Investigation of the TCF4 Aberrant Splicing in the Corneal Endothelial Cells of Patients with Fuchs Endothelial Corneal Dystrophy

Abstract

Purpose : Patients with Fuchs endothelial corneal dystrophy (FECD) frequently harbor a trinucleotide repeat (TNR) expansion in the TCF4 (RE+), suggesting that TNR is the most common causative variant. However, the causative mechanisms of patients without TNR expansion (RE-) remain unclear. We previously reported that the expression level of TCF4 mRNA is commonly upregulated in both groups. However, TCF4 has numerous isoforms with different functions, and an involvement of aberrant splicing is suggested in the pathogenesis of FECD. This study investigates the differential exon usage (DEU) in the corneal endothelial cells of patients with FECD.

Methods : Our RNA-Seq data of corneal endothelial cells obtained from patients with FECD (RE-: n = 4; RE+: n=6) and those from healthy controls (n=7) were utilized (Nakagawa T, et al. Sci Rep. 2023). Two additional data sets obtained from NGS data repositories (Nikitina AS, et al. Data Brief. 2019), (Chu Y, et al. Nucleic Acids Res. 2020) were also used. For a DEU analysis of the TCF4, the counting reads of each exon were determined by the HTSeq framework and then analyzed by the DEXSeq package.

Results : In our RNA-Seq data, we detected 27 DEUs, including 6 upregulated and 21 downregulated exons in the TCF4 region between the RE+ and controls. Between the RE- and control, 15 DEUs were detected, including 13 upregulated and 2 downregulated exons. All three RNA-Seq data sets identified common 1 upregulated DEU (E174) (located upstream of TNR) and 8 downregulated DEUs in 3 exon regions (E117-E119, E139-E143) (located downstream of TNR) between RE+ and control. Conversely, no DEUs were detected in common between the RE- and controls in three RNA-Seq analyses.

Conclusions : Our findings indicated that TNR expansion may lead to expression variations in specific exons in TCF4. Further investigation into the details of aberrant splicing in the pathogenesis of FECD is anticipated to contribute to a better understanding of the disease and identify novel therapeutic targets.

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.