Abstract
Purpose:
Fuchs endothelial corneal dystrophy (FECD) is the most common indication for corneal transplantation in the United States. While genetic analyses have linked a single chromosomal locus to the early onset form of FECD, the genetic determinants of the more common, late onset form are not fully understood. Recent data has demonstrated that aberrant epigenetic modifications lead to various disease processes including inherited syndromes, cancer, and fibrosis. We tested the hypothesis that DNA methylation changes in the corneal endothelial tissue of patients correlate with late onset FECD.
Methods:
Total DNA was extracted from 4 FECD endothelial samples retrieved from patients undergoing endothelial keratoplasty due to clinically diagnosed end-stage FECD and from 2 normal endothelial samples obtained from an eye bank. The Illumina Infinium Methylation 450k assay was used to perform global methylation analysis of over 485,000 methylation sites annotated to the coding and noncoding regions of over 99% RefSeq genes. We compared methylation profiles of a single FECD patient sample and of a sample pool derived from 3 FECD patients to contrast individual patient changes with broader population-level alterations. Beta values derived from the arrays were analyzed in R and Microsoft Excel.
Results:
The correlation structure of the patient data was consistent with the experimental variables, such that the single FECD patient clustered away from the normal and pooled samples. The FECD samples were generally hypermethylated relative to the normal controls in those sites in which methylation levels differ between FECD and normal patient samples. The 50 most highly methylated sites were annotated to genes involved in cell migration, cytoskeletal reorganization, and ion transport. Sites within TCF4, a gene previously shown to be significantly associated with FECD, were also hypermethylated in the FECD samples compared to the control samples.
Conclusions:
Global hypermethylation changes appear to occur in FECD and may result in the decreased expression of genes involved in cell migration, cytoskeletal reorganization, and ion transport. DNA methylation changes result in altered gene expression patterns in several human diseases, and our results suggest that altered DNA methylation patterns may likewise contribute to the etiology of late-onset FECD.