Single-cell spatial transcriptomics and snRNA-seq decoding the organizational principles of functional modules in the mouse amygdala

The amygdala is a functionally heterogeneous nuclear complex comprising multiple subnuclei that orchestrate diverse behaviors, making it essential for survival and reproduction. However, the precise neural mechanisms underlying these heterogeneous functions remain elusive, primarily due to limited knowledge of the amygdalas cellular heterogeneity, developmental origins, spatial organization, and gene expression profiles. Here, we integrate single-cell-resolution spatial transcriptomics with precise anatomical dissection and single-nucleus RNA sequencing to systematically map the subnuclear enrichment patterns of amygdalar cell types. We further demonstrate that developmental origin determines subnuclear positioning and propose a novel functional modular architecture based on cellular composition and gene expression signatures. Furthermore, we reveal that the central amygdala (CEA) exhibits developmental heterogeneity, with Isl1+ neurons in its medial subdivision (CEAm) predominantly originating from hypothalamic progenitors. Our findings establish a spatially resolved cellular and molecular framework for investigating amygdalar functions at cellular type resolution and understanding amygdala-related neuropsychiatric disorders.