Abstracts

Rationale: Genetic epilepsies are primarily caused by defects in ion channel genes: mutations causing amino acid substitutions or premature protein termination disrupt channel biogenesis and biophysical properties, with a nonlinear impact on disease risk and severity. There is little information about the functional effects of epilepsy mutations in the literature, despite large numbers of causative variants identified during clinical testing. This is primarily due to the large size and complex gene structure of voltage-gated ion channels, which introduces instability in plasmids used for mutagenesis, propagation, and characterization in cellular systems. Here we have designed and synthesized two ion channel specific expression vectors: pICDNA and pICJAZZ allowing easier mutagenesis and functional evaluation of these difficult-to-clone ion channels. Methods: Human, mouse, and rat sodium, potassium, calcium, and chloride ion channels (n=428) were analyzed for restriction enzyme cut sites. The multiple cloning site (MCS) of pcDNA3.1, a mammalian expression vector, was replaced with a novel MCS containing restriction sites for 35 different enzymes that cut nominal ion channel genes to create pICDNA. A linear version of pICDNA, pICJAZZ, was developed using Gibson assembly to insert the mammalian expression cassette and MCS from pICDNA into the linear pJAZZ bacterial vector. This eliminates the supercoiling and torsional strain caused by large cDNAs, like those encoding voltage-gated sodium and calcium channel alpha subunits. Vectors were validated using transformation, transfection, biogenesis and biophysical assays using standardized protocols for qualitative and quantitative analysis. Results: Vectors and cloned channels were validated by Sanger sequencing. There are no significant differences in transformation efficiencies between pICDNA and pcDNA3.1 containing rat Scn1b, mouse Kcna1, or human SCN5A channels. Human SCN5A, and rat Scn10a were easily cloned into both pICDNA and pICJAZZ. The neuronal human SCN1A and SCN2A are notoriously difficult to clone, and despite repeated attempts, we were unable to insert either into circular vectors (pcDNA 3.1, pCMV-Script, or pICDNA), however a single attempt successfully cloned each channel into the linear pICJAZZ vector. We also used pICDNA as a backbone to create a concatermeric-gene vector to study allelic dosage and heteromeric assembly. Conclusions: The demand for genetic diagnoses is rising rapidly as personalized medicine gains popularity. Current bioinformatics strategies have little predictive power for novel de novo mutations even in known epilepsy genes due to the biological and functional consequences of each mutation. Our novel ion channel vectors present new tools enabling the characterization of ion channel variants considering the allelic dosage, channel stoichiometry and functional impact of disease mutations. This will improve personalized risk prediction and pharmacotherapetuic decision making. Funding: Funding was provided by a Postdoctoral Research Award from Epilepsy Canada to ADS, and a CFI Infrastructure grant to TLK.