03016nas a2200517   4500000000100000000000100001008004100002260001200043653002900055653002200084653001000106653003200116653002300148653001700171653001400188653003100202653001700233653001100250653003000261653001400291653001200305653001400317653003500331653004100366653002700407100001300434700002200447700002700469700002200496700001600518700002300534700002200557700001800579700002300597700002000620700001800640700002000658700002000678700002200698700002400720245008400744300001200828490000800840520163600848022001402484       2023                            d  c2023-0910aAutism Spectrum Disorder10aAutistic Disorder10aBrain10aCRISPR-Associated Protein 910aCRISPR-Cas Systems10aCell Lineage10aChromatin10aDevelopmental Disabilities10aGene Editing10aHumans10aLoss of Function Mutation10aMosaicism10aNeurons10aorganoids10aRNA, Guide, CRISPR-Cas Systems10aSingle-Cell Gene Expression Analysis10aTranscription, Genetic1 aChong Li1 aJonas Simon Fleck1 aCatarina Martins-Costa1 aThomas R. Burkard1 aJan Themann1 aMarlene Stuempflen1 aAngela Maria Peer1 aÁbel Vertesy1 aJamie B. Littleboy1 aChristopher Esk1 aUlrich Elling1 aGregor Kasprian1 aNina S. Corsini1 aBarbara Treutlein1 aJuergen A. Knoblich00aSingle-cell brain organoid screening identifies developmental defects in autism  a373-3800 v6213 aThe 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.  a1476-4687