Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism

Autism spectrum disorders (ASD) are highly heritable neurodevelopmental conditions with major contributions from rare genetic variants. Most studies have focused on cortical mechanisms; even growing evidence implicates subcortical circuits in ASD etiology. To systematically map developmental and molecular alterations beyond the cortex, we profiled lineage relationships across five brain regions in an ASD mouse model. Most prominent changes emerged in the striatum, a hub for learning and motor control. Furthermore, we performed single-nucleus multiomic profiling of human putamen from ASD and neurotypical donors revealed cell-type-specific transcriptomic and regulatory alterations. Differential expression converged on synaptic and energy metabolic dysfunctions in D1 striosome medium spiny neurons (MSNs), coupled with astrocytic remodeling of synaptic support. Gene regulatory network analysis identified EGR3 and EGR1 as key transcriptional regulators of ASD-associated programs of D1 MSNs. Together, these results establish the striatum as a central node of ASD convergence and provide a multiomic resource for dissecting its subcortical mechanisms.