Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease

Abstract

The homeostasis of the transparent corneal epithelium in the eye is maintained by limbal stem cells with proper cell fates. A potential disease mechanism underlying corneal opacity has been proposed to be limbal stem cells acquiring characteristics of keratinocytes of the non-transparent epidermis. The precise cell fate differences between these two epithelial cells are however unknown. We performed a multi-omics analysis of human limbal stem cells derived from the cornea and keratinocytes from the epidermis, and characterized their similar yet distinct molecular signatures. With gene regulatory network analyses, we identified cell fate defining transcription factors and their regulatory hierarchy that are shared but also distinct for specific epithelial programs. Our findings indicate that shared transcription factors such as p63, FOXC1 and FOSL2 often regulate limbal stem cell-specific transcription factors such as PAX6, SMAD3 and OTX1. Single-cell RNA-seq analysis confirms the shared and specific transcription factors controlling the stem cell fates of the cornea and the epidermis. Importantly, genes associated with corneal opacity can cooperatively be targeted by the shared and limbal stem cell-specific transcription factors. Finally, by leveraging these key transcription factors, we identified FOSL2 as a novel candidate associated with corneal opacity. By characterizing molecular signatures, our study uncovers the distinct regulatory circuitry controlling limbal stem cell fates and corneal opacity.