In-depth examination of an iPSC-derived model of human eye development identifies multiple embryonic cell types of critical importance to ocular genesis and disease

Human ocular cell cultures commonly used for disease modeling recapitulate later stages of specialized tissue differentiation, requiring the development of new models to test genetic variants affecting earlier embryonic time points. Here we provide an in-depth characterization of a recently presented 2D model mimicking whole eye development derived from human iPSCs, known as SEAMs. Our study focused on evaluating both morphological and transcriptomic changes occurring at several time points as SEAMs formed over the course of a 28-day differentiation process, with an emphasis on an intermediate stage (Day 14) and a late stage (Day 28) of SEAM development. Transcriptomic profiling using bulk and single cell RNA sequencing was followed by clustering/annotation, pathway enrichment, ligand-receptor interaction, and differentiation trajectory analyses. Bulk RNA sequencing identified 7 major expression trends and their drivers across all time points. Single cell analyses revealed 12 and 14 partially overlapping, yet distinct clusters at Day 14 and 28, respectively, showing a progression from less (optic cup and anterior segment precursors) to more (mature retina, retinal pigmented epithelium, lens, and cornea, including limbal epithelial stem cells) differentiated cell types based on characteristic transcriptional signatures, corroborated by pseudotime and RNA velocity analyses. Establishment of a temporal baseline of SEAM development enables future investigations into how disease-causing variants may disrupt the early stages of human eye development leading to complex ocular phenotypes. Overall design: SEAM cultures were processed for transcriptomic profiling at Day 0 (reference), 14 and 28 using bulk (2 biological replicates) and single cell (1 biological replicate) RNA sequencing.