Altered endothelial cell microRNA DNA methylation patterns in Fuchs endothelial corneal dystrophy

Abstract

Purpose : There is accumulating evidence that miRNAs function as key players in the pathophysiology of human diseases. In the corneal endothelium of patients with Fuchs endothelial corneal dystrophy (FECD), multiple miRNAs have been found to be significantly downregulated, suggesting that miRNAs may play an important role in this disease. The purpose of this study was to test the hypothesis that miRNA sequences are hypermethylated in the corneal endothelium of FECD patients.

Methods : The endothelial tissue of 9 patients with FECD undergoing corneal transplantation by endothelial keratoplasty (8 DSAEK and 1 DMEK) was collected at the time of surgery and promptly processed for DNA isolation and bisulfite conversion. Four age- and gender-matched, normal endothelial tissue samples were processed simultaneously as controls. The Illumina Infinium Methylation 450k assay was used to perform global DNA methylation analysis of over 485,000 methylation sites annotated to the coding and noncoding regions of over 99% RefSeq genes. 2248 probes mapping to genomic regions containing miRNA sequences were analyzed. Beta values derived from the arrays were analyzed in R and Microsoft Excel.

Results : DNA methylation profiles of miRNA sequences were distinct between control and FECD samples. Differentially methylated probes (52) were identified in the FECD samples compared with the control samples (FDR = 0.01), with the majority of probes (38; 73%) being hypermethylated in the FECD samples. miR-199b was found to be the most hypermethylated gene and miR-1182 was the most hypomethylated gene in FECD samples. CpGs sites for all 38 hypermethylated probes were located in promoter regions. 12 of the 14 hypomethylated probes were located in promoter regions.

Conclusions : Our results found mainly hypermethylation of miRNA promoter sequences in corneal endothelial tissue of FECD patients. These epigenetic alterations may contribute to loss of corneal transparency in FECD through decreased endothelial expression of miRNAs and subsequent increased subendothelial extracellular matrix accumulation. These studies may improve the treatment of FECD by providing new insight into potential molecular targets for epigenetics-based therapy for the treatment of FECD.

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.