Patterned cPCDH expression regulates the fine organization of the neocortex

The neocortex consists of a vast number of diverse neurons that form distinct layers and intricate circuits at single-cell resolution to support complex brain functions(1). Diverse cell-surface molecules are thought to be the key to define neuronal identity and mediate inter-neuronal interaction for structural and functional organization(2–6). However, the precise mechanisms controlling the fine neuronal organization of the neocortex remain largely unclear. Here, by integrating in-depth single-cell RNA-sequencing analysis, progenitor lineage labelling and mosaic functional analysis, we report that the diverse yet patterned expression of clustered protocadherins (cPCDHs)-the largest subgroup of the Cadherin superfamily of cell adhesion molecules(7)-regulates the precise spatial arrangement and synaptic connectivity of excitatory neurons in the mouse neocortex. The expression of cPcdh genes in individual neocortical excitatory neurons is diverse yet exhibits distinct composition patterns linked to their developmental origin and spatial positioning. A reduction in functional cPCDH expression causes a lateral clustering of clonally related excitatory neurons originating from the same neural progenitor and a significant increase in synaptic connectivity. By contrast, overexpression of a single cPCDH isoform leads to a lateral dispersion of clonally related excitatory neurons and a considerable decrease in synaptic connectivity. These results suggest that patterned cPCDH expression biases fine spatial and functional organization of individual neocortical excitatory neurons in the mammalian brain.