Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo

Stem cell-derived retinal organoids recapitulate many landmarks of in vivo differentiation but lack functional maturation of distinct cell types, especially photoreceptors. Using comprehensive temporal transcriptome analyses, we show that transcriptome shift from postnatal day 6 (P6) to P10, associated with morphogenesis and synapse formation during mouse retina development, was not evident in organoids, and co-expression clusters with similar patterns included different sets of genes. Furthermore, network analysis identified divergent regulatory dynamics between developing retina in vivo and in organoids, with temporal dysregulation of specific signaling pathways and delayed or reduced expression of genes involved in photoreceptor function(s) and survival. Accordingly, addition of docosahexaenoic acid and fibroblast growth factor 1 to organoid cultures specifically promoted the maturation of photoreceptors, including cones. Our study thus identifies regulatory signals deficient in developing retinal organoids and provides experimental validation by producing a more mature retina in vitro, thereby facilitating investigations in disease modeling and therapies. [Display omitted] •Temporal delay in cell-type-specific gene expression in developing retina organoids•Dysregulation of signaling pathways during retina development in vitro•Altered expression of genes associated with photoreceptor maturation in organoids•Improved biogenesis and maintenance of photoreceptors by DHA and FGF1 Swaroop and colleagues performed transcriptome analysis of developing mouse retina in vivo and in organoids. Retinal organoid transcriptomes revealed altered expression of cell-type-specific genes associated with functional maturation and dysregulation of signaling pathways. Addition of DHA and FGF1 to organoid cultures facilitated an early and improved differentiation of photoreceptors.