Whole-brain clearing reveals region- and cell type-specific imbalances in inhibitory neurons in a mouse model for Kleefstra Syndrome

GABAergic inhibition is essential for balanced brain function and is frequently disrupted in neurodevelopmental disorders such as autism spectrum disorder (ASD). The inhibition is generated by a diverse population of GABAergic interneurons, which differ in subtype composition and spatial density across the brain. Here, we applied an unbiased whole-brain clearing and light-sheet imaging approach to systematically map the distribution of the three major GABAergic interneuron subtypes – Parvalbumin-positive (PV⁺), Somatostatin-positive (SST⁺), and Vasoactive Intestinal Polypeptide-positive (VIP⁺) cells – across the mouse brain in a model of Kleefstra Syndrome ( Ehmt1 ^+/− ), a monogenic intellectual disability disorder with a strong ASD component. Analyzing 895 brain regions we identified widespread, cell type– and region-specific alterations in GABAergic populations. Notably, we observed increased VIP⁺ neuron density in the Ehmt1 ^+/− cortex and decreased SST⁺ neuron density in sensory cortical and subcortical regions. In the basolateral amygdala (BLA), PV⁺ interneurons exhibited precocious maturation already at the juvenile stage, which persisted into adulthood and was associated with enhanced inhibitory input onto BLA principal neurons. We here demonstrate that Ehmt1 haploinsufficiency results in region– and cell-type specific changes throughout the brain. These results underscore the value of whole-brain, high-resolution mapping approaches in uncovering previously unrecognized patterns of neural vulnerability in neurodevelopmental disorders.