Abstract
Intellectual disability, affecting 2-3% of the general population, often co-occurs with neurodevelopmental disorders and is frequently caused by mutations that impair synaptic function. Kabuki syndrome (KS), a rare multisystem disorder associated with developmental delay and intellectual disability, results from mutations in either KMT2D (KS1) or KDM6A (KS2), encoding a histone methyltransferase and demethylase, respectively. The mechanisms underlying intellectual disability in KS remain poorly understood. Here, we generated human iPS cells carrying conditional Cre/lox-dependent loss-of-function mutations in KMT2D or KDM6A and differentiated them into excitatory or inhibitory neurons. Analysis revealed that KS1 and KS2 inhibitory neurons unexpectedly showed increased GABAergic synapse formation, whereas excitatory neurons displayed reduced synapse development and impaired synaptic transmission. We confirmed these findings in hippocampal neurons in vitro and in vivo using a mouse model for KS1 demonstrating a bidirectional shift: increase in inhibition and decrease in excitation. Synapse numbers and synaptic transmission in brain slices were shifted to increased inhibition/excitation ratio. Mechanistically, KS1 mutations activated neuroinflammatory signaling, impaired astrocytic function, and promoted glia-driven inhibitory synapse formation in human neurons. By integrating human neuron models with conditional KMT2D / KDM6A deletions and a Kmt2d -mutant mouse model, we identify a novel synaptic disease mechanism in KS that links chromatin remodeling defects to disrupted information transfer in neural circuits, providing a mechanistic explanation for intellectual disability. SIGNIFICANCE STATEMENT: Kabuki syndrome, a rare disorder with intellectual disability, is caused by mutations in the chromatin regulators KMT2D and KDM6A, yet its cellular pathophysiology has remained unclear. Using new Cre/lox-inducible human neuron models together with a mouse model, we reveal a conserved excitation-inhibition imbalance characterized by increased inhibitory and decreased excitatory synapse formation. Our findings establish the first mechanistic framework linking KMT2D / KDM6A mutations to synaptic dysfunction, uncover glial contributions to disease pathogenesis, and suggest potential therapeutic avenues for restoring synaptic balance. HIGHLIGHTS: KS1 and KS2 mutations cause decrease in excitatory synapses in human neuronsKS1 and KS2 mutations cause increase in inhibitory synapses in human neuronsKS1 mutation causes decrease in excitatory and increase in inhibitory synapses in miceKS1 mutant mouse astrocytes facilitate increase in inhibitory synapses in human neurons.