Description
Title: Extracellular matrix gene dysregulation and alternative splicing in Fuchs endothelial corneal dystrophy stratified by TCF4 repeat expansion status.
Purpose: Fuchs Endothelial Corneal Dystrophy (FECD) is characterised by abnormal extracellular matrix (ECM) protein accumulation and corneal endothelial cell (CEC) loss. Most European cases (~80%) are associated with a pathogenic CTG repeat expansion (≥50 repeats) in the TCF4 gene. Here we aim to define transcriptomic alterations associated with TCF4 expansion status and their contribution to ECM dysregulation.
Methods: RNA-Seq data was generated from CECs derived from FECD patients with TCF4 repeat expansion (Exp+, n=3), without TCF4 repeat expansion (Exp-, n=3) and healthy controls (n=4). Differential gene expression analysis was performed using DESeq2 and ECM-related genes were identified though Gene Ontology (GO) enrichment analysis (PANTHER). Alternative splicing events were assessed using rMATS and visualized and mapped using Intergrative Genomics Viewer (IGV) and Sashimi plots.
Results: GO analysis identified 527 ECM-related genes. Differential expression analysis revealed distinct patterns of ECM gene dysregulation between groups. In Exp+ FECD, 63 genes were upregulated and 51 downregulated compared to controls, whereas in Exp- FECD, 23 genes were upregulated and 21 downregulated, with 15 genes shared in each category. rMATS identified 14 ECM-related genes with significant alternative splicing changes unique to Exp+, 4 unique to Exp-, and 14 shared between groups. Notably, in the FN1 gene, inclusion of the EDA and EDB domains, that are critical for FN1 protein function, was increased in the Exp+, while only EDB inclusion was increased in Exp- cases.
Conclusion: TCF4 repeat expansion status is associated with distinct ECM gene expression and splicing alterations patterns, likely contributing to FECD pathogenesis through abnormal ECM accumulation.
Lay Abstract
Background: Fuch’s Endothelial Dystrophy (FECD) is a common eye disease that usually develops with age and affects both eyes. It is characterized by the abnormal accumulation of proteins in a thin inner layer of the cornea which helps cornea maintain clarity and function. These changes progressively lead to blurred vision and glare. Most people with FECD (~80% of European cases) harbor the same genetic mutation in the TCF4 gene.
Purpose: This study aims to understand how the most common TCF4 mutation affects the proteins in this important corneal layer in people with FECD.
Methods: We used advanced computer analysis to study genetic data from three groups: FECD patients with the TCF4 mutation, FECD patients without the mutation, and healthy individuals. We analyzed the differences in the genes expressed to this layer, including both activity and structure.
Results: We identified 527 genes that encode proteins related to this corneal layer and found differences in their activity. Some key genes also showed structural changes depending on the presence of TCF4 mutation.
Conclusion: The TCF4 mutation is associated with distinct changes in gene activity and structure, which likely contribute to FECD development through protein accumulation in the cornea.
| Lay Title | Investigating how the most common genetic cause of Fuchs endothelial corneal dystrophy is associated with abnormal protein expression. |
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| Role | Other |