Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity

• Published in: Cell reports methods Vol. 3; no. 8; p. 100548
• Main Authors: Tresenrider, Amy, Sridhar, Akshayalakshmi, Eldred, Kiara C, Cuschieri, Sophia, Hoffer, Dawn, Trapnell, Cole, Reh, Thomas A
• Format: Journal Article
• Language: English
• Published: United States Elsevier 28.08.2023
• Subjects: Cell Differentiation; Critical Pathways; Humans; Neurons; Organoids; Retina; neuron; single-cell sequencing; retina; organoids; cell signaling
• ISSN: 2667-2375; 2667-2375
• DOI: 10.1016/j.crmeth.2023.100548

With a critical need for more complete models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× methods produce highly concordant cell-class compositions and then expand sci-Plex to analyze the cell-class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to 6 weeks later. Our data show sci-Plex's potential to dramatically scale up the analysis of treatment conditions on relevant human models.