Contrasting Effects of Clozapine and Risperidone on Cholesterol Metabolism, Synaptic Proteins, and Transcriptional Regulation in Human LUHMES Neurons

Antipsychotic drugs elicit complex cellular responses in neurons, yet the molecular mechanisms underlying their actions remain incompletely understood. Here, we employed deep proteomic profiling (DDA/DIA-MS) in LUHMES-derived dopaminergic neurons to explore the distinct proteomic profile induced by clozapine and risperidone. Pathway analysis revealed that clozapine robustly upregulated lipid metabolic pathways, particularly those involved in cholesterol and fatty acid biosynthesis. Conversely, risperidone primarily enhanced oxidative phosphorylation and modulated synaptic architecture and protein metabolic-pathways. Functional enrichment further indicated that clozapine promotes sterol metabolism, neuronal viability, and neurite outgrowth-hallmarks of neurotrophic activity - while simultaneously suppressing neurotransmission. Importantly, quantitative analysis of the nuclear subproteome enabled us to map these opposing regulatory hubs with high precision. Mechanistically, clozapine induced a transcriptionally repressive state, marked by downregulation of chromatin-opening factors CHD5 and DPF3 (BAF complex components) and HMGN1. In parallel, upregulation of the transcriptional repressor CIC reinforced this repressive signature, suggesting diminished chromatin accessibility. Furthermore, downregulation of activity-dependent regulators CRTC3 and JUNB pointed to an attenuation of excitability-driven gene expression. In contrast, risperidone upregulated TCF4, TCF7L1, FOS, HMGN1, and coactivators RREB1 and NCOA3, promoting Wnt signaling, chromatin accessibility and synaptic plasticity. Taken together, our data unveil distinct proteomic, transcriptional and epigenetic programs orchestrated by clozapine and risperidone, providing novel molecular insights into their divergent clinical actions.