possibilities presently on offer and speculate about the power of stem cell research to gain further insights into the pathomechanisms of retinal neurodegeneration (with special emphasis on glaucoma) and to advance our therapeutic options.

Epidemiology of glaucoma in sub-saharan Africa: prevalence, incidence and risk factors

PURPOSE

The purpose of this study is to review the epidemiology of different types of glaucoma relevant to Sub-Saharan Africa (SSA) and to discuss the evidence regarding the risk factors for onset and progression of glaucoma, including risk factors for glaucoma blindness.

METHODS

Electronic databases (PubMed, MedLine, African Journals Online- AJOL) were searched using the full text, Medical Subject Headings (MeSH) terms, author(s) and title to identify publications since 1982 in the following areas: population-based glaucoma prevalence and incidence studies in SSA and in African-derived black populations outside Africa; population-based prevalence and incidence of blindness and visual impairment studies in SSA including rapid assessment methods, which elucidate the glaucoma-specific blindness prevalence; studies of risk factors for glaucoma; and publications that discussed public health approaches for the control of glaucoma in Africa.

RESULTS

Studies highlighted that glaucoma in SSA is a public health problem and predominantly open-angle glaucoma. It is the second-leading cause of blindness, has a high prevalence, an early onset and progresses more rapidly than in Caucasians. These factors are further compounded by poor awareness and low knowledge about glaucoma even by persons affected by the condition.

CONCLUSION

Glaucoma care needs to be given high priority in Vision 2020 programs in Africa. Many questions remain unanswered and there is a need for further research in glaucoma in SSA in all aspects especially epidemiology and clinical care and outcomes involving randomized controlled trials. Genetic and genome-wide association studies may aid identification of high-risk groups. Social sciences and qualitative studies, health economics and health systems research will also enhance public health approaches for the prevention of blindness due to glaucoma.

Soluble guanylate cyclase α1-deficient mice: a novel murine model for primary open angle glaucoma

Primary open angle glaucoma (POAG) is a leading cause of blindness worldwide. The molecular signaling involved in the pathogenesis of POAG remains unknown. Here, we report that mice lacking the α1 subunit of the nitric oxide receptor soluble guanylate cyclase represent a novel and translatable animal model of POAG, characterized by thinning of the retinal nerve fiber layer and loss of optic nerve axons in the context of an open iridocorneal angle. The optic neuropathy associated with soluble guanylate cyclase α1-deficiency was accompanied by modestly increased intraocular pressure and retinal vascular dysfunction. Moreover, data from a candidate gene association study suggests that a variant in the locus containing the genes encoding for the α1 and β1 subunits of soluble guanylate cyclase is associated with POAG in patients presenting with initial paracentral vision loss, a disease subtype thought to be associated with vascular dysregulation. These findings provide new insights into the pathogenesis and genetics of POAG and suggest new therapeutic strategies for POAG.