Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level [Spatial Transcriptomics]

Molecular information on the very early stages of human retinal development remains scarce due to limitations in obtaining human eye samples of less than six weeks old. Pluripotent stem cell derived retinal organoids provide an unprecedented opportunity for studying human retinal development; however their ability to fully recapitulate early retinal development has not been assessed as yet. Using a combination of scRNA-Seq and ST approaches, we present for the first time a genome wide, single cell spatio-temporal transcriptome of retinal organoid development. Our data demonstrate that retinal organoids recapitulate key events of retinogenesis including optic vesicle/cup formation, formation of a putative ciliary margin zone, emergence of RPCs and their precise and orderly differentiation to various types of retinal neurons. Combining the scRNA- with scATAC-Seq data, we were able to reveal cell type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal cell types. Our work provides the first integrated molecular and spatial atlas of human retinal organoid development that could be used to identify novel genes and key pathways that underpin human retinal development and function. Overall design: Comparative gene expression profiling analysis of RNA-seq data during retinal development using 8 samples (day10, 20, 35, 45, 60, 90, 150 and 210) of hiPSC-derived retinal organoids