Multi-omics analysis identifies coordination and hierarchy of transcription factors controlling specific epithelial cell fates in corneal epithelium [Bulk RNA-seq]

The homeostasis of the transparent corneal epithelium in the eye is maintained by the proliferation and differentiation of limbal stem cells that possess the proper cell fate. A potential disease mechanism underlying corneal opacity has been proposed to be limbal stem cells acquiring the cell fate of keratinocytes in the non-transparent epidermis. In this study, we performed a multi-omics analysis of human limbal stem cells derived from the cornea and keratinocytes from the epidermal stratum basale and characterized the similar yet distinct molecular signatures of these cells. By gene regulatory network analysis, we identified cell fate defining transcription factors and their regulatory hierarchy that are shared by the two cell types and those that regulate specific epithelial programs. Our findings indicate that shared transcription factors often regulate limbal stem cell-specific transcription factors. Single-cell RNA-seq analysis of the cornea and the epidermis confirms the shared and specific transcription factor expression patterns in the stem cells of these tissues. Finally, we showed that genes associated with corneal opacity can cooperatively be targeted by the shared and limbal stem cell-specific transcription factors. By characterizing molecular signatures, our study uncovers the distinct regulatory circuitry controlling limbal stem cell fates and corneal opacity. Overall design: siRNA knockdown of PAX6 and FOSL2 in various Limbal stem cells