Investigation of the TCF4 Splicing and Isoform Expressions 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 mutation. However, the causative genes of patients without expansion (RE-) remain unclear. We previously reported that the expression level of TCF4 mRNA is commonly upregulated in both groups (Okumura N, et al. Invest Ophthalmol Vis Sci. 2019). This study aims to investigate the splicing and isoform expressions of TCF4 in the corneal endothelium of patients with FECD of RE- and RE+.

Methods : Our RNA-Seq data of patients with FECD (RE-: n = 4; RE+: n=6) and healthy controls (n=7) were utilized (DDBJ Sequence Read Archive: DRA015078 and DRP006678). For a differential exon usage (DEU) analysis of the TCF4, the counting reads of each exon were determined by the HTSeq framework and then analyzed by the DEXSeq package. For a differential isoform expression analysis of the TCF4, a total of 93 TCF4 isoforms described in the Ensembl Genome Browser Database were subjected, and differentially expressed isoforms were identified by the DESeq2 package.

Results : DEXSeq detected 14 DEUs including 12 upregulated and 2 downregulated exons were detected between the RE- and control, while 27 DEUs including 6 upregulated and 21 downregulated exons were detected between the RE+ and control in the TCF4 region. Multiple DEUs among 21 downregulated ones in RE+ were located downstream of TNR. Three upregulated DEUs (E051, E084, and E085) overlapped, but no downregulated DEUs overlapped in the RE- and RE+ groups. The isoform-level differential expression analysis by DESeq2 identified 11 isoforms in the RE- and 6 isoforms in the RE+. Three isoforms including TCF4-204, TCF4-218, and TCF4-283 were commonly upregulated in the RE- and RE+. Interestingly, the E084 and E085 are in TCF4-204, and E051 is in TCF4-218.

Conclusions : Our current study indicated that TNR expansion might be associated with suppressing downstream DEUs in TCF4. The expression level of certain TCF4 isoforms and exons was upregulated regardless of the presence of TNR expansion, indicating the possibility of the common cause for FECD.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.