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Additional file 2: Figures S1–S5 and Supplementary Tables S2–S3.

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

Tyrosine kinase inhibitors (TKIs) are highly potent cancer therapeutics that have been linked with serious cardiotoxicity, including left ventricular dysfunction, heart failure, and QT prolongation. TKI-induced cardiotoxicity is thought to result from interference with tyrosine kinase activity in cardiomyocytes, where these signaling pathways help to control critical processes such as survival signaling, energy homeostasis, and excitation–contraction coupling. However, mechanistic understanding is limited at present due to the complexities of tyrosine kinase signaling, and the wide range of targets inhibited by TKIs. Here, we review the use of TKIs in cancer and the cardiotoxicities that have been reported, discuss potential mechanisms underlying cardiotoxicity, and describe recent progress in achieving a more systematic understanding of cardiotoxicity via the use of mechanistic models. In particular, we argue that future advances are likely to be enabled by studies that combine large-scale experimental measurements with Quantitative Systems Pharmacology (QSP) models describing biological mechanisms and dynamics. As such approaches have proven extremely valuable for understanding and predicting other drug toxicities, it is likely that QSP modeling can be successfully applied to cardiotoxicity induced by TKIs. We conclude by discussing a potential strategy for integrating genome-wide expression measurements with models, illustrate initial advances in applying this approach to cardiotoxicity, and describe challenges that must be overcome to truly develop a mechanistic and systematic understanding of cardiotoxicity caused by TKIs.

Mathematical models of cardiac electrophysiology are instrumental in determining mechanisms of cardiac arrhythmias. However, the foundation of a realistic multiscale heart model is only as strong as the underlying cell model. While there have been myriad advances in the improvement of cellular-level models, the identification of model parameters, such as ion channel conductances and rate constants, remains a challenging problem. The primary limitations to this process include: (1) such parameters are usually estimated from data recorded using standard electrophysiology voltage-clamp protocols that have not been developed with model building in mind, and (2) model parameters are typically tuned manually to subjectively match a desired output. Over the last decade, methods aimed at overcoming these disadvantages have emerged. These approaches include the use of optimization or fitting tools for parameter estimation and incorporating more extensive data for output matching. Here, we review recent advances in parameter estimation for cardiomyocyte models, focusing on the use of more complex electrophysiology protocols and global search heuristics. We also discuss future applications of such parameter identification, including development of cell-specific and patient-specific mathematical models to investigate arrhythmia mechanisms and predict therapy strategies.

Channelopathies of autoimmune origin are novel and are associated with corrected QT (QTc) prolongation and complex ventricular arrhythmias.We have recently demonstrated that anti‐SSA/Ro antibodies from patients with autoimmune diseases and with QTc prolongation on the ECG target the human ether‐à‐go‐go‐related gene (HERG) K+ channel by inhibiting the corresponding current, I Kr, at the pore region.Immunization of guinea‐pigs with a peptide (E‐pore peptide) corresponding to the extracellular loop region connecting the S5 and S6 segments of the HERG channel induces high titres of antibodies that inhibit I Kr, lengthen the action potential and cause QTc prolongation on the surface ECG. In addition, anti‐SSA/Ro‐positive sera from patients with connective tissue diseases showed high reactivity to the E‐pore peptide.The translational impact is the development of a peptide‐based approach for the diagnosis and treatment of autoimmune‐associated long QT syndrome.

This paper is the second of a series of three reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation-contraction coupling and arrhythmias: Na(+) channel and Na(+) transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on Na(+) channel function and regulation, Na(+) channel structure and function, and Na(+) channel trafficking, sequestration and complexing.

We present a minimal mathematical model of Ca(2+) spark triggering under voltage-clamp conditions in ventricular myocytes. The model predicts changes in excitation-contraction coupling 'gain' that result from diverse experimental interventions. We compare model results to several sets of data, and, in so doing, place apparent constraints on physiologically relevant model parameters. Specifically, the analysis suggests that many L-type Ca(2+) channel openings can potentially trigger each Ca(2+) spark, but the probability that an individual opening will trigger a spark is low. This procedure helps to reconcile contradictory results obtained in recent studies; moreover, this new model should be a useful tool for understanding changes in gain that occur physiologically and in disease.

Excitation-contraction coupling in the heart depends on the positive feedback process of Ca2+-induced Ca2+ release (CICR). While CICR provides for robust triggering of Ca2+ sparks, the mechanisms underlying their termination remain unknown. At present, it is unclear how a cluster of Ca2+ release channels (ryanodine receptors or RyRs) can be made to turn off when their activity is sustained by the Ca2+ release itself. We use a novel experimental approach to investigate indirectly this issue by exploring restitution of Ca2+ sparks. We exploit the fact that ryanodine can bind, nearly irreversibly, to an RyR subunit (monomer) and increase the open probability of the homotetrameric channel. By applying low concentrations of ryanodine to rat ventricular myocytes, we observe repeated activations of individual Ca2+ spark sites. Examination of these repetitive Ca2+ sparks reveals that spark amplitude recovers with a time constant of 91 ms whereas the sigmoidal recovery of triggering probability lags behind amplitude recovery by approximately 80 ms. We conclude that restitution of Ca2+ sparks depends on local refilling of SR stores after depletion and may also depend on another time-dependent process such as recovery from inactivation or a slow conformational change after rebinding of Ca2+ to SR regulatory proteins.

Time dependent refractoriness of calcium (Ca(2+)) release in cardiac myocytes is an important factor in determining whether pro arrhythmic release patterns develop. At the subcellular level of the Ca(2+) spark recent studies have suggested that recovery of spark amplitude is controlled by local sarcoplasmic reticulum (SR) refilling whereas refractoriness of spark triggering depends on both refilling and the sensitivity of the ryanodine receptor (RyR) release channels that produce sparks. Here we studied regulation of Ca(2+) spark refractoriness in mouse ventricular myocytes by examining how ß adrenergic stimulation influenced sequences of Ca(2+) sparks originating from individual RyR clusters. Our protocol allowed us to separately measure recovery of spark amplitude and delays between successive sparks and data were interpreted quantitatively through simulations with a stochastic mathematical model. We found that compared with spark sequences measured under control conditions: (1) ß adrenergic stimulation with isoproterenol accelerated spark amplitude recovery and decreased spark to spark delays; (2) activating protein kinase A (PKA) with forskolin accelerated amplitude recovery but did not affect spark to spark delays; (3) inhibiting PKA with H89 retarded amplitude recovery and increased spark to spark delays; (4) preventing phosphorylation of the RyR at serine 2808 with a knock in mouse prevented the decrease in spark to spark delays seen with ß adrenergic stimulation; (5) inhibiting either PKA or Ca(2+)/calmodulin dependent protein kinase II (CaMKII) during ß adrenergic stimulation prevented the decrease in spark to spark delays seen without inhibition. The results suggest that activation of either PKA or CaMKII is sufficient to speed SR refilling but activation of both kinases appears necessary to observe increased RyR sensitivity. The data provide novel insight into ß adrenergic regulation of Ca(2+) release refractoriness in mouse myocytes. This article is protected by copyright. All rights reserved.

Reverse rate dependence is a problematic property of antiarrhythmic drugs that prolong the cardiac action potential (AP). The prolongation caused by reverse rate dependent agents is greater at slow heart rates, resulting in both reduced arrhythmia suppression at fast rates and increased arrhythmia risk at slow rates. The opposite property, forward rate dependence, would theoretically overcome these parallel problems, yet forward rate dependent (FRD) antiarrhythmics remain elusive. Moreover, there is evidence that reverse rate dependence is an intrinsic property of perturbations to the AP. We have addressed the possibility of forward rate dependence by performing a comprehensive analysis of 13 ventricular myocyte models. By simulating populations of myocytes with varying properties and analyzing population results statistically, we simultaneously predicted the rate-dependent effects of changes in multiple model parameters. An average of 40 parameters were tested in each model, and effects on AP duration were assessed at slow (0.2 Hz) and fast (2 Hz) rates. The analysis identified a variety of FRD ionic current perturbations and generated specific predictions regarding their mechanisms. For instance, an increase in L-type calcium current is FRD when this is accompanied by indirect, rate-dependent changes in slow delayed rectifier potassium current. A comparison of predictions across models identified inward rectifier potassium current and the sodium-potassium pump as the two targets most likely to produce FRD AP prolongation. Finally, a statistical analysis of results from the 13 models demonstrated that models displaying minimal rate-dependent changes in AP shape have little capacity for FRD perturbations, whereas models with large shape changes have considerable FRD potential. This can explain differences between species and between ventricular cell types. Overall, this study provides new insights, both specific and general, into the determinants of AP duration rate dependence, and illustrates a strategy for the design of potentially beneficial antiarrhythmic drugs., Author Summary Several drugs intended to treat cardiac arrhythmias have failed because of unfavorable rate-dependent properties. That is, the drugs fail to alter electrical activity at fast heart rates, where this would be beneficial, but they do affect electrical activity at slow rates, where this is unwanted. In targeted studies, several agents have been shown to exhibit these unfavorable properties, suggesting that these rate-dependent responses may be intrinsic to ventricular muscle. To determine whether drugs with desirable rate-dependent properties could be rationally designed, we performed comprehensive and systematic analyses of several heart cell models. These analyses calculated the rate-dependent properties of changes in any model parameter, thereby generating simultaneously a large number of model predictions. The analyses showed that targets with favorable rate-dependent properties could indeed be identified, and further simulations uncovered the mechanisms underlying these behaviors. Moreover, a quantitative comparison of results obtained in different models provided new insight in why a given drug applied to different species, or to different tissue types, might produce different rate-dependent behaviors. Overall this study shows how a comprehensive and systematic approach to heart cell models can both identify novel targets and produce more general insight into rate-dependent alterations to cardiac electrical activity.