The intracellular domain of the epilepsy protein PCDH19 regulates spine density in cortical neurons in vivo via <i>Xlr</i> genes

Mosaic mutations in the X-linked cell adhesion molecule Protocadherin 19 (PCDH19) lead to epilepsy with cognitive impairment, whereas complete absence of functional protein, although possibly linked to autistic features, does not elicit any seizures. It is believed that mosaic expression of PCDH19 leads to defective neuronal communication, but whether further roles beyond cell adhesion are critical for PCDH19 function in the cortex is currently unknown. We confirm that the proteolytic processing of PCDH19, previously described in hippocampal neurons, also takes place in mouse cortical neurons in vivo and show that nuclear transport of its intracellular domain is mediated by importins. RNAseq analysis further indicates that the intracellular domain of PCDH19 leads to broad transcriptomic changes. Finally, we use in utero electroporation to provide the first in vivo data about the role of this cleaved intracellular domain in upper layer cortical neurons of male and female mice, where it reduces spine density through an increase in Xlr gene expression without affecting overall dendritic morphology. Our results suggest that PCDH19 could act as an activity sensor in a synapse to nucleus signalling pathway involved in synaptic homeostasis. Significance statement We investigate non-adhesive functions of the epilepsy-linked cell adhesion protein PCDH19 and uncover a signalling role for its intracellular domain in cortical neurons. Beyond its established function in cell adhesion, we show that proteolytic cleavage of PCDH19 and nuclear import of its intracellular fragment leads to transcriptomic changes that impact dendritic spine density through the upregulation of Xlr genes. These findings suggest that PCDH19 may act as a synaptic activity sensor, linking membrane dynamics to nuclear responses in the regulation of synaptic homeostasis.