ArticleNature methods2023
Spatiotemporal, optogenetic control of gene expression in organoids.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed, 81 citations in OpenAlex.
- Article
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- Tutorial: interrogating biology using organoid technologies.Nature protocols · 2026Review
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- Lights up on the embryonic dance: tools and applications of optogenetics in developmental biology.Genes & development · 2026Review
- Developmentally inspired synthetic kidney engineering.Nature biotechnology · 2026Review
- Signal control during tissue regeneration in adult animals.Nature reviews. Molecular cell biology · 2026Review
- Spatiotemporal cell type deconvolution leveraging tissue structure.bioRxiv : the preprint server for biology · 2026Article
- Organizers in a dish: Modeling human CNS morphogenesis.Developmental cell · 2026Review
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Optogenetic BlueGENEs engineered into a human safe harbor locus.Nucleic acids research · 2026Article
- Direct neuronal reprogramming for neurological diseases: applications, translational Challenges, and future directions.Frontiers in neuroscience · 2026Review
- Human stem cell-based embryo models: from self-organization to recapitulating development.Frontiers in cell and developmental biology · 2026Review
- Multiscale Construction, Evaluation, and Application of Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Spatial omics in 3D culture model systems: decoding cellular positioning mechanisms and microenvironmental dynamics.Journal of translational medicine · 2025Review
- Engineered Bacteria-Nano Hybrid System: The Intelligent Drug Factory for Next-Generation Cancer Immunotherapy.Pharmaceutics · 2025Review
- Engineering development: From the repressilator and toggle switch to synthetic developmental biology.Developmental biology · 2025Review
- Engineering human neuronal diversity: Morphogens and stem cell technologies for neurodevelopmental biology.Stem cell reports · 2025Review
- Organoid bioprinting to pattern the matrix microenvironment.Current opinion in biomedical engineering · 2025Article
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Authors and funding
14 authors at 2 institutions in 3 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.