[en] We report the generation and analysis of single-cell RNA-Seq data (> 38,000 cells) from mouse native retinae and induced pluripotent stem cell (iPSC)-derived retinal organoids at four matched stages of development spanning the emergence of the major retinal cell types. We combine information from temporal sampling, visualization of 3D UMAP manifolds, pseudo-time and RNA velocity analyses, to show that iPSC-derived 3D retinal organoids broadly recapitulate the native developmental trajectories. However, we observe relaxation of spatial and temporal transcriptome control, premature emergence and dominance of photoreceptor precursor cells, and susceptibility of dynamically regulated pathways and transcription factors to culture conditions in retinal organoids. We demonstrate that genes causing human retinopathies are enriched in cell-type specifying genes and identify a subset of disease-causing genes with expression profiles that are highly conserved between human retinae and murine retinal organoids. This study provides a resource to the community that will be useful to assess and further improve protocols for ex vivo recapitulation and study of retinal development.
Disciplines :
Genetics & genetic processes
Author, co-author :
Georges, Anouk ; Centre Hospitalier Universitaire de Liège - CHU > > Service d'ophtalmologie
Lavergne, Arnaud ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale
Mandai, Michiko; Laboratory for Retinal Regeneration, Center for Developmental Biology, RIKEN, Kobe, Japan
We are grateful to Tomoyo Hashiguchi for teaching the retinal organoid culture protocol and to Tomohiro Masuda and Akishi Onishi for their comments and suggestions. We thank the GIGA Genomics platform for their help both with scRNA-Seq experiments and early bio-informatic analyses (especially Wouter Coppieters and Benoit Charloteaux). We are grateful to Vincent Lambert for assisting with dissection of NaR. This work was financially supported by the “King Baudouin Foundation”, the “Global Ophthalmology Awards Program (GOAP) from Bayer”, and the “Fonds Leon Fredericq”. L.D. and L.N. are respectively postdoctoral researcher and senior associate researcher of the FRS-FNRS.
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