PT  - JOURNAL ARTICLE
AU  - Ivano Legnini
AU  - Lisa Emmenegger
AU  - Alessandra Zappulo
AU  - Ricardo Wurmus
AU  - Anna Oliveras Martinez
AU  - Cledi Cerda Jara
AU  - Anastasiya Boltengagen
AU  - Talé Hessler
AU  - Guido Mastrobuoni
AU  - Agnieszka Rybak-Wolf
AU  - Stefan Kempa
AU  - Robert Zinzen
AU  - Andrew Woehler
AU  - Nikolaus Rajewsky
TI  - Spatio-temporal, optogenetic control of gene expression in organoids
AID  - 10.1101/2021.09.26.461850
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2021.09.26.461850
4099  - http://biorxiv.org/content/early/2022/02/09/2021.09.26.461850.short
4100  - http://biorxiv.org/content/early/2022/02/09/2021.09.26.461850.full
AB  - 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 StatementThe authors have declared no competing interest.