TCF4 expansion–associated loss of FN1 intron retention drives extracellular matrix accumulation in Fuchs endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD), which is characterized by excessive extracellular matrix (ECM) accumulation and corneal endothelial cell degeneration, has trinucleotide repeat expansion in TCF4 as a major genetic risk factor. While aberrant splicing has been implicated in FECD pathogenesis, the mechanistic link between splicing abnormalities and disease-specific features remains unclear. Here, we investigated the intron retention (IR) patterns in corneal endothelial cells from FECD patients with TCF4 expansion. Initial RNA-Seq analysis using rMATS identified 486 upregulated and 89 downregulated IR events in expansion-positive FECD compared to controls. Subsequent analysis with the more stringent IRFinder algorithm revealed 10 upregulated IR events distributed across nine genes and, notably, 6 downregulated events exclusively localized within FN1, a major component of corneal guttae. While DEXSeq analysis showed reduced expression across FN1 gene regions in FECD samples, subsequent qPCR validation in an independent cohort demonstrated significantly elevated FN1 expression in both expansion-positive and expansion-negative FECD samples compared to controls. This paradoxical finding suggests that the loss of normal IR-mediated regulation may contribute to pathological FN1 overexpression in FECD. Gene ontology analysis of IR-associated genes revealed enrichment in RNA splicing and ECM-related pathways, supporting a role for IR in disease pathogenesis. Our findings reveal an association between TCF4 expansion and reduced FN1 intron retention, which correlates with ECM accumulation, suggesting a potential link between RNA processing alterations and hallmark features of FECD. These results suggest that targeting IR-mediated regulation could represent a therapeutic strategy for preventing disease progression.