DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity

Minimal phenotypes in transgenic mice with the human LOXL1/LOXL1-AS1 locus associated with exfoliation glaucoma

Exfoliation syndrome is a leading cause of secondary glaucoma worldwide. Among the risk-factors for exfoliation syndrome and exfoliation glaucoma that have been investigated, a genetic association with 15q24.1 is among the most striking. The leading candidates for the causal gene at this locus are LOXL1 and/or LOXL1-AS1, but studies have not yet coalesced in establishing, or ruling out, either candidate. Here, we contribute to studies of the 15q24.1 locus by making a partially humanized mouse model in which 166 kb of human genomic DNA from the 15q24.1 locus was introduced into the mouse genome via BAC transgenesis (B6-Tg(RP11-71M11)Andm). Transgenic expression of human genes in the BAC was only detectable for LOXL1-AS1. One cohort of 34 mice (21 experimental hemizygotes and 13 non-carrier control littermates) was assessed by slit-lamp exams and SD-OCT imaging at early (1-2 months) and mid (4-5 months) time points; fundus exams were performed at 5 months of age. A second smaller cohort (3 hemizygotes) were aged extensively (>12 months) to screen for overt abnormalities. Across all genotypes and ages, 136 slit-lamp exams, 128 SD-OCT exams, and 42 fundus exams detected no overt indices of exfoliation syndrome. Quantitatively, small, but statistically significant, age-related declines in ganglion cell complex thickness and total retinal thickness were detected in the hemizygotes at 4 months of age. Overall, this study demonstrates complexity in gene regulation from the 15q24.1 locus and suggests that LOXL1-AS1 is unlikely to be a monogenic cause of exfoliation syndrome but may contribute to glaucomatous retinal damage.

Rodent genetically modified models of glaucoma

Glaucoma, one of the leading causes of irreversible blindness worldwide, is a complex and heterogenous disease. While environmental factors are important, it is well-recognized that the disease has a strong heritable component. With the advent of large-cohort genome wide association studies, a myriad of genetic risk loci has been linked to different forms of glaucoma. Animal models have been an indispensable tool in characterizing these loci, especially if they lie within coding regions in the genome. Not only do these models connect genotype to phenotype, advancing our understanding of glaucoma pathogenesis in the process, they also have valuable utility as a platform for the pre-clinical testing of potential therapies. In this review, we will outline genetic models used for studying the major forms of glaucoma, including primary open angle glaucoma, normal tension glaucoma, primary angle closure glaucoma, pigmentary glaucoma, pseudoexfoliation glaucoma, and early onset glaucoma, including congenital and developmental glaucoma, and how studying these models have helped shed light on human glaucoma.

Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis

The phenotypic similarities between exfoliation syndrome (XFS)/exfoliation glaucoma (XFG) and pigment dispersion syndrome (PDS)/pigmentary glaucoma (PG), particularly their association with material deposition in the eye's anterior segment, have prompted investigations into genetic commonalities. This study focuses on the LOXL1 gene, conducting a comprehensive meta-analysis of three candidate gene association studies. We analyzed three single nucleotide polymorphisms (SNPs) of LOXL1: rs1048661, rs3825942, and rs2165241. Our results reveal nominal significance for the exonic SNPs rs1048661 and rs3825942 (p ≤ 0.01), but show no significant association for the intronic SNP rs2165241 (p = 0.83) with PDS/PG. There was homogeneity across study cohorts (I2 = 0), and sensitivity analyses and funnel plots confirmed a lower likelihood of bias in our findings. The lack of a statistically significant association between LOXL1 variants and PDS/PG at p < 0.05 was attributable to the insufficient statistical power of the pooled data, which ranged from 5% to 37% for the three SNPs. This study suggests no association between LOXL1 variants and PDS/PG. Further validation and exploration of XFS/XFG-associated genes in larger and more diverse cohorts would be helpful to determine the genetic correlation or distinctiveness between these conditions.

Current understanding of genetics and epigenetics in pseudoexfoliation syndrome and glaucoma

Pseudoexfoliation is a complex, progressive, and systemic age-related disorder. The early stage of deposition of extracellular fibrillar material on ocular and extraocular tissues is termed as pseudoexfoliation syndrome (PEXS). The severe advanced stage is known as pseudoexfoliation glaucoma (PEXG), which involves increased intraocular pressure and optic nerve damage. Through genome-wide association and candidate gene studies, PEX has been associated with numerous genetic risk variants in various gene loci. However, the genetic basis of the disease fails to explain certain features of PEX pathology, such as the progressive nature of the disease, asymmetric ocular manifestation, age-related onset, and only a subset of PEXS individuals developing PEXG. Increasing evidence shows an interplay of genetic and epigenetic factors in the pathology of complex, multifactorial diseases. In this review, we have discussed the genetic basis of the disease and the emerging contribution of epigenetic regulations in PEX pathogenesis, focusing on DNA methylation and non-coding RNAs. Aberrant methylation patterns, histone modifications, and post-transcriptional regulation by microRNAs lead to aberrant gene expression changes. We have reviewed these aberrant epigenetic changes in PEX pathology and their effect on molecular pathways associated with PEX. We have further discussed some possible genetic/epigenetic-based diagnoses and therapeutics for PEX. Although studies to understand the role of epigenetic regulations in PEX are just emerging, epigenetic modifications contribute significantly to PEX pathogenesis and may pave the way for better and targeted therapeutics.

MicroRNA profiles in aqueous humor between pseudoexfoliation glaucoma and normal tension glaucoma patients in a Korean population

We aimed to obtain microRNA (miRNA) profiles of patients with pseudoexfoliation (PEX) glaucoma or normal-tension glaucoma (NTG) compared to normal controls using individual aqueous humor (AH) samples and investigate the role of miRNAs in the pathogenesis of PEX glaucoma compared to NTG in Korean. AH (80-120 µl) was collected before cataract surgery or trabeculectomy from 26 Korean subjects (eleven with PEX glaucoma, age-matched eight NTG, and seven controls). RNA sequencing was conducted for RNA samples extracted from 26 AH samples. Bioinformatics analysis was performed for targets and related pathways. A total of 334 and 291 discrete miRNAs were detected in AH samples of PEX glaucoma and NTG patients, respectively. Two significantly upregulated miRNAs (hsa-miR-30d-5p and hsa-miR-320a) and ten significantly downregulated miRNAs (hsa-miR-3156-5p, hsa-miR-4458, hsa-miR-6717-5p, hsa-miR-6728-5p, hsa-miR-6834-5p, hsa-miR-6864-5p, hsa-miR-6879-5p, hsa-miR-877-3p, hsa-miR-548e-3p, and hsa-miR-6777-5p) in PEX glaucoma patients compared to control (fold-change > 2, p < 0.05) were found. In NTG patients, ten significantly upregulated and two downregulated miRNAs compared to control were found. Only hsa-miR-6777-5p was commonly downregulated in both PEX glaucoma and NTG patients. Related pathways were proteoglycans in cancer, glioma, and TGF-beta signaling pathway in PEX glaucoma. These differentially expressed miRNAs between PEX glaucoma and NTG samples suggest the possible role of miRNA in the pathogenesis of glaucoma, further implying that pathogenic mechanisms may differ between different types of glaucoma.

LOXL1 gene polymorphisms are associated with exfoliation syndrome/exfoliation glaucoma risk: An updated meta-analysis

BACKGROUND

Single nucleotide polymorphisms (SNPs) in the gene encoding LOXL1 are risk factors for exfoliation syndrome and exfoliation glaucoma. This meta-analysis comprehensively investigated the association between LOXL1 gene polymorphisms (rs1048661, rs3825942, and rs2165241) and the risk of exfoliation syndrome/exfoliation glaucoma (XFS)/(XFG).

METHODS

All eligible case-control studies, published before August 17, 2020, were searched on Medline (Ovid), PubMed, CNKI, EMBASE, and Wanfang databases.

RESULTS

In total, 5022 cases and 8962 controls were included in this meta-analysis. Significant associations between LOXL1 gene polymorphisms and XFS/XFG risk was observed in the disease types-based subgroups. In addition, in the subgroup analysis of ethnicity, positive associations between LOXL1 gene polymorphisms (rs1048661, rs3825942, and rs2165241) and XFS/XFG risk were found in Caucasians. Furthermore, rs1048661 and rs3825942 polymorphisms were related to XFS/ XFG risk in Asians; however, no significant association was observed between the LOXL1 gene rs2165241 polymorphism and XFS/XFG risk in Asians. In addition, rs1048661 and rs3825942 correlated with XFS/XFG susceptibility in Africans.

CONCLUSIONS

Our results implicate LOXL1 gene polymorphisms as XFS/XFG risk factors, especially in Caucasians.

Differential Lysyl oxidase like 1 expression in pseudoexfoliation glaucoma is orchestrated via DNA methylation

Pseudoexfoliation syndrome (PXF) is the most common cause of secondary open angle glaucoma worldwide. Single nucleotide polymorphisms (SNPs) in the gene Lysyl oxidase like 1 (LOXL1) are strongly associated with the development of pseudoexfoliation glaucoma (PXFG). However, these SNPs are also present in 50-80% of the general population, suggestive of other factors being involved in the pathogenesis of PXFG. In this study, we aimed to investigate the influence of epigenetic regulation, specifically DNA methylation, on LOXL1 expression in PXFG using human tenons fibroblasts (HTFs), aqueous humour and serum samples from donors with and without PXFG. LOXL1 expression in HTFs was measured by qPCR and Western Blotting and LOXL1 concentration in aqueous humour was determined by ELISA. Global DNA methylation levels were quantified using an ELISA for 5-methylcytosine. MeDIP assays assessed the methylation status of the LOXL1 promoter region. Expression of methylation-associated enzymes (DNMT1, DNMT3a and MeCP2) were determined by qPCR and inhibited by 0.3 μM 5-azacytidine (5-aza). Results showed that LOXL1 expression was significantly decreased in PXFG HTFs compared with Control HTFs at gene (Fold change 0.37 ± 0.05, P < 0.01) level and showed a decrease, when measured at the protein level (Fold change 0.65 ± 0.42, P = 0.22), however this was not found to be significant. LOXL1 concentration was increased in the aqueous of PXFG patients compared with Controls (2.76 ± 0.78 vs. 1.79 ± 0.33 ng/ml, P < 0.01). Increased global methylation (56.07% ± 4.87% vs. 32.39% ± 4.29%, P < 0.01) was observed in PXFG HTFs compared with Control HTFs, as was expression of methylation-associated enzymes (DNMT1 1.58 ± 0.30, P < 0.05, DNMT3a 1.89 ± 0.24, P < 0.05, MeCP2 1.63 ± 0.30, P < 0.01). Methylation-associated enzymes were also increased when measured at protein level (DNMT1 5.70 ± 2.64, P = 0.04, DNMT3a 1.79 ± 1.55, P = 0.42, MeCP2 1.64 ± 1.33, P = 0.45). LOXL1 promoter methylation was increased in patients with PXFG compared to Control patients in both blood (3.98 ± 2.24, 2.10 ± 1.29, P < 0.05) and HTF cells (37.31 ± 22.0, 8.66 ± 10.40, P < 0.01). Treatment of PXFG HTFs with in 5-azacytidine increased LOXL1 expression when compared with untreated PXFG HTFs (Fold change 2.26 ± 0.67, P < 0.05). These data demonstrate that LOXL1 expression is altered in PXFG via DNA methylation and that reversal of these epigenetic changes may represent future potential therapeutic targets in the management of PXFG.

Lysyl Oxidase Like 1: Biological roles and regulation

Lysyl Oxidase Like 1 (LOXL1) is a gene that encodes for the LOXL1 enzyme. This enzyme is required for elastin biogenesis and collagen cross-linking, polymerising tropoelastin monomers into elastin polymers. Its main role is in elastin homeostasis and matrix remodelling during injury, fibrosis and cancer development. Because of its vast range of biological functions, abnormalities in LOXL1 underlie many disease processes. Decreased LOXL1 expression is observed in disorders of elastin such as Cutis Laxa and increased expression is reported in fibrotic disease such as Idiopathic Pulmonary Fibrosis. LOXL1 is also downregulated in the lamina cribrosa in pseudoexfoliation glaucoma and genetic variants in the LOXL1 gene have been linked with an increased risk of developing pseudoexfoliation glaucoma and pseudoexfoliation syndrome. However the two major risk alleles are reversed in certain ethnic groups and are present in a large proportion of the normal population, implying complex genetic and environmental regulation is involved in disease pathogenesis. It also appears that the non-coding variants in intron 1 of LOXL1 may be involved in the regulation of LOXL1 expression. Gene alteration may occur via a number of epigenetic and post translational mechanisms such as DNA methylation, long non-coding RNAs and microRNAs. These may represent future therapeutic targets for disease. Environmental factors such as hypoxia, oxidative stress and ultraviolet radiation exposure alter LOXL1 expression, and it is likely a combination of these genetic and environmental factors that influence disease development and progression. In this review, we discuss LOXL1 properties, biological roles and regulation in detail with a focus on pseudoexfoliation syndrome and glaucoma.

LOXL1 folding in exfoliation glaucoma

Exfoliation syndrome (XFS) is an age-related disease defined by the deposition of aggregated fibrous material (XFM) in the peri-cellular space. Principal morbidity occurs in the eye, where XFM accumulates on the anterior ocular tissues. GWAS have found that certain genetic variants of lysyl oxidase-like 1 (LOXL1), a matrix cross-linking enzyme that is required for elastic fiber formation confer risk for the development of XFS, but are not a single causative factor as many genetically affected individuals do not develop XFS or subsequent glaucoma (XFG). We have found that XFG cells display defects in lysosomes, microtubules, autophagy, and mitochondria resembling defects found in cells from age-related syndromes, such as the main neurodegenerative diseases. In the majority of these diseases, the determining cellular factor is a protein containing intrinsically disordered regions (IDRs) and displaying a high propensity for aggregation. We have found that in XFG patient-derived cells, LOXL1 protein is actively subjected to autophagic clearance, suggesting that LOXL1 is undergoing aggregation. In silico analysis demonstrates that LOXL1's first 369 aa constitute an IDR with the highest disorder probability peak centering around the known risk positions. Experimentally, we have found over-expression of either unmodified LOXL1 or fluorescent chimeras preserving the well-structured N-terminus cause copious intracellular aggregation and that aggregation wanes when the high IDR peaks are deleted. Overall, our work suggests that XFS/G results from the aggregation of the LOXL1 protein coupled with a reduction of cellular proteostasis capabilities in aging, resulting in a chronic build-up of LOXL1-containing protein aggregates.

CLU Polymorphisms in Patients with Pseudoexfoliation Syndrome in Polish Population

Purpose

To evaluate CLU polymorphisms in patients with pseudoexfoliation syndrome.

Materials and Methods

We studied 81 patients (23 males and 58 females, the median age 76 years) and 91 control subjects (27 males and 64 females, the median age 75 years). Genotypes of the CLU polymorphisms (SNPs), rs3087554 and rs2279590, were determined using a commercially available validated genotyping assays. The χ ² test was performed to compare patient and control groups for possible associations between SNP genotype/allele frequency and disease state.

Results

There were no significant differences for both allele and genotype frequencies between PEX patients and controls for rs3087554 and rs2279590 polymorphisms. The haplotypes distribution shows statistically significant difference between groups (p=0.03). The haplotype (CT) more often was found in controls than in PEX patients, conferring an 18-fold decreased risk to the disease.

Conclusion

Our results indicate that CLU variants may contribute to the risk of PEX in the Polish population.

Three Single Nucleotide Polymorphisms of LOXL1' in a Turkish Population with Pseudoexfoliation Syndrome and Pseudoexfoliation Glaucoma

Objectives:

To investigate the three single nucleotide polymorphisms (SNPs) (rs3825942, rs1048661, and rs2165241) of the LOXL1 gene in pseudoexfoliation syndrome (XFS) and pseudoexfoliation glucoma (XFG) in the Turkish population.

Materials and Methods:

DNA was obtained from blood samples of 48 XFS, 58 XFG, and 171 control subjects. Three LOXL1 SNPs (rs3825942, rs1048661, rs2165241) were investigated with real time PCR, a probe-based genotyping method, and melting curve analysis.

Results:

All three SNPs of LOXL1 were significantly associated with XFS (rs3825942 p=3.54x10^-6, odds ratio [OR]=∞; rs1048661 p=0.008, OR=2.18; rs2165241 p=8.69x10^-9, OR=4.30) and XFG (rs3825942 p=3.41x10^-7, OR=∞; rs1048661 p=1.75x10^-5, OR=3.78; rs2165241 p=3.85x10^-11 OR=4.90). No significant differences were observed between the XFS and XFG groups for any of the SNPs. The GG genotype of rs3825942 was more valuable for distinguishing pseudoexfoliative cases from healthy individuals. The homozygous TT genotype of rs2165241 was associated with 6-fold increased XFS risk (p=8.15x10^-8, OR=6.32) and 7-fold increased XFG risk (p=1.45x10^-10 OR=7.95). The GGT haplotype consisting of all three risk alleles was associated with a 7.45-fold higher risk of XFS/XFG (p=8.65x10^-14, OR=7.45). Presence of T allele of rs2165241 conferred 3 times higher risk for men than women (p=6.78x10^-5, OR=3.202).

Conclusion:

LOXL1 SNPs are associated with increased risk for pseudoexfoliation in the Turkish population. T allele of rs2165241 was found to be the most important characterized risk factor for our cohort. All SNP distributions were similar to other European and American populations.

A Role for Clusterin in Exfoliation Syndrome and Exfoliation Glaucoma?

The multifunctional protein clusterin (CLU) is a secreted glycoprotein ubiquitously expressed throughout the body, including in the eye. Its primary function is to act as an extracellular molecular chaperone, preventing the precipitation and aggregation of misfolded extracellular proteins. Clusterin is commonly identified at fluid-tissue interfaces, and has been identified in most body fluids. It is a component of exfoliation material, and CLU mRNA is reduced in eyes with exfoliation syndrome compared with controls. SNPs located in the CLU genomic region have been associated with Alzheimer disease (AD) at the genome-wide level and several CLU SNPs located in an apparent regulatory region have been nominally associated with XFS/XFG in Caucasians with European ancestry and in south Indians. Interestingly, clusterin associates with altered elastic fibers in human photoaged skin and prevents UV-induced elastin aggregation in vitro. In light of the known geographic risk factors for XFS/XFG, which could include UV light, investigations of CLU-geographic interactions could be of interest. Future studies investigating rare CLU variation and other complex interactions including gene-gene interactions in XFS/XFG cases and controls may also be fruitful. Although CLU has been considered as a therapeutic target in AD, cancer and dry eye, a role for clusterin in XFS/XFG needs to be better defined before therapeutic approaches involving CLU can be entertained.

Exfoliation Syndrome: A Disease of Autophagy and LOXL1 Proteopathy

Exfoliation syndrome (XFS) is an age-related disease involving the deposition of aggregated fibrillar material (exfoliation material) at extracellular matrices in tissues that synthesize elastic fibers. Its main morbidity is in the eye, where exfoliation material accumulations form on the surface of the ciliary body, iris, and lens. Exfoliation glaucoma (XFG) occurs in a high proportion of persons with XFS and can be a rapidly progressing disease. Worldwide, XFG accounts for about 25% of open-angle glaucoma cases. XFS and XFG show a sharp age-dependence, similarly to the many age-related diseases classified as aggregopathies. Progress in understanding the cellular bases for XFS/XFG has been slowed by a lack of experimental models. Working with primary human tenon fibroblasts (TF) derived from trabeculectomies of XFG patients and age-matched primary open-glaucoma controls, we found that TF from XFG cells display many of the functional features observed in cells from other protein aggregate diseases, such as Parkinson, Alzheimer, Huntington, and age-related macular degeneration. We have documented defects in lysosomal positioning, microtubule organization, autophagy processing rate, and mitochondrial health. In regard to failure of lysosomal and autophagosome positioning in XFG cells, we have found that XFG TF are unable to establish the transnuclear microtubule organizing center that is required for efficient centripetal vesicular locomotion along microtubules. In regard to potential sources of the autophagy malfunction, we have directed our attention to a potential role of the lysyl oxidase-like 1 protein (LOXL1), the elastic fiber catalyst that displays variant-dependent association with risk for XFG. Our experiments show that (a) in XFG cells, a substantial fraction of LOXL1 is processed for degradation by the autophagic system; (b) most of the LOXL1 N-terminus domain exists in a highly disordered state, a condition known to greatly increase the frequency of polypeptide misfolding; (c) that maximum misfolding occurs at amino acid position 153, the location of the high risk variant G153D; and (d) that replacement of glycine (G) by aspartate (D) there results in a substantial decrease in disorder within the 20 amino acid surrounding domain. Finally, we show that clusterin, a protein that can be induced by the presence of intracellular, or extracellular aggregates, is uniformly overexpressed in XFG TF. The implications of our results for a theory relating XFG to cellular aggregopathy are discussed.

Molecular Genetics of Pigment Dispersion Syndrome and Pigmentary Glaucoma: New Insights into Mechanisms

We explore the ideas and advances surrounding the genetic basis of pigment dispersion syndrome (PDS) and pigmentary glaucoma (PG). As PG is the leading cause of nontraumatic blindness in young adults and current tailored interventions have proven ineffective, a better understanding of the underlying causes of PDS, PG, and their relationship is essential. Despite PDS being a subclinical disease, a large proportion of patients progress to PG with associated vision loss. Decades of research have supported a genetic component both for PDS and conversion to PG. We review the body of evidence supporting a genetic basis in humans and animal models and reevaluate classical mechanisms of PDS/PG considering this new evidence.

Major review: Exfoliation syndrome; advances in disease genetics, molecular biology, and epidemiology

Exfoliation syndrome (XFS) is a common age-related disorder that leads to deposition of extracellular fibrillar material throughout the body. The most recognized disease manifestation is exfoliation glaucoma (XFG), which is a common cause of blindness worldwide. Recent developments in XFS genetics, cell biology and epidemiology have greatly improved our understanding of the etiology of this complex inherited disease. This review summarizes current knowledge of XFS pathogenesis, identifies gaps in knowledge, and discusses areas for future research.

LOXL1 Gene Polymorphism With Exfoliation Syndrome/Exfoliation Glaucoma: A Meta-Analysis

AIM

There were several studies that have researched the associations between lysyl oxidase-like 1 (LOXL1) gene polymorphism and the susceptibility to exfoliation syndrome (XFS)/exfoliation glaucoma (XFG), but results have been inconclusive.

MATERIALS AND METHODS

A meta-analysis was performed for deriving more exact estimation of the relationship. Twenty-five studies were selected for studying rs1048661 and rs3825942. Sixteen studies were selected for studying rs2165241.

RESULTS

Single nucleotide polymorphism (SNP) rs1048661 was found to be associated with XFS/XFG, but the risk allele in white populations was found to be G, as opposite to the T allele in Japanese, Chinese, and Korean populations. The SNP rs3825942 was significantly associated with XFS in this black South African population. However, the AA genotype of rs3825942 confers XFS risk in this population, as opposed to the GG genotype described in all other populations. SNP rs2165241 was found to be associated with XFS/XFG, but the risk allele in white populations was found to be T, as opposite to the "C" allele in Japanese and Korean populations.

CONCLUSIONS

Our meta-analysis indicates that rs1048661 ("G" alleles) had weak association with XFG/XFS; rs3825942 ("G" alleles) had strongly association with XFG/XFS; and rs2165241("T" alleles) had significant risk with XFG/XFS in some ethnicity.

Biological effect of LOXL1 coding variants associated with pseudoexfoliation syndrome

Pseudoexfoliation (PEX) syndrome is a systemic disease involving the extracellular matrix. It increases the risk of glaucoma, an irreversible cause of blindness, and susceptibility to heart disease, stroke and hearing loss. Single nucleotide polymorphisms (SNPs) in the LOXL1 (Lysyl oxidase-like 1) gene are the major known genetic risk factor for PEX syndrome. Two coding SNPs, rs1048861 (G > T; Arg141Leu) and rs3825942 (G > A; Gly153Asp), in the LOXL1 gene are strongly associated with the disease risk in multiple populations worldwide. In the present study, we investigated functional effects of these SNPs on the LOXL1 protein. We show through molecular modelling that positions 141 and 153 are likely surface residues and hence possible recognition sites for protein-protein interactions; the Arg141Leu and Gly153Asp substitutions cause charge changes that would lead to local differences in protein electrostatic potential and in turn the potential to modify protein-protein interactions. In RFL-6 rat fetal lung fibroblast cells ectopically expressing the LOXL1 protein variants related to PEX (Arg141_Gly153, Arg141_Asp153 or Leu141_Gly153), immunoprecipitation of the secreted variants showed differences in their processing by endogenous proteins, possibly Bone morphogenetic protein-1 (BMP-1) that cleaves and leads to enzymatic activation of LOXL1. Immunofluorescence labelling of the ectopically expressed protein variants in RFL-6 cells showed no significant difference in their extracellular accumulation tendency. In conclusion, this is the first report of a biological effect of the coding SNPs in the LOXL1 gene associated with PEX syndrome, on the LOXL1 protein. The findings indicate that the disease associated coding variants themselves may be involved in the manifestation of PEX syndrome.

What's in a Gene? Pseudoexfoliation Syndrome and Pigment Dispersion Syndrome in the Same Patient

Pseudoexfoliation syndrome (PXS) and pigment dispersion syndrome (PDS) are two of the commonest disorders to produce secondary open-angle glaucoma through trabecular meshwork blockage. Each is a defined clinical entity, and while genetics likely play a significant role in the pathogenesis of both, the specific genes involved appear to be distinct. There is surprisingly little published in the literature regarding the coexistence of PDS and PXS in the same patient. We present the intriguing case of a patient who developed PDS in one eye and PXS in the other. This unusual case acts as a platform for an interesting discussion of the genomics of PXS and PDS.

Lysyl oxidase-like 1 polymorphisms in a southwestern Greek cataract population with pseudoexfoliation syndrome

Purpose

The aim of this study was to determine the possible association of rs1048661 and rs3825942 single nucleotide polymorphisms (SNPs) in the lysyl oxidase-like 1 (LOXL1) gene of cataract patients from southwestern Greece with pseudoexfoliation (PEX) syndrome.

Patients and methods

Ninety-three patients with PEX syndrome and 74 without PEX syndrome were recruited with the principal diagnosis being cataract. LOXL1 SNPs, rs1048661 and rs3825942, were genotyped by using polymerase chain reaction.

Results

The G allele of rs1048661 was found in 96.7% in the PEX group as compared to 80.5% of non-PEX alleles (P=19×10⁻⁴; Odds ratio [OR] =5.37; 95% confidence interval [CI] =1.68–17.12). Similarly, the G allele of rs3825942 was found in 72.1% of the PEX group as compared to 41.8% of non-PEX alleles (P=4×10⁻⁵; OR =3.78; 95% CI =1.98–7.23). The T and A allele frequencies of rs1048661 and rs3825942, respectively, were underrepresented in the PEX group patients as compared to non-PEX group.

Conclusion

Our data confirm previously reported association between LOXL1 polymorphisms and PEX syndrome in a southwestern Greek population. A significant association was found for the G allele of rs1048661 and rs3825942 demonstrating that the GG haplotype is a high-risk factor for the development of PEX syndrome.

Ethnicity-Based Differences in the Association of LOXL1 Polymorphisms with Pseudoexfoliation/Pseudoexfoliative Glaucoma: A Meta-Analysis

Pseudoexfoliation (PEX) is an age-related disorder of the extracellular matrix; it is strongly associated with glaucoma, the leading cause of irreversible blindness worldwide. We conducted an ethnic-based meta-analysis of the association of LOXL1 polymorphisms with PEX/pseudoexfoliative glaucoma (PEXG). Association studies were retrieved systematically from PubMed, EMBASE, and Web of Knowledge. Allelic and genotype frequencies of rs3825942, rs1048661, and rs2165241 were compared between PEX/PEXG and controls. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using a random effects model. Overall, 39 independent cohorts were included. Rs3825942 (G) was an at risk allele for PEX/PEXG in Caucasians, Japanese, Koreans, Chinese, South Asians, and Middle Easterners, but protective in Black South Africans (OR = 0.10, 95%CI:0.06-0.16). Rs1048661 (G) was an at risk allele for PEX/PEXG in Caucasians, South Asians, Middle Easterners and Black South Africans, but was protective in Japanese (OR = 0.03, 95%CI:0.02-0.06) and Koreans (OR = 0.10, 95%CI:0.05-0.22). These associations we-re confirmed for the genotypic recessive models. Rs2165241 (C) was a protective allele for PEX/PEXG in Caucasians, but was an at risk allele in Japanese (OR = 7.49, 95%CI:3.22-17.41) and Koreans (OR = 6.63, 95%CI:2.60-16.90). This was confirmed for the genotypic dominant model. Other genetic and/or environmental factors may modify the effect of LOXL1 polymorphisms in certain ethnic groups.

LOXL1 gene variants and their association with pseudoexfoliation glaucoma (XFG) in Spanish patients

Background

LOXL1 gene is the most important genetic risk factor known so far for pseudoexfoliation glaucoma (XFG). Our purpose was to evaluate the potential association of individual genetic variants of the lysyl oxidase-like 1 (LOXL1) gene and haplotypes with XFG in Spanish patients.

Methods

Blood samples were collected from a total of 105 Spanish patients with XFG and 200 healthy controls. The entire LOXL1 gene along with the promoter, coding and non-coding regions including the 5´- and 3´-untranslated regions, were sequenced using next-generation sequencing in 99 XFG patients. SNPs rs16958477 (promoter), rs1048661 (exon 1), rs3825942 (exon 1), rs2165241 (intron 1) and rs3522 (exon 7) in LOXL1 were genotyped by restriction fragment-length polymorphism (RFLP) in all Spanish control participants and in six additional XFG patients, and a case–control association study was performed.

Comparisons of the allelic and genotypic frequencies were performed using standard χ² test with Bonferroni and Pearson corrections. Logistic regression analyses were permormed using Sigmaplot v11. Haplotypes frequencies were performed using HaploView 4.0.

Results

Sequencing of the LOXL1 gene in XFG participants identified a total of 212 SNPs, of which 49 exhibited allelic frequencies with significant differences between cases and controls, and 66 were not previously described. The allele frequencies of SNPs rs16958477, rs1048661, rs3825942, rs2165241, were significantly associated with an increased risk for XFG, however the SNP rs3522 was not.

The haplotype frequencies of SNPs rs16958477, rs1048661, rs3825942 and rs2165241 and their association with XFG indicated that the CGGT haplotype, containing all four risk alleles, and the AGGT haplotype, which carries the protective allele of rs16958477 and three risk alleles of the other three SNPs, were significantly associated with XFG (p = 4.5×10⁻⁶, and p = 8.8×10⁻⁶), conferring more than 2-fold increased disease susceptibility.

Conclusions

SNPs of the LOXL1 gene are associated with XFG in the Spanish population. This information adds new support to the distinct risk association frequencies of LOXL1 alleles with XFG in Western European and Asian populations. Identification and validation of additional SNPs along the entire LOXL1 gene of XFG cases may provide insightful information on their potential role in the pathogenesis of this disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-015-0221-y) contains supplementary material, which is available to authorized users.

Association of clusterin (CLU) variants and exfoliation syndrome: An analysis in two Caucasian studies and a meta-analysis

Exfoliation syndrome (XFS) is an important risk factor for glaucoma (XFG) worldwide. LOXL1 variants are highly associated with XFS in most populations; however, the high frequency of risk alleles in normal individuals and the reversal of risk alleles in different ethnic populations suggest that other factors contribute to XFS pathogenesis. Clusterin (CLU) is an extracellular matrix chaperone that prevents protein aggregation and is highly expressed in ocular tissues affected by XFS. Studies examining common CLU variants for association with XFS have been inconsistent. The purpose of this study was to evaluate CLU variants for association with XFS in two independent datasets from the United States (222 cases and 344 controls) and Israel (92 cases and 102 controls). Seven tag SNPs that captured >95% of alleles at r(2) greater than 0.8 across the CLU genomic region were genotyped using TaqMan assays. Genotypes for an additional SNP, rs2279590, were imputed using phased haplotypes of HapMap reference CEU samples. Of the 8 CLU SNPs selected for the study, none were significantly associated with XFS in either case-control group (age and sex adjusted P > 0.14 and 0.36, respectively, in the US and Israeli datasets), or when they were meta-analyzed together (age and sex adjusted P > 0.13). Haplotype analysis using all 8 SNPs or only the promoter region SNPs also did not show significant associations of CLU with XFS in the combined US and Israeli dataset (P > 0.28). Meta-analysis of the data from this study and previous studies in Caucasian populations (1184 cases and 978 controls) resulted in statistically significant association of rs2279590 with XFS (summary OR = 1.18, 95% CI: 1.03-1.33, P = 0.01). Significant association between rs2279590 and XFS was also found in Indian populations (summary OR = 0.76, 95% CI: 0.61-0.96; P = 0.02); however, significant heterogeneity between the Caucasian and Indian populations possibly due to reversal of the risk allele precluded an overall meta-analysis for rs2279590 (Q = 0.001, I(2) = 91%). No significant association was identified for rs3087554 in either Caucasian populations (summary OR = 0.90, 95% CI: 0.77-1.05, P = 0.17) or Indian populations (summary OR = 0.89, 95% CI: 0.72-1.10, P = 0.28), or in both populations combined (1705 cases and 3713 controls; summary OR = 0.90, 95% CI: 0.79-1.01, P = 0.08). Significant heterogeneity precluded the addition of the Japanese data to the meta-analysis for rs3087554 (Q = 0.006, I(2) = 87%). Our results suggest that common CLU variants may contribute to modest XFS risk but even larger datasets are required to confirm these findings.

Evaluation of genetic polymorphisms in clusterin and tumor necrosis factor-alpha genes in South Indian individuals with pseudoexfoliation syndrome

PURPOSE

The aim of this study was to explore the potential association of genetic variants across clusterin (CLU) and tumor necrosis factor-alpha (TNF-α) genes in South Indian individuals with pseudoexfoliation syndrome (PEXS) and pseudoexfoliation glaucoma (PEXG).

MATERIALS AND METHODS

A total of 523 individuals including 299 unrelated cases (150 PEXS and 149 PEXG) and 224 age- and ethnically-matched healthy controls were recruited for genetic analysis. Six single-nucleotide polymorphisms (SNPs) including, five CLU SNPs (rs11136000, rs2279590, rs9331888, rs9331931, rs3087554) and one promoter SNP (rs1800629) of TNF-α were genotyped in all study subjects. Genotyping of CLU SNPs were performed using the TaqMan allelic discrimination assay while TNF-α SNP was genotyped using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) analysis. Association analysis was performed by determining the distributions of genotype and allele frequencies, Hardy-Weinberg equilibrium, and chi-square p values and odds ratios as implemented in the Golden Helix SNP & Variation Suite (SVS).

RESULTS

Five CLU SNPs did not show any significant differences in allele frequencies between patients and control subjects (rs3087554, p = 0.919, OR = 1.01, 95% CI: 0.77-1.33; rs2279590, p = 0.432, OR = 1.12, 95% CI: 0.84-1.51; rs9331931, p = 0.310, OR = 1.24, 95% CI: 0.81-1.89; rs11136000, p = 0.072, OR = 1.31, 95% CI: 0.97-1.76; rs9331888, p = 0.911, OR = 1.01, 95% CI: 0.78-1.31). The investigation of TNF-α SNP established a significant association with PEXS and PEXG (p = 0.042, OR = 0.61, 95% CI: 0.38-0.99). However, this association did not remain significant after Bonferroni correction.

CONCLUSIONS

Our data suggest that genetic variants in CLU and TNF-α genes do not play a major role in the development of PEXS and PEXG in the South Indian population.

Ocular and systemic manifestations of exfoliation syndrome

Exfoliation syndrome is an age-related disease characterized by the production and progressive accumulation of a fibrillar extracellular material in many ocular tissues. It leads to the most common identifiable cause of open-angle glaucoma worldwide, comprising the majority of glaucoma in some countries. The material in the eye appears as white deposits on the anterior lens surface and/or pupillary border. During pupillary movement, the iris scrapes exfoliation material from the lens surface, while the material on the lens causes rupture of iris pigment epithelial cells, with concomitant pigment dispersion into the anterior chamber and its deposition on anterior chamber structures. Exfoliation material can be found in many different organs. It is an ischemic disease and is associated with elevated serum homocysteine. Systemic associations include transient ischemic attacks, hypertension, angina, myocardial infarction, cerebrovascular and cardiovascular disease, aortic aneurysm, Alzheimer disease, and hearing loss. The discovery in 2007 of nonsynonymous single nucleotide polymorphisms in the LOXL1 (lysyl oxidase-like 1) gene are expected to make a major impact not only in understanding exfoliation syndrome, but in leading to new avenues of therapy.

Animal models of exfoliation syndrome, now and future

At present, no animal models fully embody exfoliation syndrome or exfoliation glaucoma. Both genetic and environmental factors appear critical for disease manifestation, and both must be considered when generating animal models. Because mice provide a powerful mammalian platform for modeling complex disease, this paper focuses on mouse models of exfoliation syndrome and exfoliation glaucoma.

A common variant mapping to CACNA1A is associated with susceptibility to exfoliation syndrome

Exfoliation syndrome (XFS) is the most common recognizable cause of open-angle glaucoma worldwide. To better understand the etiology of XFS, we conducted a genome-wide association study (GWAS) of 1,484 cases and 1,188 controls from Japan and followed up the most significant findings in a further 6,901 cases and 20,727 controls from 17 countries across 6 continents. We discovered a genome-wide significant association between a new locus (CACNA1A rs4926244) and increased susceptibility to XFS (odds ratio (OR) = 1.16, P = 3.36 × 10(-11)). Although we also confirmed overwhelming association at the LOXL1 locus, the key SNP marker (LOXL1 rs4886776) demonstrated allelic reversal depending on the ancestry group (Japanese: OR(A allele) = 9.87, P = 2.13 × 10(-217); non-Japanese: OR(A allele) = 0.49, P = 2.35 × 10(-31)). Our findings represent the first genetic locus outside of LOXL1 surpassing genome-wide significance for XFS and provide insight into the biology and pathogenesis of the disease.

The association of LOXL1 polymorphisms with exfoliation syndrome/glaucoma: Meta-analysis

AIM

To investigate the association of lysyl oxidase-like 1 (LOXL1) single nucleotide polymorphisms (SNPs) with exfoliation syndrome (XFS)/exfoliation glaucoma (XFG).

METHODS

Published manuscripts from PubMed and EMBASE were identified until May 2014. Summary odds ratios (ORs) and 95% confidence intervals (CIs) for LOXL1 (rs1048661, rs2165241 and rs3825942) polymorphisms and the risk of XFS/XFG were estimated using random- or fixed- effect model.

RESULTS

The three LOXL1 polymorphisms (rs1048661, rs3825942, and rs2165241) were associated with an increased risk for XFS/XFG among Caucasians, with OR 2.19(1.96-2.45), 8.8 (6.05-12.79) and 3.41 (3.11-3.73), respectively. On the contrast, the rs1048661 and rs2165241, but not rs3825942 polymorphism, have a potential protective effect on XFS/XFG in Asians, with OR 0.06 (0.02-0.18), 0.15 (0.09-0.25), respectively.

CONCLUSION

There is strong evidence that LOXL1 polymorphisms are associated with XFS/XFG risk. The strength of risk might be ethnicity-dependent.

Associations of polymorphisms of LOXL1 gene with primary open-angle glaucoma: a meta-analysis based on 5,293 subjects

OBJECTIVE

Previous studies indicated that the relationship between lysyl oxidase-like 1 (LOXL1) gene polymorphisms and primary open-angle glaucoma (POAG) remains inconsistent. In the present study, we aimed to perform a meta-analysis to investigate the association of LOXL1 polymorphisms with POAG risk.

METHODS

Literatures were electronically searched in the PubMed, EMBASE, CNKI, Wanfang, and VIP databases. The published literatures, which are case-control or cohort studies on the relationship between the polymorphisms (rs1048661, rs3825942, rs2165241) of the LOXL1 gene and POAG, were documented.

RESULTS

We included 13 literatures including 5,293 subjects for the present study. A meta-analysis showed that the risk of POAG in individuals carrying the C allele of rs2165241 was 1.26 times higher compared with those carrying the T allele (odds ratio (OR)=1.26, 95% confidence interval (CI): 1.09~1.46) in the total population. In the Caucasian population, we also found that individuals carrying the C allele of rs2165241 have an increased risk for POAG compared to those subjects carrying the T allele (OR=1.42, 95% CI: 1.19~1.69, p=0.0001). In addition, we found that the rs1048661 polymorphism was associated with POAG in the Asian population (OR=1.17, 95% CI: 1.02~1.35, p=0.03), and rs3825942 was associated with POAG in the Caucasian population (OR=2.69, 95% CI: 1.61~4.47, p<0.001).

CONCLUSIONS

The polymorphisms of the LOXL1 gene were associated with the susceptibility of POAG.

The interactions of genes, age, and environment in glaucoma pathogenesis

Glaucoma, a progressive degenerative condition that results in the death of retinal ganglion cells, is one of the leading causes of blindness, affecting millions worldwide. The mechanisms underlying glaucoma are not well understood, although years of studies have shown that the largest risk factors are elevated intraocular pressure, age, and genetics. Eleven genes and multiple loci have been identified as contributing factors. These genes act by a number of mechanisms, including mechanical stress, ischemic/oxidative stress, and neurodegeneration. We summarize the recent advances in the understanding of glaucoma and propose a unified hypothesis for glaucoma pathogenesis. Glaucoma does not result from a single pathological mechanism, but rather a combination of pathways that are influenced by genes, age, and environment. In particular, we hypothesize that, in the presence of genetic risk factors, exposure to environment stresses results in an earlier age of onset for glaucoma. This hypothesis is based upon the overlap of the molecular pathways in which glaucoma genes are involved. Because of the interactions between these processes, it is likely that there are common therapies that may be effective for different subtypes of glaucoma.

Lack of association between lysyl oxidase-like 1 polymorphisms and primary open angle glaucoma: a meta-analysis

AIM

To study the associations between lysyl oxidase-like 1 (LOXL1) polymorphisms and primary open angle glaucoma (POAG) remain inconsistent. In this study, we have performed a meta-analysis to investigate the association of LOXL1 polymorphisms with POAG risk.

METHODS

Published literature from PubMed and other databases were retrieved. All studies evaluating the association between LOXL1 polymorphisms (rs2165241, rs1048661, rs3825942) and POAG risk were included. Pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using random- or fixed-effects model.

RESULTS

Twelve studies were identified as eligible articles, with thirteen (2098 cases and 16 473 controls), thirteen (1795 cases and 2916 controls) and sixteen population cohorts (2456 cases and 2846 controls) for the association of rs2165241, rs1048661 and rs3825942 with POAG risk respectively. Overall analyses showed no association between each LOXL1 polymorphism and POAG risk, and the negative associations were remained when the subjects were stratified as Caucasian and Asian. The heterozygote of rs2165241 was associated with reduced POAG risk in hospital-based populations (TC vs CC: OR, 0.79, 95%CI: 0.63-0.99), and rs1048661 was associated with increased POAG risk in hospital-based populations in a dominant model (TT vs CC+CT: OR, 1.23, 95%CI: 1.01-1.50); however, these associations were not found in population-based subjects.

CONCLUSION

This meta-analysis suggests that LOXL1 polymorphisms are not associated with POAG risk. Given the limited sample size, the associations of LOXL1 polymorphisms with POAG risk in hospital-based populations await further investigation.

Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population

The common variants in lysyl oxidase-like 1 gene (LOXL1) are associated with exfoliation glaucoma (XFG) patients developed through exfoliation syndrome (XFS). However, the risk allele of a variant in LOXL1 has been found to be inverted between Asian and Caucasian populations. Therefore, we newly performed a genome-wide association study using 201 XFS/XFG and 697 controls in Japanese, and identified 34 genome-wide significant single-nucleotide polymorphisms (SNPs) distributing in not only LOXL1 but also TBC1D21 and PML at the 15q24.1 locus. These SNPs were confirmed by an independent population consisted of 121 XFS/XFG and 263 controls in Japanese. Moreover, further analyses revealed a unique haplotype structure only from the combination of TBC1D21 and LOXL1 variants showing a high XFS/XFG susceptibility specific for the Asian population. Although there still should be other gene(s) in the other region(s) contributing to the disease process, these results suggested that the combination of newly discovered variants in these genes might be useful for precise XFG risk assessment, as well as for elucidating the molecular mechanism of XFG pathogenesis through XFS.

Association between polymorphisms in lysyl oxidase-like 1 and susceptibility to pseudoexfoliation syndrome and pseudoexfoliation glaucoma

The present knowledge on the association of single nucleotide polymorphisms (SNPs) of lysyl oxidase-like 1 (LOXL1) with pseudoexfoliation syndrome (PEXS) and pseudoexfoliation glaucoma (PEXG) is controversial and inconclusive. This meta-analysis sought to derive a more precise estimation of the effects of LOXL1 SNP loci (rs1048661, rs3825942, and rs2165241) on PEXS/PEXG. Literature searches were conducted on the PubMed, EMBASE, ISI Web of Science, and Cochrane Library databases through October 2013. Twelve studies describing 1810 cases and 1790 controls met the inclusion criteria. The strengths of the associations found through the meta-analysis were assessed with pooled odds ratios and their 95% confidence intervals (CI). A meta-regression analysis was also used to examine the influence of the study and population characteristics. The results indicated that rs1048661 TT carriers had 92.1% and 40.4% less risk of developing PEXS/PEXG than did the controls in the Caucasian and Asian populations, respectively. Carriers of rs3825942 AA or rs2165241 CC also had significantly less PEXS/PEXG susceptibility than did the non-carriers. Meta-regression showed that in Caucasians, the male proportion (slope: 0.272; 95% CI: 0.167–0.376; P = 0.0001) and mean age (slope: 0.796; 95% CI: 0.375–1.217; P = 0.0002) of the PEXS/PEXG subjects correlated positively with the effect of rs3825942 on PEXS/PEXG susceptibility. The meta-analysis suggested that LOXL1 rs1048661 TT, rs3825942 AA, and rs2165241 CC were associated with a reduced risk of developing PEXS/PEXG.

Regional pathology in glaucoma--an overlooked link to neuroprotective strategies

Primary open-angle glaucoma (POAG) is the second commonest cause of blindness in the world. It is a neurodegenerative disease characterized by retinal ganglion cell loss. The molecular mechanism leading to glaucoma damage is unclear. Understanding the pathways that favor neuronal survival plus those that predispose to neuronal demise in POAG may have direct implications for other neurodegenerative diseases. POAG is a heterogeneous disease. A small subset of POAG patients develop damage in a highly focal form with a discrete sector of the optic nerve manifesting well delineated neuronal loss. It is hypothesized that this pattern of nerve loss indicates the optic nerve is not molecularly homogeneous. Genetic analysis of patients with isolated focal forms of POAG may enable new genes to be identified in glaucoma. Finding the responsible genes in POAG is a critical first step. The potential implications are earlier disease detection with resultant optimized visual preservation. Future treatment options could develop that include altered gene regulation, gene silencing or introducing repair genes. Determining the molecular causes for regional neuronal susceptibility could lead to identification of pathways underlying disease and ultimately effective patient-specific neuroprotective strategies.

Evaluation of lysyl oxidase-like 1 gene polymorphisms in pseudoexfoliation syndrome in a Korean population

PURPOSE

The purpose of this study was to evaluate association profiles of lysyl oxidase-like 1 (LOXL1) gene polymorphisms with pseudoexfoliation syndrome (XFS) in a Korean population.

METHODS

A total of 110 Korean patients with XFS and 127 control subjects were included in this study. Genotypes of three single nucleotide polymorphisms (SNPs) of LOXL1 (rs1048661, rs3825942, and rs2165241) were analyzed with direct sequencing, and a case-control association study was performed. Genotype frequencies of each SNP were compared according to the XFS phenotypes.

RESULTS

All three SNPs were significantly associated with XFS. The T allele at rs1048661 (odds ratio [OR] = 14.29, 95% confidence interval [CI] = 6.25-33.3) and the C allele at rs2165241 (OR = 7.14, 95% CI = 1.59-33.3) were risk alleles in Korean subjects, which was consistent with findings in other Asian populations. However, our findings were opposite to results from Caucasian populations in which the risk alleles at rs1048661 and rs2165241 were G and T, respectively. At the rs3825942, the G allele (OR = 12.50, 95% CI = 2.94-50.0) was a risk allele for XFS, which was similar to results from most other ethnic groups except black South Africans in whom the A allele increased the risk. In the haplotype analysis, the T-G-C haplotype composed of all three risk alleles was significantly overrepresented in XFS and conferred an 11.36 fold (95% CI = 5.97-23.49) increased likelihood of XFS. There was no significant association between the genotype frequencies of the three SNPs and the XFS phenotypes.

CONCLUSIONS

Three SNPs of LOXL1 (rs1048661, rs3825942, and 2,165,241) are highly associated with XFS in a Korean population. The risk alleles of these SNPs were similar to those of other Asian populations, such as Japanese or Chinese, but differed from non-Asian populations, suggesting that still unidentified genetic or environmental factors may contribute to disease expression.

The genetics of pigment dispersion syndrome and pigmentary glaucoma

We review the inheritance patterns and recent genetic advances in the study of pigment dispersion syndrome (PDS) and pigmentary glaucoma (PG). Both conditions may result from combinations of mutations in more than one gene or from common variants in many genes, each contributing small effects. We discuss the currently known genetic loci that may be related with PDS/PG in humans, the role of animal models in expanding our understanding of the genetic basis of PDS, the genetic factors underlying the risk for conversion from PDS to PG and the relationship between genetic and environmental--as well as anatomical--risk factors.

The rationale for targeting the LOX family in cancer

The therapeutic targeting of extracellular proteins is becoming hugely attractive in light of evidence implicating the tumour microenvironment as pivotal in all aspects of tumour initiation and progression. Members of the lysyl oxidase (LOX) family of proteins are secreted by tumours and are the subject of much effort to understand their roles in cancer. In this Review we discuss the roles of members of this family in the remodelling of the tumour microenvironment and their paradoxical roles in tumorigenesis and metastasis. We also discuss how targeting this family of proteins might lead to a new avenue of cancer therapeutics.

Evaluation of CNTNAP2 gene polymorphisms for exfoliation syndrome in Japanese

PURPOSE

To investigate the contactin-associated protein-like 2 (CNTNAP2) gene for single-nucleotide polymorphisms (SNPs) in Japanese patients with the exfoliation syndrome (XFS).

METHODS

One hundred and eight unrelated Japanese patients with the XFS, and 199 normal controls were studied. Genomic DNA was extracted from the leukocytes of the peripheral blood, and 8 SNPs, rs826802, rs1404699, rs7803992, rs700308, rs4725736, rs2107856, rs2141388, and rs6970064, were amplified by polymerase chain reaction (PCR), directly sequenced, and genotyped.

RESULTS

The allele frequencies of rs1404699 (p=8.57XE-3, odds ratio (OR)=1.59, 95% confidential intervals (CI); 1,12-2.24) and rs7803992 (p=5.43XE-4, OR=1.86, 95% CI; 1.31-2.65) were statistically significantly different between XFS and controls. In addition, there were significant differences in these genotype frequencies (p=0.0197 and 1.75XE-3). The allele and the genotype frequencies of rs2107856 and rs2141388, which were statistically significant SNPs in an earlier study, were not significantly different.

CONCLUSIONS

The variants, rs1404699 and rs7803992, of CNTNAP2 should be associated with XFS in the Japanese population.

Variations in LOXL1 associated with exfoliation glaucoma do not affect amine oxidase activity

PURPOSE

Lysyl oxidase-like 1 (LOXL1) is a copper-dependant amine oxidase that plays an essential role in elastogenesis. Two non-synonymous single-nucleotide polymorphisms of LOXL1, R141L (rs1048661) and G153D (rs3825942), have been reported to significantly increase susceptibility to exfoliation glaucoma (XFG). To evaluate the impact of the R141L and G153D variations on the amine oxidase activity of LOXL1, we generated four different haplotypes of LOXL1 with R141L and G153D and assessed the amine oxidase activity of the LOXL1 variant proteins.

METHODS

The four different haplotype variants of LOXL1 were created by oligonucleotide-directed mutagenesis in an LOXL1 expression vector. Recombinant LOXL1 variant proteins were purified by nickel-affinity chromatography. The amine oxidase activities of the LOXL1 variant proteins were assessed using peroxidase-coupled fluorometric assays.

RESULTS

All of the haplotype variants of LOXL1 (141R-153G, 141R-153D, 141L-153G, and 141L-153D) showed β-aminopropionitrile-inhibitable amine oxidase activity toward elastin, type I collagen, and cadaverine, indicating that each LOXL1 variant functions as an amine oxidase. However, there were no significant differences in amine oxidase activity between the LOXL1 haplotype variants toward the tested substrates.

CONCLUSIONS

The R141L and G153D variations in the NH(2)-terminal region of LOXL1 do not affect the amine oxidase activity of LOXL1. This is consistent with recent genetic findings on the reversal of risk alleles of R141L and G153D in different ethnic backgrounds. Our results suggest that other unknown genetic factors or molecular mechanisms may be more relevant to the development of XFG.

An approach to predict the risk of glaucoma development by integrating different attribute data

Primary open-angle glaucoma (POAG) is one of the major causes of blindness worldwide and considered to be influenced by inherited and environmental factors. Recently, we demonstrated a genome-wide association study for the susceptibility to POAG by comparing patients and controls. In addition, the serum cytokine levels, which are affected by environmental and postnatal factors, could be also obtained in patients as well as in controls, simultaneously. Here, in order to predict the effective diagnosis of POAG, we developed an “integration approach” using different attribute data which were integrated simply with several machine learning methods and random sampling. Two data sets were prepared for this study. The one is the “training data set”, which consisted of 42 POAG and 42 controls. The other is the “test data set” consisted of 73 POAG and 52 controls. We first examined for genotype and cytokine data using the training data set with general machine learning methods. After the integration approach was applied, we obtained the stable accuracy, using the support vector machine method with the radial basis function. Although our approach was based on well-known machine learning methods and a simple process, we demonstrated that the integration with two kinds of attributes, genotype and cytokines, was effective and helpful in diagnostic prediction of POAG.

Association of lysyl oxidase-like 1 gene polymorphisms with exfoliation syndrome in Koreans

PURPOSE

To evaluate the association of the lysyl oxidase-like 1 (LOXL1) single nucleotide polymorphisms (SNPs) in the Korean population with exfoliation syndrome (XFS) and to investigate the association between the SNPs and phenotypes of XFS.

METHODS

Eighty-nine unrelated patients with XFS and 146 unrelated control subjects were recruited. LOXL1 SNPs, rs1048661, rs3825942, and rs2165241, were genotyped by direct DNA sequencing. Association between cases and controls was analyzed and phenotypic features of XFS were compared in terms of the SNPs.

RESULTS

The three SNPs were found to be significantly associated with XFS. After adjusting for rs3825942, rs2165241, and other factors influencing the prevalence of XFS, only rs1048661 among three SNPs remained significant (95% confidence interval=4.11-35.78, p=6.11×10(-6)). T allele and TT genotype of rs1048661 and C allele and CC genotype of rs2165241 were associated with XFS, showing risk alleles and genotypes opposite to those reported in Caucasians. In the haplotype analysis, T-G-C was the only risk haplotype (p=3.35×10(-12)), which was not associated with XFS in Caucasians. No significant differences were noted in the allele and genotype frequencies depending on phenotypic features of XFS.

CONCLUSIONS

Three LOXL1 SNPs are associated with XFS in the Korean population. Risk alleles and genotypes of rs1048661 and rs2165241 in Korean have a similar pattern with those of East Asians, including Japanese and Northern Chinese, while they have a different pattern from those of Caucasians.

Review: The role of LOXL1 in exfoliation syndrome/glaucoma

Exfoliation syndrome is a common cause of open-angle glaucoma. It is characterized by microscopic flakes of protein-rich material being deposited in both ocular and non-ocular tissues. While its mechanism is poorly understood, family- and population-based studies have established that the disorder has a strong genetic component. A further understanding of the relevant gene variants might help reveal the molecular mechanism behind exfoliation. The most-strongly associated genetic variants are found in the lysyl oxidase-like 1 (LOXL1) gene. However, two major risk alleles in the LOXL1 coding region are reversed between ethnic groups. It now appears the strong association between LOXL1 and XFS is due to non-coding variants that have not yet been identified. Such variants might alter LOXL1 expression, which is decreased in the late stages of exfoliation syndrome/glaucoma. Here we discuss LOXL1 as a risk gene for exfoliation syndrome and glaucoma.

Genetics and genomics of pseudoexfoliation syndrome/glaucoma

Pseudoexfoliation (PEX) syndrome, one of the most common causes of glaucoma, represents a complex, multifactorial, late-onset disease of worldwide significance. The etiopathogenesis involves both genetic and non-genetic factors. The PEX-specific tissue alterations are caused by a generalized fibrotic matrix process, which has been characterized as a stress-induced elastosis associated with the excessive production and abnormal cross-linking of elastic microfibrils into fibrillar PEX aggregates. The identification of lysyl oxidase-like 1 (LOXL1) as a major genetic risk factor for PEX syndrome and PEX glaucoma further supports a role of elastogenesis and elastosis in the pathophysiology of PEX, as LOXL1 is a pivotal cross-linking enzyme in elastic fiber formation and stabilization. The available data suggest that LOXL1 is markedly dysregulated depending on the stage of the fibrotic process. While transient upregulation of LOXL1 during the early stages of PEX fibrogenesis participates in the formation and aggregation of abnormal PEX fiber deposits, the decreased expression of LOXL1 during the advanced stages of the disease may affect elastin metabolism and promote elastotic processes, e.g. in the lamina cribrosa, predisposing to glaucoma development. However, in view of the low penetrance of the PEX-associated risk variants of LOXL1, other genetic and/or environmental factors must contribute to the risk of developing the PEX phenotype. Some evidence exists for the contribution of additional genes with relatively small effects, e.g. clusterin (CLU), contactin-associated protein-like 2 (CNTNAP2), apolipoprotein E (APOE), glutathione S-transferases (GSTs), and tumor necrosis factor-alpha (TNFA), in certain study populations. Several environmental conditions associated with PEX, such as oxidative stress as well as pro-fibrotic cytokines and growth factors, can regulate expression of LOXL1 and elastic proteins in vitro and may therefore act as co-modulating external factors. Ultimately, both detection and functional characterization of yet unidentified genetic and non-genetic factors may lead to the development of more precise screening tools for the risk of PEX glaucoma.

Evaluation of LOXL1 polymorphisms in exfoliation syndrome in the Uygur population

PURPOSE

In Uygur populations, exfoliation syndrome (XFS) and exfoliation glaucoma (XFG) occurred at a high frequency. In this study, we evaluate the association profiles of the lysyl oxidase-like 1 (LOXL1) gene polymorphisms with XFS in the Uygur population.

METHODS

Sixty-four unrelated Uygur patients with XFS and 127 Uygur control subjects were included in this study. Genotypes of the three single nucleotide polymorphisms (SNPs) of LOXL1 (rs1048661, rs2165241, and rs3825942) were analyzed by direct sequencing, and a case-control association study was performed.

RESULTS

The three SNPs were significantly associated with XFS and XFG individually. The G allele of rs1048661 (OR [95%CI]: 1.92 [1.14-3.22]), G of rs3825942 (OR [95%CI]: 4.86 [2.02-11.68]), and T of rs2165241 (OR [95%CI]: 3.98 [2.54-6.25]) were risk alleles for the disorder. The genotypes GG for rs1048661 (OR [95%CI]: 2.13 [1.14-3.97]), GG for rs3825942 (OR [95%CI]: 5.68 [2.28-14.17]), and TT for rs2165241 (OR [95%CI]: 6.13 [2.68-14.01]) were risk genotypes for the disease. The haplotypes G-G for the SNPs rs1048661and rs3825942, G-T for the SNPs rs1048661 and rs2165241, and SNPs rs3825942 and rs2165241 were found to be significantly associated with XFS/G. The haplotypes G-G-T for the three SNPs were determined to be significantly associated with XFS/G. There were significant differences of the allelic and genotypic proportion in different gender/age patients and controls for all three SNPs. T allele of rs2165241 and G of rs3825942 were risk alleles for the disorder in both the male and female groups. G allele of rs1048661 was a risk allele for the disorder in the below 65-year-old group. T of rs2165241 was a risk allele for the disorder in both age groups. G of rs3825942 was a risk allele for the disorder in the over 65-year-old group. The genotypes also showed significant differences in the below 65-year-old group of rs1048661, both groups of rs2165241, and over 65-year-old group of rs3825942.

CONCLUSIONS

LOXL1 is a susceptibility gene of XFS/XFG in Uygur populations. The risk alleles of rs1048661, rs3825942 and rs2165241 in Uygur subjects were found to be similar to those of populations in Iceland and the United States and different from Han populations in China. The genotypic and allelic distributions of these SNPs are similar between XFS and XFG.

No association of LOXL1 gene polymorphisms with Alzheimer's disease

Aggregation of amyloid-beta is one of the major characteristics in brains of patients with Alzheimer's disease (AD). Although several mechanisms behind the formation of such aggregates have been suggested the regulatory factors are still unknown. The present study aimed at investigating the association of lysyl oxidase-like 1 (LOXL1) polymorphisms with AD diagnosis and cerebrospinal fluid biomarkers (CSF) for the disease. Proteins of the lysyl oxidase (LOX) family are involved in cross-linking extracellular matrix proteins to insoluble fibers and have been associated with neurodegenerative diseases including AD. Genetic polymorphisms in LOXL1 (rs1048661, rs3825942, and rs2165241) have been linked to exfoliation syndrome and exfoliation glaucoma, conditions that have shown association with AD. The polymorphisms were genotyped by Taqman allelic discrimination in a study sample including AD patients (n = 318) and controls (n = 575). In a subgroup of the population, the polymorphisms were analyzed in relation to APOE ε4 genotype and to CSF (T-tau, P-tau, and Aβ(1-42)). No evidence for associations of these polymorphisms with risk for AD or any of the studied CSF biomarkers measured was found. These results do not support LOXL1 as being a major risk gene for AD.

Lack of association between LOXL1 gene polymorphisms and primary open angle glaucoma in the Saudi Arabian population

PURPOSE

To investigate whether major single nucleotide polymorphisms (SNPs) in the LOXL1 gene associated with pseudoexfoliation glaucoma are associated with primary open angle glaucoma (POAG) in the Saudi Arabian population.

METHODS

The regions of the LOXL1 gene associated with pseudoexfoliation glaucoma, encompassing the three common SNPs, (rs1048661, rs3825942 and rs2165241), were sequenced in a Saudi Arabian dataset consisting of 96 POAG cases and 101 healthy controls.

RESULTS

The allele frequency of the G exfoliation risk allele for SNP rs1048661 in POAG cases and controls was 0.75 and 0.76 (p = 0.886), respectively and the allele frequency difference was not statistically significant (p = 0.866). There was no statistically significant difference in the genotypes between patients and controls (p = 0.261 and 0.156 for genotypes G/G and G/T respectively). As for SNP rs3825942, the frequency of the "G" allele in the POAG patients was comparable to that in the controls (p = 0.477) and there was no statistically significant difference in genotype G/G and A/G frequency in the study groups. As for SNP rs2165241, the "T" allele frequency in the POAG patients (0.46) was slightly higher than the frequency in controls (0.39), but this difference was not statistically significant (p = 0.176).

CONCLUSION

The Saudi Arabian POAG population, similar to all other populations studied to date, demonstrates no association with SNPs associated with pseudoexfoliation glaucoma.

LOXL1 promoter haplotypes are associated with exfoliation syndrome in a U.S. Caucasian population

PURPOSE

LOXL1 is a major genetic risk factor for exfoliation syndrome (ES) and exfoliation glaucoma (EG). Recent evidence documenting reversal of risk alleles for the disease-associated missense variants R141L and G153D suggests that these variants are not causative and that they may be proxies for other unknown functional LOXL1 variants. The purpose of this study was to investigate the disease association of LOXL1 variants spanning the gene region, including the 5' and 3' regulatory regions, in a U.S. Caucasian case-control sample.

METHODS

Twenty-five LOXL1 single-nucleotide polymorphisms (SNPs), distributed throughout the gene, were genotyped in 196 Caucasian patients with ES/EG and 201 matched controls. Genotype data were analyzed for single SNP associations, SNP interactions, and haplotype associations.

RESULTS

Promoter region haplotypes that included the risk alleles for rs12914489, a SNP located in the distal promoter region and independently associated with ES, and rs16958477, a SNP previously shown to affect gene transcription, were associated with increased disease risk (P=0.0008; odds ratio [OR], 2.34; 95% confidence interval [CI], 1.42-3.85) and with protective effects (P=2.3 × 10(-6); OR, 0.38; 95% CI, 0.25-0.57). Haplotypes containing rs12914489 and rs16958477 risk and protective alleles also significantly influenced the disease risk associated with missense alleles R141L and G153D.

CONCLUSIONS

LOXL1 promoter haplotypes were identified that are significantly associated with ES/EG in a U.S. Caucasian population. These results suggest that promoter region SNPs can influence LOXL1 gene expression, potentially causing a reduction of enzyme activity that may predispose to disease.

Learning in glaucoma genetic risk assessment

Genome Wide Association (GWA) studies are powerful tools to identify genes involved in common human diseases, and are becoming increasingly important in genetic epidemiology research. However, the statistical approaches behind GWA studies lack capability in taking into account the possible interactions among genetic markers; and true disease variants may be lost in statistical noise due to high threshold. A typical GWA study reports a few highly suspected signals, e.g. Single-nucleotide polymorphisms (SNPs), which usually account for a tiny portion of overall genetic risks for the disease of interest. This study proposes a computational learning approach in addition to parametric statistical methods along with a filtering mechanism, to build glaucoma genetic risk assessment model. Our data set was obtained from Singapore Malay Eye Study (SiMES), genotyped on Illumina 610 quad arrays. We constructed case-control data set with 233 glaucoma and 458 healthy samples. A standard case-control association test was conducted on post-QC dataset with more than 500k SNPs. Genetic profile is constructed using genotype information from a list of 412 SNPs filtered by a relaxed pvalue threshold of 1 × 10(-3), and forms the feature space for learning. Among the five learning algorithms we performed, Support Vector Machines with radial kernel (SVM-radial) achieved the best result, with area under curve (ROC) of 99.4% and accuracy of 95.9%. The result illustrates that, learning approach in post GWAS data analysis is able to accurately assess genetic risk for glaucoma. The approach is more robust and comprehensive than individual SNPs matching method. We will further validate our results in several other data sets obtained in consequential population studies conducted in Singapore.