Abstract Aims Cardiac electrical activity is extraordinarily robust. However, when it goes wrong it can have fatal consequences. Electrical activity in the heart is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. Whilst there is considerable variability in cardiac ion channel expression levels between individuals, studies in rodents have indicated that there are modules of ion channels whose expression co-vary. The aim of this study was to investigate whether meta-analytic co-expression analysis of large-scale gene expression data sets could identify modules of co-expressed cardiac ion channel genes in human hearts that are of functional importance. Methods and Results Meta-analysis of 3653 public human RNA-seq datasets identified a strong correlation between expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was also observed in human adult heart tissue samples. In silico modeling suggested that co-expression of CACNA1C and KCNH2 would limit the variability in action potential duration seen with variations in expression of ion channel genes and reduce susceptibility to early afterdepolarizations, a surrogate marker for pro-arrhythmia. We also found that levels of KCNH2 and CACNA1C expression are correlated in human induced pluripotent stem cell derived cardiac myocytes and the levels of CACNA1C and KCNH2 expression were inversely correlated with the magnitude of changes in repolarization duration following inhibition of IKr. Conclusions Meta-analytic approaches of multiple independent human gene expression datasets can be used to identify gene modules that are important for regulating heart function. Specifically, we have verified that there is co-expression of CACNA1C and KCNH2 ion channel genes in human heart tissue, and in silico analyses suggest that CACNA1C-KCNH2 co-expression increases the robustness of cardiac electrical activity. Translational Perspective Here, we show, using meta-analysis of multiple independent human gene expression datasets, that there is co-expression of KCNH2-CACNA1C in human heart tissue which was then confirmed in human cardiac myocytes derived from induced pluripotent stem cells. Both in silico and functional studies show that the co-expression of CACNA1C and KCNH2 increases the robustness of cardiac electrical signalling. Our data also suggest that those patients who express higher levels of CACNA1C and KCNH2 are likely to be more susceptible to arrhythmias when exposed to drugs that block IKr, the major cause of drug-induced cardiac arrhythmias.

Extracellular field potentials were recorded from hiPSC-CM monolayers using a Maestro-APEX multi-electrode array (MEA) system (Axion Biosystems, Atlanta, GA, USA). Briefly, cell monolayers were maintained for 20-30 days in STEMDiff cardiomyocte maintenance media (STEM CELL Technologies), on EStim classic 48 well MEA plates (Axion Biosystems, Atlanta, USA), prior to recording. Monolayers, maintained at 37°C, were paced at 1 Hz and signals digitized at 12.5 kHz using AxIS v2.5.1.10 software (Axion Biosystems, Atlanta, GA, USA). Field potential durations were measured from the peak depolarization spike to the peak of the repolarization wave. After 30 minutes of pacing equilibration, Electrograms were recorded for 5 minutes in control conditions, 5 minutes in the presence of cisapride (200nM), and for 5 minutes in the presence of cisparide + nifedipine (50 nM) and measurements averaged over the last 10 beats of each recording period. This allowed for the possibility that if there was any beat to beat variation this could be averaged out over the ten beats. Twelve wells were plated for each line and all wells from which signals were recorded (n=7-12) were included in the analysis.

MEA guide.txt (description of contents of raw data files and how to extract the data)

The data set contains 6 raw dat files (matlab files):

           Plate1_baseline.mat

           Plate1_cis.mat

           Plate1_nif.mat

           Plate2_baseline.mat

           Plate2_cis.mat

           Plate2_nif.mat