Abstract
Autism spectrum disorder (ASD) has been associated with diverse genetic factors and molecular changes. Yet, how pathophysiology emerges during development and contributes to clinical heterogeneity remains unclear. Here we use spatial and single-cell transcriptomics of genetically diverse patient-derived organoids of the prenatal cortex to map the spatial architecture of ASD pathogenesis. We find abnormal partitioning of progenitor and neuron zones alongside local patches of disorganized neurons that vary in distribution among patients. Such spatially mosaic disarray persists into neuronal maturation and is consistent with impaired adhesion between progenitors. Our findings suggest that the spatial landscape of biological processes leading to ASD may be more heterogeneous than previously thought. We propose a model in which different patterns of scattered abnormalities, arising from spatially mosaic pathogenesis during prenatal brain development, contribute to the wide range of symptoms and brain structure variations observed in ASD patients. Spatial and single-cell transcriptomics of patient-derived brain organoids reveal disrupted progenitor–neuron organization and local neuronal disarray, implicating spatially mosaic pathogenesis in autism heterogeneity.