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To identify possible genetic variants influencing expression of  EPHA2  (Ephrin-receptor Type-A2), a tyrosine kinase receptor that has been shown to be important for lens development and to contribute to both congenital and age related cataract when mutated, the extended promoter region of  EPHA2  was screened for variants. SNP rs6603883 lies in a PAX2 binding site in the  EPHA2  promoter region. The C (minor) allele decreased  EPHA2  transcriptional activity relative to the T allele by reducing the binding affinity of PAX2. Knockdown of  PAX2  in human lens epithelial (HLE) cells decreased endogenous expression of  EPHA2 . Whole RNA sequencing showed that extracellular matrix (ECM), MAPK-AKT signaling pathways and cytoskeleton related genes were dysregulated in  EPHA2  knockdown HLE cells. Taken together, these results indicate a functional non-coding SNP in  EPHA2  promoter affects PAX2 binding and reduces EPHA2 expression. They further suggest that decreasing  EPHA2  levels alters MAPK, AKT signaling pathways and ECM and cytoskeletal genes in lens cells that could contribute to cataract. These results demonstrate a direct role for PAX2 in EPHA2 expression and help delineate the role of EPHA2 in development and homeostasis required for lens transparency.

Functional non-coding polymorphism in an EPHA2 promoter PAX2 binding site modifies expression and alters the MAPK and AKT pathways