Applications of Dynamic Clamp to Cardiac Arrhythmia Research: Role in Drug Target Discovery and Safety Pharmacology Testing

Advances in induced pluripotent stem cell-derived cardiac myocytes: technological breakthroughs, key discoveries and new applications

A transformation is underway in precision and patient-specific medicine. Rapid progress has been enabled by multiple new technologies including induced pluripotent stem cell-derived cardiac myocytes (iPSC-CMs). Here, we delve into these advancements and their future promise, focusing on the efficiency of reprogramming techniques, the fidelity of differentiation into the cardiac lineage, the functional characterization of the resulting cardiac myocytes, and the many applications of in silico models to understand general and patient-specific mechanisms controlling excitation-contraction coupling in health and disease. Furthermore, we explore the current and potential applications of iPSC-CMs in both research and clinical settings, underscoring the far-reaching implications of this rapidly evolving field.

Optimization of a cardiomyocyte model illuminates role of increased INa,L in repolarization reserve

Cardiac ion currents may compensate for each other when one is compromised by a congenital or drug-induced defect. Such redundancy contributes to a robust repolarization reserve that can prevent the development of lethal arrhythmias. Most efforts made to describe this phenomenon have quantified contributions by individual ion currents. However, it is important to understand the interplay between all major ion-channel conductances, as repolarization reserve is dependent on the balance between all ion currents in a cardiomyocyte. Here, a genetic algorithm was designed to derive profiles of nine ion-channel conductances that optimize repolarization reserve in a mathematical cardiomyocyte model. Repolarization reserve was quantified using a previously defined metric, repolarization reserve current, i.e., the minimum constant current to prevent normal action potential repolarization in a cell. The optimization improved repolarization reserve current up to 84% compared to baseline in a human adult ventricular myocyte model and increased resistance to arrhythmogenic insult. The optimized conductance profiles were not only characterized by increased repolarizing current conductances but also uncovered a previously unreported behavior by the late sodium current. Simulations demonstrated that upregulated late sodium increased action potential duration, without compromising repolarization reserve current. The finding was generalized to multiple models. Ultimately, this computational approach, in which multiple currents were studied simultaneously, illuminated mechanistic insights into how the metric's magnitude could be increased and allowed for the unexpected role of late sodium to be elucidated.NEW & NOTEWORTHY Genetic algorithms are typically used to fit models or extract desired parameters from data. Here, we use the tool to produce a ventricular cardiomyocyte model with increased repolarization reserve. Since arrhythmia mitigation is dependent on multiple cardiac ion-channel conductances, study using a comprehensive, unbiased, and systems-level approach is important. The use of this optimization strategy allowed us to find robust profiles that illuminated unexpected mechanistic determinants of key ion-channel conductances in repolarization reserve.

Leak current, even with gigaohm seals, can cause misinterpretation of stem cell-derived cardiomyocyte action potential recordings

AIMS

Human-induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have become an essential tool to study arrhythmia mechanisms. Much of the foundational work on these cells, as well as the computational models built from the resultant data, has overlooked the contribution of seal-leak current on the immature and heterogeneous phenotype that has come to define these cells. The aim of this study is to understand the effect of seal-leak current on recordings of action potential (AP) morphology.

METHODS AND RESULTS

Action potentials were recorded in human iPSC-CMs using patch clamp and simulated using previously published mathematical models. Our in silico and in vitro studies demonstrate how seal-leak current depolarizes APs, substantially affecting their morphology, even with seal resistances (Rseal) above 1 GΩ. We show that compensation of this leak current is difficult due to challenges with obtaining accurate measures of Rseal during an experiment. Using simulation, we show that Rseal measures (i) change during an experiment, invalidating the use of pre-rupture values, and (ii) are polluted by the presence of transmembrane currents at every voltage. Finally, we posit that the background sodium current in baseline iPSC-CM models imitates the effects of seal-leak current and is increased to a level that masks the effects of seal-leak current on iPSC-CMs.

CONCLUSION

Based on these findings, we make recommendations to improve iPSC-CM AP data acquisition, interpretation, and model-building. Taking these recommendations into account will improve our understanding of iPSC-CM physiology and the descriptive ability of models built from such data.

INNOVATIVE TECHNIQUES AND NEW INSIGHTS: Studying cardiac ionic currents and action potentials in physiologically relevant conditions

Cardiac arrhythmias are associated with various forms of heart diseases. Ventricular arrhythmias present a significant risk for sudden cardiac death. Atrial fibrillations predispose to blood clots leading to stroke and heart attack. Scientists have been developing patch-clamp technology to study ion channels and action potentials (APs) underlying cardiac excitation and arrhythmias. Beyond the traditional patch-clamp techniques, innovative new techniques were developed for studying complex arrhythmia mechanisms. Here we review the recent development of methods including AP-Clamp, Dynamic Clamp, AP-Clamp Sequential Dissection, and Patch-Clamp-in-Gel. These methods provide powerful tools for researchers to decipher how the dynamic systems in excitation-Ca2+ signaling-contraction feedforward and feedback to control cardiac function and how their dysregulations lead to heart diseases.

Patch-Clamp Recordings of Action Potentials From Human Atrial Myocytes: Optimization Through Dynamic Clamp

Introduction: Atrial fibrillation (AF) is the most common cardiac arrhythmia. Consequently, novel therapies are being developed. Ultimately, the impact of compounds on the action potential (AP) needs to be tested in freshly isolated human atrial myocytes. However, the frequent depolarized state of these cells upon isolation seriously hampers reliable AP recordings.

Purpose: We assessed whether AP recordings from single human atrial myocytes could be improved by providing these cells with a proper inward rectifier K⁺ current (I_K1), and consequently with a regular, non-depolarized resting membrane potential (RMP), through “dynamic clamp”.

Methods: Single myocytes were enzymatically isolated from left atrial appendage tissue obtained from patients with paroxysmal AF undergoing minimally invasive surgical ablation. APs were elicited at 1 Hz and measured using perforated patch-clamp methodology, injecting a synthetic I_K1 to generate a regular RMP. The injected I_K1 had strong or moderate rectification. For comparison, a regular RMP was forced through injection of a constant outward current. A wide variety of ion channel blockers was tested to assess their modulatory effects on AP characteristics.

Results: Without any current injection, RMPs ranged from −9.6 to −86.2 mV in 58 cells. In depolarized cells (RMP positive to −60 mV), RMP could be set at −80 mV using I_K1 or constant current injection and APs could be evoked upon stimulation. AP duration differed significantly between current injection methods (p < 0.05) and was shortest with constant current injection and longest with injection of I_K1 with strong rectification. With moderate rectification, AP duration at 90% repolarization (APD₉₀) was similar to myocytes with regular non-depolarized RMP, suggesting that a synthetic I_K1 with moderate rectification is the most appropriate for human atrial myocytes. Importantly, APs evoked using each injection method were still sensitive to all drugs tested (lidocaine, nifedipine, E-4031, low dose 4-aminopyridine, barium, and apamin), suggesting that the major ionic currents of the atrial cells remained functional. However, certain drug effects were quantitatively dependent on the current injection approach used.

Conclusion: Injection of a synthetic I_K1 with moderate rectification facilitates detailed AP measurements in human atrial myocytes. Therefore, dynamic clamp represents a promising tool for testing novel antiarrhythmic drugs.

Dynamic Clamp in Electrophysiological Studies on Stem Cell-Derived Cardiomyocytes-Why and How?

ABSTRACT

Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are supposed to be a good human-based model, with virtually unlimited cell source, for studies on mechanisms underlying cardiac development and cardiac diseases, and for identification of drug targets. However, a major drawback of hPSC-CMs as a model system, especially for electrophysiological studies, is their depolarized state and associated spontaneous electrical activity. Various approaches are used to overcome this drawback, including the injection of "synthetic" inward rectifier potassium current (IK1), which is computed in real time, based on the recorded membrane potential ("dynamic clamp"). Such injection of an IK1-like current results in quiescent hPSC-CMs with a nondepolarized resting potential that show "adult-like" action potentials on stimulation, with functional availability of the most important ion channels involved in cardiac electrophysiology. These days, dynamic clamp has become a widely appreciated electrophysiological tool. However, setting up a dynamic clamp system can still be laborious and difficult, both because of the required hardware and the implementation of the dedicated software. In the present review, we first summarize the potential mechanisms underlying the depolarized state of hPSC-CMs and the functional consequences of this depolarized state. Next, we explain how an existing manual patch clamp setup can be extended with dynamic clamp. Finally, we shortly validate the extended setup with atrial-like and ventricular-like hPSC-CMs. We feel that dynamic clamp is a highly valuable tool in the field of cellular electrophysiological studies on hPSC-CMs and hope that our directions for setting up such dynamic clamp system may prove helpful.

Constant-potential environment for activating and synchronizing cardiomyocyte colonies with on-chip ion-depleting perm-selective membranes

In this study, an ion depleted zone created by an ion-selective membrane was used to impose a high and uniform constant extracellular potential over an entire ∼1000 cell rat cardiomyocyte (rCM) colony on-a-chip to trigger synchronized voltage-gated ion channel activities while preserving cell viability, thus extending single-cell voltage-clamp ion channel studies to an entire normalized colony. Image analysis indicated that rCM beating was strengthened and accelerated (by a factor of ∼2) within minutes of ion depletion and the duration of contraction and relaxation phases was significantly reduced. After the initial synchronization, the entire colony responds collectively to external potential changes such that beating over the entire colony can be activated or deactivated within 0.1 s. These newly observed collective dynamic responses, due to simultaneous ion channel activation/deactivation by a uniform constant-potential extracellular environment, suggest that perm-selective membrane modules on cell culture chips can facilitate studies of extracellular cardiac cell electrical communication and how ion-channel related pathologies affect cardiac cell synchronization. The future applications of this new technology can lead to better drug screening platforms for cardiotoxicity as well as platforms that can facilitate synchronized maturation of pluripotent stem cells into colonies with high electrical connectivity.

Canard analysis reveals why a large Ca2+ window current promotes early afterdepolarizations in cardiac myocytes

The pumping of blood through the heart is due to a wave of muscle contractions that are in turn due to a wave of electrical activity initiated at the sinoatrial node. At the cellular level, this wave of electrical activity corresponds to the sequential excitation of electrically coupled cardiac cells. Under some conditions, the normally-long action potentials of cardiac cells are extended even further by small oscillations called early afterdepolarizations (EADs) that can occur either during the plateau phase or repolarizing phase of the action potential. Hence, cellular EADs have been implicated as a driver of potentially lethal cardiac arrhythmias. One of the major determinants of cellular EAD production and repolarization failure is the size of the overlap region between Ca2+ channel activation and inactivation, called the window region. In this article, we interpret the role of the window region in terms of the fast-slow structure of a low-dimensional model for ventricular action potential generation. We demonstrate that the effects of manipulation of the size of the window region can be understood from the point of view of canard theory. We use canard theory to explain why enlarging the size of the window region elicits EADs and why shrinking the window region can eliminate them. We also use the canard mechanism to explain why some manipulations in the size of the window region have a stronger influence on cellular electrical behavior than others. This dynamical viewpoint gives predictive power that is beyond that of the biophysical explanation alone while also uncovering a common mechanism for phenomena observed in experiments on both atrial and ventricular cardiac cells.

Functional Impact of BeKm-1, a High-Affinity hERG Blocker, on Cardiomyocytes Derived from Human-Induced Pluripotent Stem Cells

I_Kr current, a major component of cardiac repolarization, is mediated by human Ether-à-go-go-Related Gene (hERG, K_v11.1) potassium channels. The blockage of these channels by pharmacological compounds is associated to drug-induced long QT syndrome (LQTS), which is a life-threatening disorder characterized by ventricular arrhythmias and defects in cardiac repolarization that can be illustrated using cardiomyocytes derived from human-induced pluripotent stem cells (hiPS-CMs). This study was meant to assess the modification in hiPS-CMs excitability and contractile properties by BeKm-1, a natural scorpion venom peptide that selectively interacts with the extracellular face of hERG, by opposition to reference compounds that act onto the intracellular face. Using an automated patch-clamp system, we compared the affinity of BeKm-1 for hERG channels with some reference compounds. We fully assessed its effects on the electrophysiological, calcium handling, and beating properties of hiPS-CMs. By delaying cardiomyocyte repolarization, the peptide induces early afterdepolarizations and reduces spontaneous action potentials, calcium transients, and contraction frequencies, therefore recapitulating several of the critical phenotype features associated with arrhythmic risk in drug-induced LQTS. BeKm-1 exemplifies an interesting reference compound in the integrated hiPS-CMs cell model for all drugs that may block the hERG channel from the outer face. Being a peptide that is easily modifiable, it will serve as an ideal molecular platform for the design of new hERG modulators displaying additional functionalities.

Use of Patient Health Records to Quantify Drug-Related Pro-arrhythmic Risk

There is an increasing expectation that computational approaches may supplement existing human decision-making. Frontloading of models for cardiac safety prediction is no exception to this trend, and ongoing regulatory initiatives propose use of high-throughput in vitro data combined with computational models for calculating proarrhythmic risk. Evaluation of these models requires robust assessment of the outcomes. Using FDA Adverse Event Reporting System reports and electronic healthcare claims data from the Truven-MarketScan US claims database, we quantify the incidence rate of arrhythmia in patients and how this changes depending on patient characteristics. First, we propose that such datasets are a complementary resource for determining relative drug risk and assessing the performance of cardiac safety models for regulatory use. Second, the results suggest important determinants for appropriate stratification of patients and evaluation of additional drug risk in prescribing and clinical support algorithms and for precision health.

In vitro data and computational models can assist with calculating pro-arrhythmic risk

We use patient health records and FDA Adverse Event Reporting System reports

Use of such datasets helps assess relative drug risk and cardiac safety models

We quantify how patient characteristics can affect arrhythmia incidence

Ultrarapid Delayed Rectifier K+ Channelopathies in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Atrial fibrillation (AF) is the most common cardiac arrhythmia. About 5-15% of AF patients have a mutation in a cardiac gene, including mutations in KCNA5, encoding the K_v1.5 α-subunit of the ion channel carrying the atrial-specific ultrarapid delayed rectifier K⁺ current (I_Kur). Both loss-of-function and gain-of-function AF-related mutations in KCNA5 are known, but their effects on action potentials (APs) of human cardiomyocytes have been poorly studied. Here, we assessed the effects of wild-type and mutant I_Kur on APs of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). We found that atrial-like hiPSC-CMs, generated by a retinoic acid-based differentiation protocol, have APs with faster repolarization compared to ventricular-like hiPSC-CMs, resulting in shorter APs with a lower AP plateau. Native I_Kur, measured as current sensitive to 50 μM 4-aminopyridine, was 1.88 ± 0.49 (mean ± SEM, n = 17) and 0.26 ± 0.26 pA/pF (n = 17) in atrial- and ventricular-like hiPSC-CMs, respectively. In both atrial- and ventricular-like hiPSC-CMs, I_Kur blockade had minimal effects on AP parameters. Next, we used dynamic clamp to inject various amounts of a virtual I_Kur, with characteristics as in freshly isolated human atrial myocytes, into 11 atrial-like and 10 ventricular-like hiPSC-CMs, in which native I_Kur was blocked. Injection of I_Kur with 100% density shortened the APs, with its effect being strongest on the AP duration at 20% repolarization (APD₂₀) of atrial-like hiPSC-CMs. At I_Kur densities < 100% (compared to 100%), simulating loss-of-function mutations, significant AP prolongation and raise of plateau were observed. At I_Kur densities > 100%, simulating gain-of-function mutations, APD₂₀ was decreased in both atrial- and ventricular-like hiPSC-CMs, but only upon a strong increase in I_Kur. In ventricular-like hiPSC-CMs, lowering of the plateau resulted in AP shortening. We conclude that a decrease in I_Kur, mimicking loss-of-function mutations, has a stronger effect on the AP of hiPSC-CMs than an increase, mimicking gain-of-function mutations, whereas in ventricular-like hiPSC-CMs such increase results in AP shortening, causing their AP morphology to become more atrial-like. Effects of native I_Kur modulation on atrial-like hiPSC-CMs are less pronounced than effects of virtual I_Kur injection because I_Kur density of atrial-like hiPSC-CMs is substantially smaller than that of freshly isolated human atrial myocytes.

Transgenic Rabbit Models in Proarrhythmia Research

Drug-induced proarrhythmia constitutes a potentially lethal side effect of various drugs. Most often, this proarrhythmia is mechanistically linked to the drug's potential to interact with repolarizing cardiac ion channels causing a prolongation of the QT interval in the ECG. Despite sophisticated screening approaches during drug development, reliable prediction of proarrhythmia remains very challenging. Although drug-induced long-QT-related proarrhythmia is often favored by conditions or diseases that impair the individual's repolarization reserve, most cellular, tissue, and whole animal model systems used for drug safety screening are based on normal, healthy models. In recent years, several transgenic rabbit models for different types of long QT syndromes (LQTS) with differences in the extent of impairment in repolarization reserve have been generated. These might be useful for screening/prediction of a drug's potential for long-QT-related proarrhythmia, particularly as different repolarizing cardiac ion channels are impaired in the different models. In this review, we summarize the electrophysiological characteristics of the available transgenic LQTS rabbit models, and the pharmacological proof-of-principle studies that have been performed with these models—highlighting the advantages and disadvantages of LQTS models for proarrhythmia research. In the end, we give an outlook on potential future directions and novel models.

Validation of quantitative measure of repolarization reserve as a novel marker of drug induced proarrhythmia

Repolarization reserve, the robustness of a cell to repolarize even when one of the repolarization mechanisms is failing, has been described qualitatively in terms of ionic currents, but has not been quantified by a generic metric that is applicable to drug screening. Prolonged repolarization leading to repolarization failure is highly arrhythmogenic. It may lead to ventricular tachycardia caused by triggered activity from early afterdepolarizations (EADs), or it may promote the occurrence of unidirectional conduction block and reentry. Both types of arrhythmia may deteriorate into ventricular fibrillation (VF) and death. We define the Repolarization Reserve Current (RRC) as the minimum constant current necessary to prevent normal repolarization of a cell. After developing and testing RRC for nine computational ionic models of various species, we applied it experimentally to atrial and ventricular human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM), and isolated guinea-pig ventricular cardiomyocytes. In simulations, repolarization was all-or-none with a precise, model-dependent critical RRC, resulting in a discrete shift in the Action Potential Duration (APD) - RRC relation, in the occurrence of EADs and repolarization failure. These data were faithfully reproduced in cellular experiments. RRC allows simple, fast, unambiguous quantification of the arrhythmogenic propensity in cardiac cells of various origins and species without the need of prior knowledge of underlying currents and is suitable for high throughput applications, and personalized medicine applications.

Required GK1 to Suppress Automaticity of iPSC-CMs Depends Strongly on IK1 Model Structure

Human-induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs) are a virtually endless source of human cardiomyocytes that may become a great tool for safety pharmacology; however, their electrical phenotype is immature: they show spontaneous action potentials (APs) and an unstable and depolarized resting membrane potential (RMP) because of lack of I_K1. Such immaturity hampers their application in assessing drug safety. The electronic overexpression of I_K1 (e.g., through the dynamic clamp (DC) technique) is an option to overcome this deficit. In this computational study, we aim to estimate how much I_K1 is needed to bring hiPSC-CMs to a stable and hyperpolarized RMP and which mathematical description of I_K1 is most suitable for DC experiments. We compared five mature I_K1 formulations (Bett, Dhamoon, Ishihara, O’Hara-Rudy, and ten Tusscher) with the native one (Paci), evaluating the main properties (outward peak, degree of rectification), and we quantified their effects on AP features (RMP, V˙max, APD₅₀, APD₉₀ (AP duration at 50 and 90% of repolarization), and APD₅₀/APD₉₀) after including them in the hiPSC-CM mathematical model by Paci. Then, we automatically identified the critical conductance for I_K1 ( G_{K1, critical}), the minimally required amount of I_K1 suppressing spontaneous activity. Preconditioning the cell model with depolarizing/hyperpolarizing prepulses allowed us to highlight time dependency of the I_K1 formulations. Simulations showed that inclusion of mature I_K1 formulations resulted in hyperpolarized RMP and higher V˙max, and observed G_{K1, critical} and the effect on AP duration strongly depended on I_K1 formulation. Finally, the Ishihara I_K1 led to shorter (−16.3%) and prolonged (+6.5%) APD₉₀ in response to hyperpolarizing and depolarizing prepulses, respectively, whereas other models showed negligible effects. Fine-tuning of G_K1 is an important step in DC experiments. Our computational work proposes a procedure to automatically identify how much I_K1 current is required to inject to stop the spontaneous activity and suggests the use of the Ishihara I_K1 model to perform DC experiments in hiPSC-CMs.

Dynamic clamping human and rabbit atrial calcium current: narrowing ICaL window abolishes early afterdepolarizations

Key points

Early‐afterdepolarizations (EADs) are abnormal action potential oscillations and a known cause of cardiac arrhythmias. Ventricular EADs involve reactivation of a Ca²⁺ current (I_CaL) in its ‘window region’ voltage range. However, electrical mechanisms of atrial EADs, a potential cause of atrial fibrillation, are poorly understood.

Atrial cells were obtained from consenting patients undergoing heart surgery, as well as from rabbits. I_CaL was blocked with nifedipine and then a hybrid patch clamp/mathematical‐modelling technique, ‘dynamic clamping’, was used to record action potentials at the same time as injecting an artificial, modifiable, I_CaL (I_CaL,D‐C).

Progressively widening the I_CaL,D‐C window region produced EADs of various types, dependent on window width. EAD production was strongest upon moving the activation (vs. inactivation) side of the window.

EADs were then induced by a different method: increasing I_CaL,D‐C amplitude and/or K⁺ channel‐blockade (4‐aminopyridine). Narrowing of the I_CaL,D‐C window by ∼10 mV abolished these EADs.

Atrial I_CaL window narrowing is worthy of further testing as a potential anti‐atrial fibrillation drug mechanism.

Abstract

Atrial early‐afterdepolarizations (EADs) may contribute to atrial fibrillation (AF), perhaps involving reactivation of L‐type Ca²⁺ current (I_CaL) in its window region voltage range. The present study aimed (i) to validate the dynamic clamp technique for modifying the I_CaL contribution to atrial action potential (AP) waveform; (ii) to investigate the effects of widening the window I_CaL on EAD‐propensity; and (iii) to test whether EADs from increased I_CaL and AP duration are supressed by narrowing the window I_CaL. I_CaL and APs were recorded from rabbit and human atrial myocytes by whole‐cell‐patch clamp. During AP recording, I_CaL was inhibited (3 µm nifedipine) and replaced by a dynamic clamp model current, I_CaL,D‐C (tuned to native I_CaL characteristics), computed in real‐time (every 50 µs) based on myocyte membrane potential. I_CaL,D‐C‐injection restored the nifedipine‐suppressed AP plateau. Widening the window I_CaL,D‐C, symmetrically by stepwise simultaneous equal shifts of half‐voltages (V_0.5) of I_CaL,D‐C activation (negatively) and inactivation (positively), generated EADs (single, multiple or preceding repolarization failure) in a window width‐dependent manner, as well as AP alternans. A stronger EAD‐generating effect resulted from independently shifting activation V_0.5 (asymmetrical widening) than inactivation V_0.5; for example, a 15 mV activation shift produced EADs in nine of 17 (53%) human atrial myocytes vs. 0 of 18 from inactivation shift (P < 0.05). In 11 rabbit atrial myocytes in which EADs were generated either by increasing the conductance of normal window width I_CaL,D‐C or subsequent 4‐aminopyridine (2 mm), window I_CaL,D‐C narrowing (10 mV) abolished EADs of all types (P < 0.05). The present study validated the dynamic clamp for I_CaL, which is novel in atrial cardiomyocytes, and showed that EADs of various types are generated by widening (particularly asymmetrically) the window I_CaL, as well as abolished by narrowing it. Window I_CaL narrowing is a potential therapeutic mechanism worth pursuing in the search for improved anti‐AF drugs.

Early‐afterdepolarizations (EADs) are abnormal action potential oscillations and a known cause of cardiac arrhythmias. Ventricular EADs involve reactivation of a Ca²⁺ current (I_CaL) in its ‘window region’ voltage range. However, electrical mechanisms of atrial EADs, a potential cause of atrial fibrillation, are poorly understood.

Atrial cells were obtained from consenting patients undergoing heart surgery, as well as from rabbits. I_CaL was blocked with nifedipine and then a hybrid patch clamp/mathematical‐modelling technique, ‘dynamic clamping’, was used to record action potentials at the same time as injecting an artificial, modifiable, I_CaL (I_CaL,D‐C).

Progressively widening the I_CaL,D‐C window region produced EADs of various types, dependent on window width. EAD production was strongest upon moving the activation (vs. inactivation) side of the window.

EADs were then induced by a different method: increasing I_CaL,D‐C amplitude and/or K⁺ channel‐blockade (4‐aminopyridine). Narrowing of the I_CaL,D‐C window by ∼10 mV abolished these EADs.

Atrial I_CaL window narrowing is worthy of further testing as a potential anti‐atrial fibrillation drug mechanism.

Machine learning in drug development: Characterizing the effect of 30 drugs on the QT interval using Gaussian process regression, sensitivity analysis, and uncertainty quantification

Prolonged QT intervals are a major risk factor for ventricular arrhythmias and a leading cause of sudden cardiac death. Various drugs are known to trigger QT interval prolongation and increase the proarrhythmic potential. Yet, how precisely the action of drugs on the cellular level translates into QT interval prolongation on the whole organ level remains insufficiently understood. Here we use machine learning techniques to systematically characterize the effect of 30 common drugs on the QT interval. We combine information from high fidelity three-dimensional human heart simulations with low fidelity one-dimensional cable simulations to build a surrogate model for the QT interval using multi-fidelity Gaussian process regression. Once trained and cross-validated, we apply our surrogate model to perform sensitivity analysis and uncertainty quantification. Our sensitivity analysis suggests that compounds that block the rapid delayed rectifier potassium current I Kr have the greatest prolonging effect of the QT interval, and that blocking the L-type calcium current I CaL and late sodium current I NaL shortens the QT interval. Our uncertainty quantification allows us to propagate the experimental variability from individual block-concentration measurements into the QT interval and reveals that QT interval uncertainty is mainly driven by the variability in I Kr block. In a final validation study, we demonstrate an excellent agreement between our predicted QT interval changes and the changes observed in a randomized clinical trial for the drugs dofetilide, quinidine, ranolazine, and verapamil. We anticipate that both the machine learning methods and the results of this study will have great potential in the efficient development of safer drugs.

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows

Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Consortium and major international projects. It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility, portability and scalability as critical unmet needs in this area. Scientific workflows are a well-recognized strategy for addressing these needs in scientific computing. While there are good examples if the use of scientific workflows in bioinformatics, medical informatics, biomedical imaging and data analysis, there are fewer examples in multi-scale computational modeling in general and cardiac electrophysiology in particular. Cardiac electrophysiology simulation is a mature area of multi-scale computational biology that serves as an excellent use case for developing and testing new scientific workflows. In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale cardiac cell and tissue model that is expandable, modular and portable. The workflow described leverages Python and Kepler-Python actor for plotting and pre/post-processing. During all stages of the workflow design, we rely on freely available open-source tools, to make our workflow freely usable by scientists.

We present a computational workflow as a proof of concept for integration and implementation of a reusable and reproducible cardiac multi-scale electrophysiology model that is expandable, modular and portable. This framework enables scientists to create intuitive, user-friendly and flexible end-to-end automated scientific workflows using a graphical user interface. Kepler is an advanced open-source platform that supports multiple models of computation. The underlying workflow engine handles scalability, provenance, reproducibility aspects of the code, performs orchestration of data flow, and automates execution on heterogeneous computing resources. One of the main advantages of workflow utilization is the integration of code written in multiple languages Standardization occurs at the interfaces of the workflow elements and allows for general applications and easy comparison and integration of code from different research groups or even multiple programmers coding in different languages for various purposes from the same group. A workflow driven problem-solving approach enables domain scientists to focus on resolving the core science questions, and delegates the computational and process management burden to the underlying Workflow. The workflow driven approach allows scaling the computational experiment with distributed data-parallel execution on multiple computing platforms, such as, HPC resources, GPU clusters, Cloud etc. The workflow framework tracks software version information along with hardware information to allow users an opportunity to trace any variation in workflow outcome to the system configurations.

A Hybrid Model for Safety Pharmacology on an Automated Patch Clamp Platform: Using Dynamic Clamp to Join iPSC-Derived Cardiomyocytes and Simulations of Ik1 Ion Channels in Real-Time

An important aspect of the Comprehensive In Vitro Proarrhythmia Assay (CiPA) proposal is the use of human stem cell-derived cardiomyocytes and the confirmation of their predictive power in drug safety assays. The benefits of this cell source are clear; drugs can be tested in vitro on human cardiomyocytes, with patient-specific genotypes if needed, and differentiation efficiencies are generally excellent, resulting in a virtually limitless supply of cardiomyocytes. There are, however, several challenges that will have to be surmounted before successful establishment of hSC-CMs as an all-round predictive model for drug safety assays. An important factor is the relative electrophysiological immaturity of hSC-CMs, which limits arrhythmic responses to unsafe drugs that are pro-arrhythmic in humans. Potentially, immaturity may be improved functionally by creation of hybrid models, in which the dynamic clamp technique joins simulations of lacking cardiac ion channels (e.g., I_K1) with hSC-CMs in real-time during patch clamp experiments. This approach has been used successfully in manual patch clamp experiments, but throughput is low. In this study, we combined dynamic clamp with automated patch clamp of iPSC-CMs in current clamp mode, and demonstrate that I_K1 conductance can be added to iPSC-CMs on an automated patch clamp platform, resulting in an improved electrophysiological maturity.