3D epigenomic landscape of human retinal pigment epithelium [RNA-seq]

While ongoing RPE cells transplantation clinical trials worldwide, the absence of standardized quality metrics for stem cell-derived RPE represents a significant gap. In this study, we aim to systematically dissect epigenomic divergence among human primary RPE (hRPE), induced pluripotent stem cell-derived RPE (iPSC-RPE), and immortalized ARPE-19 cells through multi-omic analyses.

Our study elucidated the distinct functional characteristics of the three types of RPE and their underlying epigenetic regulatory mechanisms, with a particular focus on the development and functional maturation of iPSC-RPE. We further revealed cell-type-specific regulatory blueprints: hRPE exhibits strong extracellular matrix (ECM) organization capacity through 3D-epigenomic (3D genome folding and epigenomic state) regulation, as exemplified by the enrichment of the RUNX1 motif, whereas iPSC-RPE retains signatures of RPE development and weak ECM function, marked by transcription factors such as Hand1, OTX2, PAX6, and ECM-associated genes.