TY - JOUR
KW - Autism Spectrum Disorder
KW - Autistic Disorder
KW - Brain
KW - CRISPR-Associated Protein 9
KW - CRISPR-Cas Systems
KW - Cell Lineage
KW - Chromatin
KW - Developmental Disabilities
KW - Gene Editing
KW - Humans
KW - Loss of Function Mutation
KW - Mosaicism
KW - Neurons
KW - organoids
KW - RNA, Guide, CRISPR-Cas Systems
KW - Single-Cell Gene Expression Analysis
KW - Transcription, Genetic
AU - Chong Li
AU - Jonas Simon Fleck
AU - Catarina Martins-Costa
AU - Thomas R. Burkard
AU - Jan Themann
AU - Marlene Stuempflen
AU - Angela Maria Peer
AU - Ábel Vertesy
AU - Jamie B. Littleboy
AU - Christopher Esk
AU - Ulrich Elling
AU - Gregor Kasprian
AU - Nina S. Corsini
AU - Barbara Treutlein
AU - Juergen A. Knoblich
AB - The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
BT - Nature
DA - 2023-09
DO - 10.1038/s41586-023-06473-y
IS - 7978
LA - eng
N2 - The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
PY - 2023
SP - 373
EP - 380
T2 - Nature
TI - Single-cell brain organoid screening identifies developmental defects in autism
VL - 621
SN - 1476-4687
ER -