Dysregulation of Multiple Solute Carrier genes and Metabolic Deficits in SLC1A4-Mutant Human iPSC-Derived Hippocampal Neurons

Abstract

Mutations in SLC1A4, which encodes the neuronal amino acid transporter ASCT1, disrupt metabolic and synaptic homeostasis, contributing to neurodevelopmental deficits commonly observed in autism spectrum disorder (ASD). To investigate the underlying molecular mechanisms of SLC1A4-related disorders, we utilized human iPSC-derived hippocampal neurons and applied an integrated multi-omics approach, combining electrophysiology, calcium imaging, metabolomics, proteomics, and transcriptomics. Our findings reveal an initial phase of early neuronal hyperexcitability, driven by increased sodium and potassium currents, followed by a progressive decline in synaptic activity at later stages. Metabolomic analysis identified elevated glycine, serine, and glutamate levels during early differentiation, contributing to excitotoxicity, whereas later glutamate depletion and extracellular matrix (ECM) disruption were associated with synaptic dysfunction. Proteomics data further showed dysregulation in metabolic pathways, amino acid biosynthesis, and fatty acid metabolism pathways during early time points, and in later stage dysregulation in metabolic and ECM-receptor interactions. Additionally, transcriptomic analysis revealed dysregulation in calcium signaling, amino acid metabolism pathways such as valine, leucine and isoleucine degradation, tryptophan metabolism, and glycine, serine, and threonine metabolism. Further investigation of SLC-family transporter genes uncovered disruptions in glutamate and glycine transport, establishing a direct link between amino acid transport dysfunction and neuronal deficits. Collectively, our study demonstrates that SLC1A4 mutations lead to dysregulation of multiple solute carrier protein genes causing metabolic stress, excitability defects, and synaptic abnormalities, providing a molecular framework for understanding SLC1A4-related neurodevelopmental disorders and identifying potential therapeutic targets.