Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments
Authors: Yang Janice , Daily Neil , Pullinger Taylor K. , Wakatsuki Tetsuro , Sobie Eric A. 
Published: January 2024

AbstractHuman induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help understand the ionic underpinnings of, and to simulate, various cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters.We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created simulated datasets by applying various protocols to a population ofin silicocells with known conductance variations, and we fitted to those datasets. We found that calibrating models to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation held regardless of whether the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses.Author SummaryMany drug treatments or environmental factors can trigger cardiac arrhythmias, which are dangerous and often unpredictable. Human cardiomyocytes derived from donor stem cells have proven to be a promising model for studying these events, but variability in donor genetic background and cell maturation methods, as well as overall immaturity of stem cell-derived cardiomyocytes relative to the adult heart, have hindered reproducibility and reliability of these studies. Mathematical models of these cells can aid in understanding the underlying electrophysiological contributors to this variability, but determining these models’ parameters for multiple cell preparations is challenging. In this study, we tackle these limitations by developing a computational method to simultaneously estimate multiple model parameters using data from imaging-based experiments, which can be easily scaled to rapidly characterize multiple cell lines. This method can generate many personalized models of individual cell preparations, improving drug response predictions and revealing specific differences in electrophysiological properties that contribute to variability in cardiac maturity and arrhythmia susceptibility.GLOSSARYModel/parameter calibration: tuning one or more parameters in the computational model so that the model output more closely matches experimental dataExperiment/protocol optimization: the process of determining what type and amount of data is sufficient but also feasible for our model calibration goalsProtocol conditions – buffer calcium, potassium, or sodium concentrations; addition or removal of stimulus; pacing rates; channel block; etc.Protocol length(?) – number of protocol conditionsProtocol data type(?) –AP, CaT, or both; normalized or non-normalized dataModel prediction: using the calibrated computational model to simulate response tonew (unseen)conditions, drugs, or perturbations (in our case, IKrblock)Papers on independent validation/predictionComputational pipeline: the full process of iPSC-CM computational model calibration; Includes iPSC-CM data acquisition/simulation -> data processing -> parameter calibration using genetic algorithm -> validation of calibrated models on an unseen condition (i.e. evaluating model predictions)