SMPD4 mediated sphingolipid metabolism regulates brain and primary cilia development

SMPD4 (neutral sphingomyelinase-3/nSMase3) has recently been shown to be a new cause of microcephaly in a cohort of twenty-three pediatric patients. The function of nSMases in brain development and how SMPD4 variants cause human microcephaly and cerebellar hypoplasia was previously unknown.We developed an iPSC model to complement our mouse study. We found iPSC models from human SMPD4 patient and CRISPR/Cas9-induced SMPD4 knockout lines demonstrate a proliferation defect, increased cell death, loss of neural progenitors, and shortened primary cilia. Treatment with exogenous ceramide significantly rescues the cilia defect. SMPD4 patient and knockout cells have altered WNT signaling. We provide evidence that SMPD4 controls brain development by providing ceramide for primary ciliogenesis, suggesting a novel therapeutic strategy for SMPD4 mediated disease. Overall design: We generated an SMPD4 knockout iPSC line (SMPD4 KO). We generated neural rosettes (NR) containing neural progenitor cells from control, KO, and patient iPSCs. We extracted RNA from these three lines for neural rosettes at eight days in culture and stem cells (iPSCs) and compared RNA expression patterns.