Authors :
Presenting Author: Syed Wafa, MA, MS – Northwestern University
Timothy Fenton, PhD – University of California, Davis
Ghazaleh Yazdani, MS – University of California, Davis
Christopher Thompson, PhD – Northwestern University
Roy Ben-Shalom, PhD – University of California, Davis
Alfred George, Jr., MD – Northwestern University
Rationale:
The SCN2A gene, which encodes the neuronal voltage-gated sodium channel NaV1.2, is associated with a wide range of neurodevelopmental disorders, including developmental and epileptic encephalopathy, self-limited infantile epilepsy, and autism. SCN2A channels are primarily expressed in axons and dendrites of excitatory neurons, where they drive action potential initiation and propagation. Pathogenic SCN2A mutations affecting protein structure and function modulate neuronal responses to synaptic inputs leading to seizures and impaired cognitive function in SCN2A-related disorders. However, the net effects of complex SCN2A channel dysfunction on neuronal excitability are difficult to predict, and the relationship between specific channel biophysical perturbations and resulting changes to neuronal physiology is unclear. Here, we determined the relationships among structural, biophysical, and neurophysiological consequences of 115 SCN2A mutations.
Methods:
We used open-source resources to annotate topological and physiochemical features of each variant and performed voltage-clamp recordings to determine functional consequences. In parallel, we leveraged in vitro voltage-clamp recordings to build in silico Hodgkin-Huxley models of each variant, which we used to simulate heterozygous channel dysfunction in a benchmarked model of a neocortical pyramidal neuron. We probed neuronal defects resulting from SCN2A channel dysfunction and the neuronal impact of modulating individual biophysical properties using interpretable machine learning. Specifically, we measured and predicted dendritic backpropagation of spikes, somatic firing frequency, and spike shape at axon terminals to determine how specific changes in SCN2A channel biophysics impact action potential boosting, somatic excitability, and neurotransmitter release, respectively.
Results:
We discovered that variant location within the SCN2A protein is a predictor of channel dysfunction accounting for 38.8% of the variance in channel biophysical properties. Mutations in the channel pore are associated with lower current density with 33 variants exhibiting non-functional channels. 68 variants displayed loss- or gain-of-function or mixed biophysical defects, and cluster analysis revealed channel inactivation kinetics as a key driver of channel dysfunction. Neuronal simulations indicated that the ability of SCN2A channels to recover from inactivation strongly influenced neuronal excitability with slower recovery of SCN2A channels from inactivation dampening neuronal excitability by potentiating somato-dendritic potassium conductances that promote membrane repolarization between action potentials.
Conclusions:
Overall, our work elucidated a granular genotype-phenotype relationship landscape of SCN2A-related disorders highlighting key molecular and cellular mechanisms of pathophysiology and allowing the intuitive prediction of the physiological impact of new SCN2A variants with any pattern of channel dysfunction. In addition, our work established a quantitative framework for investigating the physiological impact of genetic perturbations in the nervous system.
Funding: American Epilepsy Society Predoctoral Research Fellowship