A Multiplex Human Pluripotent Stem Cell Platform Defines Molecular and Functional Subclasses of Autism-Related Genes

Autism is a clinically heterogeneous neurodevelopmental disorder characterized by impaired social interactions, restricted interests, and repetitive behaviors. Despite significant advances in the genetics of autism, understanding how genetic changes perturb brain development and affect clinical symptoms remains elusive. Here, we present a multiplex human pluripotent stem cell (hPSC) platform, in which 30 isogenic disease lines are pooled in a single dish and differentiated into prefrontal cortex (PFC) lineages to efficiently test early-developmental hypotheses of autism. We define subgroups of autism mutations that perturb PFC neurogenesis and are correlated to abnormal WNT/βcatenin responses. Class 1 mutations (8 of 27) inhibit while class 2 mutations (5 of 27) enhance PFC neurogenesis. Remarkably, autism patient data reveal that individuals carrying subclass-specific mutations differ clinically in their corresponding language acquisition profiles. Our study provides a framework to disentangle genetic heterogeneity associated with autism and points toward converging molecular and developmental pathways of diverse autism-associated mutations. [Display omitted] •hPSC-based multiplex platform for interrogation of autism-associated mutations•Prefrontal cortex paradigm in hPSCs identifies autism-related neurogenesis defects•Abnormal WNT/βcatenin responses in class of autism genes with neurogenesis defects•Endophenotypes in hPSCs correlate with clinical data in autism patients Large-scale sequencing studies have identified hundreds of autism-associated genes, yet a systematic understanding of their functional consequences during human neurodevelopment remains elusive. Cederquist et al. develop a pooled human pluripotent stem cell-based phenotypic screening platform and identify subclasses of autism genes with convergent molecular, developmental, and clinical associations.