Pathogenic KIF1A variants differentially disrupt axonal trafficking and impede synaptic development

The nervous system relies on billions of neurons connected through trillions of synapses to support a vast array of vital functions. Despite the critical importance of this synaptic network, the cellular mechanisms dictating synapse formation during human neurodevelopment remain unclear. Long-distance trafficking of synaptic components is critical for both synaptogenesis and the maintenance of synaptic function across lifespan. The microtubule motor KIF1A has a highly conserved role in the trafficking of synaptic vesicle precursors, while mutations in <i>KIF1A</i> are causal for the neurodevelopmental and neurodegenerative disease <i>KIF1A</i>-Associated Neurological Disorder (KAND). Here, we employ isogenic human induced pluripotent stem cells (iPSCs) gene-edited to express pathogenic <i>KIF1A</i> variants to assess how disparate mutations alter synaptic trafficking and function. We compared the effects of both loss-of-function and gain-of-function mutations on KIF1A motor activity. We found that both null (p.C92*) and hypoactive (p.P305L) mutations induce delayed neurite outgrowth, mislocalization of synaptic cargos, and decreased synapse density. Conversely, the hyperactive KIF1A mutation (p.R350G) supports neurite outgrowth but leads to aberrant motility of synaptic vesicle precursors along the axon. Further, live imaging reveals that hyperactive KIF1A induces deficits in the microtubule-dependent patterning of presynaptic components along the developing axon, suggesting a failure to respond to cytoskeletal cues directing cargo delivery. Functional analysis of neuronal activity via multi-electrode arrays reveals delayed synaptic maturation in loss-of-function mutations (p.P305L, p.C92*). In contrast, the hyperactive p.R350G mutation exhibits accelerated activity maturation and possible excitotoxicity. Together, these data provide insights detailing how pathogenic variants in KIF1A causative for KAND exhibit distinct effects at the molecular level that lead to significant downstream deficits in synaptic function in human neurons.