Epigenetically dysregulated genes and pathways implicated in the pathogenesis of non-syndromic high myopia

Abstract

Myopia, commonly referred to as nearsightedness, is one of the most common causes of visual disability throughout the world. It affects more people worldwide than any other chronic visual impairment condition. Although the prevalence varies among various ethnic groups, the incidence of myopia is increasing in all populations across globe. Thus, it is considered a pressing public health problem. Both genetics and environment play a role in development of myopia. To elucidate the epigenetic mechanism(s) underlying the pathophysiology of high-myopia, we conducted methylation profiling in 18 cases and 18 matched controls (aged 4-12 years), using Illumina MethylationEPIC BeadChips array. The degree of myopia was variable among subjects, ranging from -6 to -15D. We identified 1541 hypermethylated CpGs, representing 1745 genes (2.0-fold or higher) (false discovery rate (FDR) p ≤ 0.05), multiple CpGs were p < 5 × 10^-8 with a receiver operating characteristic area under the curve (ROC-AUC) ≥ 0.75 in high-myopia subjects compared to controls. Among these, 48 CpGs had excellent correlation (AUC ≥ 0.90). Herein, we present the first genome-wide DNA methylation analysis in a unique high-myopia cohort, showing extensive and discrete methylation changes relative to controls. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination.

Figure 1

(A–D) Receiver operating characteristic curve analysis of methylation profiles. ROC analysis for four excellent CpG sites [(A) cg12711743: LRRC8C; (B) cg05367846: MICAL3; (C) cg00765710: PGBD2; and (D) cg16232979: TPM4]. At each locus, the FDR p-value for methylation difference between myopia subjects and controls was significantly different. ROC: Receiver operating characteristic; AUC: Area Under Curve; 95% CI: 95% Confidence Interval.

Figure 2

Heatmap and hierarchical clustering of myopia cases based on DNA methylation. Heat map showing hypermethylation variation in myopia cases compared with controls. The Heat map in hierarchical clustering analysis represented DNA methylation levels from completely methylated (red) to unmethylated (green).

Figure 3

Three dimensional PCA (PCA 3D).

Figure 4

Functional enrichment analysis of differentially methylated genes involved in transporter activity, translation regulator activity, catalytic activity, receptor activity, signal transducer activity, structural molecule activity and binding activity with their respective percentages given.

Figure 5

Pathways analysis of significant DNA methylation variations and network analysis performed using Ingenuity Pathway Analysis (IPA). Schematic location of nodes such as on extracellular space, plasma membrane, cytoplasm and nucleus is depicted.