The transcriptomic signature of DEPDC5 KO induced mTOR hyperactivation in human neurons and its response to rapamycin treatment.

Objective: Mutations of the DEP Domain Containing 5 gene (DEPDC5), a mechanistic Target of Rapamycin (mTOR) inhibitor involved in amino acid sensing, are associated with neurological diseases such as epilepsy and/or autism spectrum disorder (ASD). Loss of DEPDC5 impacts early neuronal development via mTOR hyperactivity. Although, in the mTOR-hyperactivity-associated syndrome tuberous sclerosis, mTOR inhibitors have proven to be beneficial in treating epilepsy, ASD-associated symptoms are ameliorated only partially. Similarly, the mTOR inhibitor rapamycin (RAPA) only partially rescues phenotypes induced by loss of DEPDC5 in animal models, suggesting some pathological mechanisms independent of mTOR.

Methods: We dissected these mechanisms by identifying the DEPDC5-associated gene networks and how they are targeted by RAPA in an isogenic primary human neural progenitor (phNPC) DEPDC5 knock-out cell model.

Results: We confirm that loss of DEPDC5 leads to hyperactivation of mTOR, paralleled by altered expression of mTOR-associated genes. These effects were partially (up to 33% of genes) attenuated by RAPA treatment applying a clinically comparable concentration. We did not observe an association of the differentially expressed genes with ASD or epilepsy risk genes in general. However, we identified a significant association with gene networks known to be differentially regulated in cortex samples of individuals with ASD, which were still significantly deregulated after RAPA treatment. Furthermore, genes not rescued in differentiated neurons were specifically associated with synaptic pruning and early cortical development. The observed increase in neuronal markers was confirmed morphologically. RAPA treatment recovered the increased differentiation but not the morphological changes.

Significance: These new insights on the human gene network of DEPDC5 show evidence for pathological mechanisms that are not attenuated by the currently administered RAPA concentrations or that are independent of mTOR. These mechanisms should be considered as potential targets for future therapies.