Spatiotemporal, optogenetic control of gene expression in organoids

Nat Methods. 2023 Oct;20(10):1544-1552. doi: 10.1038/s41592-023-01986-w. Epub 2023 Sep 21.

Abstract

Organoids derived from stem cells have become an increasingly important tool for studying human development and modeling disease. However, methods are still needed to control and study spatiotemporal patterns of gene expression in organoids. Here we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes in programmable spatiotemporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. Spatial and single-cell transcriptomic analyses showed that this local induction was sufficient to generate stereotypically patterned organoids 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.

MeSH terms

  • Cell Differentiation
  • Gene Expression
  • Hedgehog Proteins* / metabolism
  • Humans
  • Optogenetics*
  • Organoids / metabolism

Substances

  • Hedgehog Proteins