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Single Cell RNA-Sequencing Reveals the Inner Complexity of Stem Cell-derived Retinal Organoids

Review of “Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina” from STEM CELLS by Stuart P. Atkinson

Recent advances have permitted the derivation of three‐dimensional retinal organoids containing structures akin to the developing eye from human pluripotent stem cells [1, 2]; however, we currently lack robust methods to accurately define and characterize the heterogeneous cell types within these organoids over time. 

While a few studies have reported single-cell RNA sequencing (scRNA‐Seq) in human retinal tissue and organoids [3-5] (See the STEM CELLS article here!), researchers from the laboratory of Majlinda Lako (Newcastle University, Newcastle-upon-Tyne, UK) postulated that such studies have yet to reveal the full complexity of retinal organoids. In their new STEM CELLS study, Collin et al. hoped to now accomplish this feat via the application of high-throughput Integrated Fluidic Circuits (IFC) for scRNA‐Seq to interrogate hESC‐derived retinal organoids through a differentiation time course [6]. 

The authors began by generating retinal organoids from human embryonic stem cells (hESCs) and applying scRNA‐Seq at three distinct time points (60, 90, and 200 days) to reveal the presence of nine different cell clusters. Encouragingly, five of the cultures corresponded crucial retinal cell types - retinal pigment epithelium, retinal ganglion cells, cone photoreceptors, rod photoreceptors, and Müller glia - while the other four clusters expressed genes typical of mitotic cells, extracellular matrix components, and homeostasis.

Interestingly, further analysis of cell clustering established that while mitotic cells and retinal ganglion cells exhibited a decreasing presence over time, the increased formation of distinct retinal pigment epithelium and the emergence of cone and rod photoreceptors from photoreceptor precursors occurred over time accompanied by a general rise in Müller glia number. Overall, pseudo‐time analysis of cluster evolution suggested that the generation of retinal organoids from hESCs resembled in vivo development, as evidenced by the mitotic cell cluster starting the differentiation journey with a vast majority of Müller glia completing the timeline.

Overall, the authors of this fascinating new study establish the potential of scRNA‐Seq to reveal the inherent complexity of retinal organoids and, in doing so, demonstrate how hESC differentiation into retinal organoids mimics healthy retinal development. Can this strategy now be applied to other organoid systems and perhaps disease models?

For more on organoids and single cell analysis, stay tuned to the Stem Cells Portal


  1. Nakano T, Ando S, Takata N, et al., Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell 2012;10:771-785.
  2. Eiraku M, Takata N, Ishibashi H, et al., Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 2011;472:51-6.
  3. Welby E, Lakowski J, Di Foggia V, et al., Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells. Stem Cell Reports 2017;9:1898-1915.
  4. Phillips MJ, Jiang P, Howden S, et al., A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types. Stem Cells 2018;36:313-324.
  5. Langer KB, Ohlemacher SK, Phillips MJ, et al., Retinal Ganglion Cell Diversity and Subtype Specification from Human Pluripotent Stem Cells. Stem Cell Reports 2018;10:1282-1293.
  6. Collin J, Queen R, Zerti D, et al., Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina. STEM CELLS 2019;37:593-598.