A genome-wide association study for corneal curvature identifies the platelet-derived growth factor receptor alpha gene as a quantitative trait locus for eye size in white Europeans

• Introduction
• Methods
• Results
• Discussion

Abstract

Purpose: Corneal curvature is a key determinant of the refractive power of the eye. Variants in two genes, FKBP12-rapamycin complex-associated protein 1 (FRAP1) on chromosome 1p36.2 and platelet-derived growth factor receptor alpha (PDGFRA) on chromosome 4q12, have shown genome-wide significant association with normal variation in corneal curvature in a study of subjects of Asian origin. Variants at the PDGFRA locus have also shown genome-wide significant association with corneal astigmatism. Whether these variants influence other ocular parameters such as axial length has yet to be reported. We performed a genome-wide association study for corneal curvature in white European subjects from a population-based birth cohort, with the aim of replicating and extending the above findings.

Methods: White European children participating in the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort were examined at age about 15.5 years (95% confidence interval=15.45 to 15.48 years). Radius of corneal curvature and axial eye length were measured with an IOLmaster. DNA samples were genotyped with Illumina HumanHap550 arrays and untyped variants imputed using MACH, with CEU individuals from HapMap release 22, Phase II NCBI B36, Single Nucleotide Polymorphism database 126 as the reference panel. Association between corneal curvature and single nucleotide polymorphism (SNP) genotype was tested, genome-wide, using mach2qtl, with sex as a covariate (n=2023; 46.6% male).

Results: The variant exhibiting the strongest evidence for association with corneal curvature (rs6554163; p=2.8×10⁻⁶) was located in the same linkage disequilibrium block as the previously discovered PDGFRA variants. Meta-analysis of the current and prior findings enhanced the evidence for association (rs17084051, p=4.5×10⁻¹⁴). rs6554163 genotype predicted 1.0% of variation in corneal curvature. In addition, these PDGFRA variants were associated with axial eye length, predicting 0.6% of the normal trait variation (p=5.3×10⁻⁴). Each copy of the minor allele of variants at the locus also increased the risk of corneal astigmatism in this white European cohort (odds ratio [OR]=1.24, 95% confidence interval=1.07–1.45; p=0.006).

Conclusion: As in Asians, variants at the PDGFRA locus influence corneal curvature (and corneal astigmatism). However, rather than affecting corneal curvature in isolation, this locus influences the size of the eye while maintaining its scaling.

Sharp vision requires light to be focused precisely onto the photoreceptor layer of the retina by the combined action of the cornea and the crystalline lens. The cornea is the major refracting element, and its curvature must be carefully coordinated with the dimensions of the other component parts of the growing eye during childhood. A failure in this coordination leads to the refractive errors myopia and hyperopia, while asymmetry of the cornea’s curvature in different orientations, corneal astigmatism, can similarly impair vision [1]. Refractive errors are widespread: For instance, they now affect more than 40% of the population in the United States [2] and the majority of children leaving high school in Hong Kong, Singapore, and Taiwan [3,4]. Excessive corneal steepness is a hallmark feature of keratoconus, and excessive flatness of cornea plana [5,6].

Apart from the overall size of the eye, known predictors of corneal curvature include height and sex. To date, however, little is known about the genetic regulation of eye size at the molecular level, despite ocular component dimensions being heritable [7-9]. Recent genome-wide association studies (GWASs) have begun to address this question, with loci associated with corneal curvature [10], corneal astigmatism [11], refractive error [12,13], and high myopia [14-18] having been reported, mostly in subjects of Chinese ethnicity. As yet, few of these GWAS findings have been replicated independently or have already failed to replicate in subjects of the same or different ethnicity when examined in more detail [19-22]. Our aim was to replicate, in a large collection of European children, associations detected in prior studies on corneal curvature and astigmatism in Asians, which implicated the involvement of the platelet-derived growth factor receptor alpha (PDGFRA) gene in the determination of both traits and the FKBP12-rapamycin complex-associated protein 1 (FRAP1, also known as MTOR) gene in determining corneal curvature [10,11].

Taken at an average age of 15.5 years, corneal curvature measurements in a sample of 2,023 white European children from a UK birth cohort had a Gaussian distribution and a mean value of 7.82 mm (95% confidence interval [CI]=7.81 to 7.83) and, on average, were lower (steeper) in girls than boys (Table 1 and Figure 1). A GWAS for corneal curvature did not yield any SNP markers with a p value <5×10⁻⁸, a value widely accepted as indicating genome-wide significance [32]. However, the SNP with the lowest p value in our GWAS (rs6554163, p=2.8×10⁻⁶; Table 2) was located at the 3′ end of the PDGFRA gene on chromosome 4 (Figure 2), which was recently identified by Han et al. [10] as one of two genes harboring genome-wide significant variants influencing corneal curvature in four Asian samples. rs6554163 resides in a region of low recombination frequency on chromosome 4 spanning approximately 0.16 Mb and that includes only the PDGFRA gene (Figure 2). A meta-analysis of the results from the present white European sample and the four samples recruited from Singapore by Han et al. [10], which comprised Chinese adults (SP2), Malay adults (SiMES), Indian adults (SINDI), and Chinese children (SCORM), enhanced the evidence for association observed in the initial study (combined meta-analysis including ALSPAC and Asian samples, p=4.5×10⁻¹⁴ for SNP rs17084051; Appendix 1). The study by Han et al. [10] identified a second genome-wide significant locus associated with corneal curvature in Asians, centered on the FRAP1 gene at chromosome 1p36.2. However, there was no evidence of replication for this locus in our sample of white European children (all p>0.05; Appendix 1).

Han et al.’s [10] findings were consistent with a single causal variant being responsible for the association between SNP genotypes in the PDGFRA region and corneal curvature. However, GWAS results alone cannot distinguish from among a set of associated SNPs which (if any) is the causal variant. Nevertheless, because of the high linkage disequilibrium (LD) and similar allele frequencies of the associated SNPs, each of the SNPs in the associated PDGFRA region can be regarded as a surrogate for the (presumed single) causal variant. In support of this reasoning, including the imputed genotype dosage of SNP rs6554163 as a covariate in the corneal curvature GWAS completely removed evidence of association with other variants in the region (Appendix 1). We used linear regression models to evaluate the extent the lead SNP rs6554163 in the PDGFRA gene influenced not just corneal curvature but also the potentially related traits, axial eye length and body height. Under an additive model of SNP effects, rs6554163 retained an association with corneal curvature of equivalent magnitude before and after controlling for height (Table 3): Standardized beta coefficient before=–0.167 (95% CI=−0.093 to −0.241) and after=–0.163 (95% CI=−0.091 to −0.235). In both models, rs6554163 predicted 1.0% of the variation in corneal curvature. This SNP was also found to exert a comparable influence on axial length, which again was unaffected by statistically controlling for height (Table 4): Standardized beta coefficient before=–0.128 (95% CI=−0.056 to −0.200) and after=–0.125 (95% CI=−0.054 to −0.195). In both cases, rs6554163 predicted 0.6% of the variation in axial length. There was little evidence of association between the rs6554163 genotype and height itself: Standardized beta coefficient=–0.012 (95% CI=−0.049 to 0.074; p=0.69). The average effect of the PDGFRA gene variant on corneal curvature, axial length, and height is presented in Figure 3.

Separate from Han et al.’s [10] work, a GWAS performed by Fan et al. [11] demonstrated that variants in the same region of the PDGFRA gene that influenced corneal curvature also influenced the risk of corneal astigmatism. Fan et al. [11] surveyed five Asian cohorts recruited from Singapore, namely, the four cohorts listed above in the relation to Han et al.’s [10] work, plus a sample of Chinese parent-infant trios (STARS). For the lead SNP in that study (rs7677751, MAF 0.19 to 0.26), each copy of the minor allele was associated with an increased risk of individuals being classified as a corneal astigmat (OR=1.26, 95% CI=1.16 to 1.36, in the meta-analysis of five studies). In our white European subjects, SNP rs6554163 located in the PDGFRA high LD region was associated with the risk of corneal astigmatism to a similar degree and in the same direction as that observed in the Asian subjects studied by Fan et al. [11]. Specifically, each copy of the minor allele of rs6554163 was associated with an increased risk (OR) of corneal astigmatism of 1.24 (95% CI=1.07 to 1.45; p=0.006) in the ALSPAC subjects (Table 5). In contrast to these results for corneal astigmatism, the rs6554163 genotype did not predict an individual being classified as myopic versus non-myopic (Table 5): Each copy of the minor allele was associated with an OR for myopia of 0.98 (95% CI=0.79 to 1.20; p=0.78). In these latter analyses, sex was associated with corneal astigmatism (being more frequent in girls than boys; OR=1.406, 95% CI=1.174 to 1.683; p<0.001) but was not associated with myopia (Table 5).

To investigate whether variants at the PDGFRA locus contribute in cis to inter-individual variation in PDGFRA gene expression, we performed eQTL (expression quantitative trait locus) GWAS analyses. Whole genome gene expression (transcriptome) array results for EBV-transformed lymphoblastoid cell lines and high-density genotype data were available for 875 of the children from the ALSPAC birth cohort. However, for each of the two probes used to monitor PDGFRA expression on the transcriptome array, there was no evidence of a major eQTL on chromosome 4 in the vicinity of the PDGFRA gene (Appendix 1). This suggests that (at least in these cell lines) variants at the PDGFRA locus do not act as cis regulatory factors that influence the gene’s expression level.

An antibody to PDGFRA was used to assess the protein’s ultrastructural distribution in the normal human cornea. Antibody labeling was strongest in the epithelium, all layers of which were stained, but especially the superficial layer of squamous cells (Figure 4A). Labeling was less abundant in the corneal stroma, but was present in the keratocyte cells and their surrounding extracellular matrix (Figure 4B–C). The endothelial layer and Descemet’s membrane exhibited weaker labeling (Figure 4D–E). Negative control sections showed no background labeling (Figure 4F).

Our finding of a strong association between variants in the PDGFRA gene and corneal curvature, with an effect of equivalent size and direction to that observed by Han et al. [10], suggests that PDGFRA variants influence corneal curvature in both Asians and white Europeans. Likewise, our finding that these same variants were associated with corneal astigmatism in the ALSPAC subjects, and that the size and direction of effect matched those reported by Fan et al. [11], implies that these PDGFRA variants influence corneal astigmatism in Asians and white Europeans, as well. By contrast, the lack of replication for the FRAP1 gene locus in our sample of white European children suggests that the FRAP1 variants influencing corneal curvature in Asians [10] are not present in Europeans, or are not well tagged by common SNPs in Europeans. Notably, patterns of LD in this region are markedly different between European (CEU) and Asian (CHB+JPT) HapMap individuals (Appendix 1). While our article was under review, Mishra et al. [33] also reported that PDGFRA variants (but not FRAP1 variants) influenced corneal curvature in a sample of Australian subjects of European ancestry (1,788 twins and their families, plus 1,013 members of a birth cohort). These authors did not examine the effects of PDGRFA variants on corneal astigmatism or axial length.

Previous phenotype-correlation analyses in mice [34] and chickens [35-37] support the existence of three types of genetic “effects” that act together to determine the size of the component parts of the vertebrate eye (or, more precisely, that proportion under genetic control). These are (i) genetic effects that allometrically scale the size of the eye and body, (ii) effects that purely govern eye size, and (iii) effects restricted to determining the dimensions of each individual ocular component. The PDGFRA variants studied here have the characteristics of genetic effects in the second group, since (as judged by the inheritance of copies of the minor A allele of SNPs such as rs6554163; Figure 3) they act to reduce corneal curvature (i.e., steepen it) and to reduce axial eye length. As visual function is exquisitely dependent on the careful scaling of the eye’s component parts, observing such pleiotropy is not surprising. In terms of identifying genetic variants that influence susceptibility to disorders such as refractive error, variants that affect the expression level or function of PDGFRA would not seem likely candidates given this pleiotropic scaling role. Indeed, subjects’ genotypes for SNP rs6554163 were not associated with the presence/absence of myopia in ALSPAC subjects. Thus, PDGFRA variants appear to exert a risk of corneal astigmatism but not spherical refractive error.

Corneal curvature tends to increase (flatten) markedly during the first few years of life and then remain relatively stable during the remainder of childhood and early adulthood [38-40]. Thus, the association between corneal curvature and PDGFRA variants identified in the 15-year-old children examined here is likely to persist as they age, consistent with the associations previously observed in child and adult Asian populations [10]. However, axial length follows a different pattern of post-natal growth to that of corneal curvature, generally continuing to increase throughout childhood and even into early adulthood [38-40]. This suggests that although these traits share common genetic determinants, there may be differences in the age and/or duration over which these variants exert their effects. It will be of interest to explore further how the association of PDGFRA and axial length alters over the lifecourse, in would-be emmetropes and myopes.

Situated on chromosome 4q12, PDGFRA encodes the alpha isoform of a transmembrane tyrosine kinase receptor for members of the PDGF family. The gene is very widely expressed and has important roles in development and cell proliferation. We observed PDGFRA antibody labeling in all of the major cell types of the normal human cornea, as reported previously [41]. Protein levels appeared highest in the epithelium, followed by stromal keratocytes, and lower still in the endothelium. Antibody labeling was not restricted to the cell membrane in any of the three cell types, consistent [42] with the presence of intracellular stores of PDGFRA, which would permit mobilization to the cell surface in response to external stimuli. Variants in PDGFRA have previously been associated with susceptibility to several cancer types, certain developmental anomalies (see Genetic Association), and several red blood cell quantitative traits [43]. Pertinent to the association with corneal curvature and axial length, members of the PDGF family are known to modulate multiple aspects of extracellular matrix biology [44-48]. However, the specific physiologic mechanism through which PDGFRA gene variation exerts an effect on eye size awaits elucidation.