Cell types of the human retina and its organoids at single-cell resolution: developmental convergence, transcriptomic identity, and disease map

Abstract

How closely human organoids recapitulate cell-type diversity and cell-type maturation of their target organs is not well understood. We developed human retinal organoids with multiple nuclear and synaptic layers. We sequenced the RNA of 158,844 single cells from these organoids at six developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable 'developed' state at a rate similar to human retina development in vivo and the transcriptomes of organoid cell types converged towards the transcriptomes of adult peripheral retinal cell types. The expression of disease-associated genes was significantly cell-type specific in adult retina and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in adult human retinas.

Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development

“…S4J-Q). Of particular interest is CYP26A1, a transcript implicated in marking a rod-free zone in the chicken (da Silva and Cepko, 2017), and selectively expressed in RPCs and Müller glia of both the developing and mature primate fovea (Cowan et al, 2019; Peng et al, 2019). We then validated enrichment of CYP26A1 and DIO2 transcript expressions and co-expression of SFRP1 or RLBP1 within macula cells of the GW18 retina (Fig 4B-C).…”

“…Bulk RNA-Seq cannot resolve cell-type specific changes in gene expression. Furthermore, the extent to which retinal organoids fully recapitulate in vivo development at the individual cell level is still not entirely clear (Cowan et al, 2019). The combinatorial use of scRNA-Seq and human developing retinal tissue in our dataset overcomes some of these limitations.…”

“…30 or 42 days in culture organoids). This suggests that while the treatment of organoids with DAPT does stimulate photoreceptor specification, the differentiation trajectory of these organoid-derived cones varies markedly from that seen in vivo , even though more mature organoid-derived cones and native cones eventually show broadly similar gene expression profiles (Cowan et al, 2019).…”

“…The emergence of single-cell RNA sequencing (scRNA-Seq) technologies provides a powerful tool to comprehensively classify cell types of the central nervous system and the gene regulatory networks that control their development (Fan et al, 2018; Farrell et al, 2018; Liu et al, 2017; Tasic et al, 2018; Wagner et al, 2018; Zeisel et al, 2018; Zhong et al, 2018). Studies in both macaque and human have examined the diversity of cellular subtypes within the mature retina (Cowan et al, 2019; Lukowski et al, 2019; Peng et al, 2019; Voigt et al, 2019). Furthermore, recent studies in mouse using scRNA-Seq analysis have identified changes in gene expression across retinal development, including progenitor maturation and specification/differentiation of each of the major classes of retinal cell types (Buenaventura et al, 2019; Clark et al, 2019; Lo Giudice et al, 2019).…”

Otx2 and Oc1 directly regulate the transcriptional program of cone photoreceptor development

“…The data presented here bring a greater understanding of the processes that might lead to the development of cell-based therapies to treat retinal disease. In particular, human iPSC-derived organoids produce few cones, especially relative to rod production 18,67 . The engraftment of stem-cell derived cones, the generation of cones from endogenous stem cells, and/or the use of cones for in vitro screens of potential therapies, would all benefit from an efficient production of cones.…”