Integrative transcriptomics and electrophysiological profiling of hiPSC-derived neurons identifies novel druggable pathways in Koolen-de Vries Syndrome

Abstract

Koolen-de Vries Syndrome (KdVS) is a neurodevelopmental disorder (NDD) with no treatment options due to a lack of understanding of its underlying pathophysiology. To investigate neuronal activity in KdVS, human induced pluripotent stem cell (hiPSC)-derived neurons from KdVS and control subjects were cultured on microelectrode arrays (MEAs). Our study identified reduced network burst rates, indicating disorganized network activity in KdVS neurons. To bridge molecular and functional aspects of the syndrome, we developed an experimental framework, MEA-seq, that integrates network activity measurements with high-throughput transcriptome profiling. This approach identified a negative correlation between the expression of the NDD-associated gene CLCN4 and the network burst rate. Consequently, knockdown of CLCN4 in KdVS neurons restored the activity to control level, confirming a causal relationship between increased CLCN4 expression and reduced network burst rate. Additionally, we identified a positive correlation between mitochondrial gene expression and the network burst rate, and identified impaired mitochondrial function in KdVS hiPSC-derived neurons. The transcriptomic signature of KdVS neurons was then used for computational screening against drug perturbation signatures of the LINCS Consortium database, predicting other drug targets and compounds capable of reversing the expression of affected genes in KdVS neurons. We selected 10 compounds for experimental validation, identifying the antioxidant phloretin and the Rho-kinase inhibitor fasudil as potential candidates for restoring the network activity dysfunction in KdVS. We conclude that the integrative molecular and electrophysiological of hiPSC-derived neurons with MEA-seq has excellent potential for identifying novel drugs and druggable pathways for KdVS and other NDDs.