Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, the lack of knowledge of the developmental origin, cell fate determination, and identity of human LSCs hindered the establishment of differentiation protocols for hPSC-derived LSCs and hold back their clinical application. Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells. Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hPSCs-derived LSCs and their progeny - the transit amplifying cells. Furthermore, several new makers of LSCs were identified, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.