Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC Commitment in Early Human Retinogenesis

Summary

The development of the mammalian retina is a complicated process involving the generation of distinct types of neurons from retinal progenitor cells (RPCs) in a spatiotemporal-specific manner. The progression of RPCs during retinogenesis includes RPC proliferation, cell-fate commitment, and specific neuronal differentiation. In this study, by performing single-cell RNA sequencing of cells isolated from human embryonic stem cell (hESC)-derived 3D retinal organoids, we successfully deconstructed the temporal progression of RPCs during early human retinogenesis. We identified two distinctive subtypes of RPCs with unique molecular profiles, namely multipotent RPCs and neurogenic RPCs. We found that genes related to the Notch and Wnt signaling pathways, as well as chromatin remodeling, were dynamically regulated during RPC commitment. Interestingly, our analysis identified that CCND1, a G ₁-phase cell-cycle regulator, was coexpressed with ASCL1 in a cell-cycle-independent manner. Temporally controlled overexpression of CCND1 in retinal organoids demonstrated a role for CCND1 in promoting early retinal neurogenesis. Together, our results revealed critical pathways and novel genes in early retinogenesis of humans.

Graphical Abstract

Highlights

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  Fate transition occurring in RPC is concomitant with onset of retinal neurogenesis

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  Molecular dynamics underlying RPC commitment are dissected

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  CCND1 promotes retinal neurogenesis in a cell-cycle-independent manner

Abstract

Retinogenesis is a complicated process involving generating distinct types of neurons from retinal progenitor cells (RPCs) in a spatiotemporal-specific manner. By taking the advantage of hESC-derived retinal organoids and single-cell RNA sequencing, Fan, Liu, Hu and colleagues show the genetic program dynamics during RPC progression. Their results revealed critical pathways and novel genes involved in early retinogenesis of humans.