Abstract
Organoids derived from stem cells become increasingly important to study human development and to model disease. However, methods are needed to control and study spatio-temporal patterns of gene expression in organoids. To this aim, we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatio-temporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. High-resolution spatial transcriptomic and single-cell analyses showed that this local induction was sufficient to generate stereotypically patterned organoids in three dimensions and revealed new insights into SHH’s contribution to gene regulation in neurodevelopment.
With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
In this new version of our manuscript, we provide an extensive characterization, based on spatial transcriptomic and single-cell RNA sequencing analyses, of neural organoids upon localized induction of Sonic Hedgehog (SHH). These data are shown in a new panel of Figure 3 (previously Figure 4), the new Figure 4 (previously not present), and supplementary figures 5, 6 and 7. The previous Figure 2 is now reported in the Supplementary materials as Figure S1, and previous Figure 3 is now Figure 2. The abstract, main text and the supplementary text have been updated accordingly. Given new contributions, the order of the authors has been updated.
