Cardiac safety pharmacology: from human ether-a-gogo related gene channel block towards induced pluripotent stem cell based disease models

Artificial Intelligence-Driven Algorithm for Drug Effect Prediction on Atrial Fibrillation: An in silico Population of Models Approach

Background: Antiarrhythmic drugs are the first-line treatment for atrial fibrillation (AF), but their effect is highly dependent on the characteristics of the patient. Moreover, anatomical variability, and specifically atrial size, have also a strong influence on AF recurrence. Objective: We performed a proof-of-concept study using artificial intelligence (AI) that enabled us to identify proarrhythmic profiles based on pattern identification from in silico simulations. Methods: A population of models consisting of 127 electrophysiological profiles with a variation of nine electrophysiological variables (G _Na , I _NaK , G _K1, G _CaL , G _Kur , I _KCa , [Na] _ext , and [K] _ext and diffusion) was simulated using the Koivumaki atrial model on square planes corresponding to a normal (16 cm²) and dilated (22.5 cm²) atrium. The simple pore channel equation was used for drug implementation including three drugs (isoproterenol, flecainide, and verapamil). We analyzed the effect of every ionic channel combination to evaluate arrhythmia induction. A Random Forest algorithm was trained using the population of models and AF inducibility as input and output, respectively. The algorithm was trained with 80% of the data (N = 832) and 20% of the data was used for testing with a k-fold cross-validation (k = 5). Results: We found two electrophysiological patterns derived from the AI algorithm that was associated with proarrhythmic behavior in most of the profiles, where G _K1 was identified as the most important current for classifying the proarrhythmicity of a given profile. Additionally, we found different effects of the drugs depending on the electrophysiological profile and a higher tendency of the dilated tissue to fibrillate (Small tissue: 80 profiles vs Dilated tissue: 87 profiles). Conclusion: Artificial intelligence algorithms appear as a novel tool for electrophysiological pattern identification and analysis of the effect of antiarrhythmic drugs on a heterogeneous population of patients with AF.

Generation and characterization of iPSC-derived renal proximal tubule-like cells with extended stability

The renal proximal tubule is responsible for re-absorption of the majority of the glomerular filtrate and its proper function is necessary for whole-body homeostasis. Aging, certain diseases and chemical-induced toxicity are factors that contribute to proximal tubule injury and chronic kidney disease progression. To better understand these processes, it would be advantageous to generate renal tissues from human induced pluripotent stem cells (iPSC). Here, we report the differentiation and characterization of iPSC lines into proximal tubular-like cells (PTL). The protocol is a step wise exposure of small molecules and growth factors, including the GSK3 inhibitor (CHIR99021), the retinoic acid receptor activator (TTNPB), FGF9 and EGF, to drive iPSC to PTL via cell stages representing characteristics of early stages of renal development. Genome-wide RNA sequencing showed that PTL clustered within a kidney phenotype. PTL expressed proximal tubular-specific markers, including megalin (LRP2), showed a polarized phenotype, and were responsive to parathyroid hormone. PTL could take up albumin and exhibited ABCB1 transport activity. The phenotype was stable for up to 7 days and was maintained after passaging. This protocol will form the basis of an optimized strategy for molecular investigations using iPSC derived PTL.

Assay Procedures for Compound Testing of hiPSC-Derived Cardiomyocytes Using Multiwell Microelectrode Arrays

The cardiac action potential requires a precise timing of activation and inactivation of ion channel subtypes. Deviations, for example, due to blockage of specific voltage-gated potassium channels, can result in live-threatening arrhythmias. Due to the limitations of standard cellular assays based on cells which artificially express only single ion channel subtypes, many potentially interesting compounds are discarded during drug development. More predictive functional assays are required. With the upcoming of human stem-cell derived cardiomyocytes (hiPS-CM) these assays are available, supporting even the design of patient-derived disease models. Microelectrode array systems allow to noninvasively record and evaluate cardiac field action potentials. In this chapter we describe how to cultivate hiPS-CM on two parallelized MEA systems and suggest an experimental strategy for compound tests.

Predicting cardiac safety using human induced pluripotent stem cell-derived cardiomyocytes combined with multi-electrode array (MEA) technology: A conference report

Safety pharmacology studies that evaluate drug candidates for potential cardiovascular liabilities remain a critical component of drug development. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have recently emerged as a new and promising tool for preclinical hazard identification and risk assessment of drugs. Recently, Pluriomics organized its first User Meeting entitled 'Combining Pluricyte® Cardiomyocytes & MEA for Safety Pharmacology applications', consisting of scientific sessions and live demonstrations, which provided the opportunity to discuss the application of hiPSC-CMs (Pluricyte® Cardiomyocytes) in cardiac safety assessment to support early decision making in safety pharmacology. This report summarizes the outline and outcome of this Pluriomics User Meeting, which took place on November 24-25, 2016 in Leiden (The Netherlands). To reflect the content of the communications presented at this meeting we have cited key scientific articles and reviews.

The assessment of electrophysiological activity in human-induced pluripotent stem cell-derived cardiomyocytes exposed to dimethyl sulfoxide and ethanol by manual patch clamp and multi-electrode array system

INTRODUCTION

Recently, electrophysiological activity has been effectively measured in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) to predict drug-induced arrhythmia. Dimethyl sulfoxide (DMSO) and ethanol have been used as diluting agents in many experiments. However, the maximum DMSO and ethanol concentrations that can be effectively used in the measurement of electrophysiological parameters in hiPSC-CMs-based patch clamp and multi-electrode array (MEA) have not been fully elucidated.

METHODS

We investigated the effects of varying concentrations of DMSO and ethanol used as diluting agents on several electrophysiological parameters in hiPSC-CMs using patch clamp and MEA.

RESULTS

Both DMSO and ethanol at concentrations>1% in external solution resulted in osmolality >400mOsmol/kg, but pH was not affected by either agent. Neither DMSO nor ethanol led to cell death at the concentrations examined. However, resting membrane potential, action potential amplitude, action potential duration at 90% and 40%, and corrected field potential duration were decreased significantly at 1% ethanol concentration. DMSO at 1% also significantly decreased the sodium spike amplitude. In addition, the waveform of action potential and field potential was recorded as irregular at 3% concentrations of both DMSO and ethanol. Concentrations of up to 0.3% of either agent did not affect osmolality, pH, cell death, or electrophysiological parameters in hiPSC-CMs.

DISCUSSION

Our findings suggest that 0.3% is the maximum concentration at which DMSO or ethanol should be used for dilution purposes in hiPSC-CMs-based patch clamp and MEA.

The Use of Ratiometric Fluorescence Measurements of the Voltage Sensitive Dye Di-4-ANEPPS to Examine Action Potential Characteristics and Drug Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) and higher throughput platforms have emerged as potential tools to advance cardiac drug safety screening. This study evaluated the use of high bandwidth photometry applied to voltage-sensitive fluorescent dyes (VSDs) to assess drug-induced changes in action potential characteristics of spontaneously active hiPSC-CM. Human iPSC-CM from 2 commercial sources (Cor.4U and iCell Cardiomyocytes) were stained with the VSD di-4-ANEPPS and placed in a specialized photometry system that simultaneously monitors 2 wavebands of emitted fluorescence, allowing ratiometric measurement of membrane voltage. Signals were acquired at 10 kHz and analyzed using custom software. Action potential duration (APD) values were normally distributed in cardiomyocytes (CMC) from both sources though the mean and variance differed significantly (APD90: 229 ± 15 ms vs 427 ± 49 ms [mean ± SD, P < 0.01]; average spontaneous cycle length: 0.99 ± 0.02 s vs 1.47 ± 0.35 s [mean ± SD, P < 0.01], Cor.4U vs iCell CMC, respectively). The 10-90% rise time of the AP (Trise) was ∼6 ms and was normally distributed when expressed as 1/[Formula: see text] in both cell preparations. Both cell types showed a rate dependence analogous to that of adult human cardiac cells. Furthermore, nifedipine, ranolazine, and E4031 had similar effects on cardiomyocyte electrophysiology in both cell types. However, ranolazine and E4031 induced early after depolarization-like events and high intrinsic firing rates at lower concentrations in iCell CMC. These data show that VSDs provide a minimally invasive, quantitative, and accurate method to assess hiPSC-CM electrophysiology and detect subtle drug-induced effects for drug safety screening while highlighting a need to standardize experimental protocols across preparations.

Specific prediction of clinical QT prolongation by kinetic image cytometry in human stem cell derived cardiomyocytes

INTRODUCTION

A priority in the development and approval of new drugs is assessment of cardiovascular risk. Current methodologies for screening compounds (e.g. HERG testing) for proarrhythmic risk lead to many false positive and false negative results, resulting in the attrition of potentially therapeutic compounds in early development, and the advancement of other candidates that cause adverse effects. With improvements in the technologies of high content imaging and human stem cell differentiation, it is now possible to directly screen compounds for arrhythmogenic tendencies in human stem cell derived cardiomyocytes (hSC-CMs).

METHODS

A training panel of 90 compounds consisting of roughly equal numbers of QT-prolonging and negative control (non-QT-prolonging) compounds, and a follow-up blinded study of 35 compounds including 16 from the 90 compound panel and 2 duplicates, were evaluated for prolongation of the calcium transient in hSC-CMs using kinetic image cytometry (KIC), a specialized form of high content analysis.

RESULTS

The KIC-hSC-CM assay identified training compounds that prolong the calcium transient with 98% specificity, 97% precision, 80% sensitivity, and 89% accuracy in predicting clinical QT prolongation by these compounds. The follow-up study of 35 blinded compounds confirmed the reproducibility and strong diagnostic accuracy of the assay.

DISCUSSION

The correlation of the KIC-hSC-CM results to clinical observations met or surpassed traditional preclinical assessment of cardiac risk utilizing animal models. Thus, the KIC-hSC-CM assay, which can be accomplished in high throughput and at relatively low cost, is an effective new model system for testing chemicals for cardiovascular risk.

Large-scale production of human pluripotent stem cell derived cardiomyocytes

Regenerative medicine, including preclinical studies in large animal models and tissue engineering approaches as well as innovative assays for drug discovery, will require the constant supply of hPSC-derived cardiomyocytes and other functional progenies. Respective cell production processes must be robust, economically viable and ultimately GMP-compliant. Recent research has enabled transition of lab scale protocols for hPSC expansion and cardiomyogenic differentiation towards more controlled processing in industry-compatible culture platforms. Here, advanced strategies for the cultivation and differentiation of hPSCs will be reviewed by focusing on stirred bioreactor-based techniques for process upscaling. We will discuss how cardiomyocyte mass production might benefit from recent findings such as cell expansion at the cardiovascular progenitor state. Finally, remaining challenges will be highlighted, specifically regarding three dimensional (3D) hPSC suspension culture and critical safety issues ahead of clinical translation.

Isolation and characterization of embryonic stem cell-derived cardiac Purkinje cells

The cardiac Purkinje fiber network is composed of highly specialized cardiomyocytes responsible for the synchronous excitation and contraction of the ventricles. Computational modeling, experimental animal studies, and intracardiac electrical recordings from patients with heritable and acquired forms of heart disease suggest that Purkinje cells (PCs) may also serve as critical triggers of life-threatening arrhythmias. Nonetheless, owing to the difficulty in isolating and studying this rare population of cells, the precise role of PC in arrhythmogenesis and the underlying molecular mechanisms responsible for their proarrhythmic behavior are not fully characterized. Conceptually, a stem cell-based model system might facilitate studies of PC-dependent arrhythmia mechanisms and serve as a platform to test novel therapeutics. Here, we describe the generation of murine embryonic stem cells (ESC) harboring pan-cardiomyocyte and PC-specific reporter genes. We demonstrate that the dual reporter gene strategy may be used to identify and isolate the rare ESC-derived PC (ESC-PC) from a mixed population of cardiogenic cells. ESC-PC display transcriptional signatures and functional properties, including action potentials, intracellular calcium cycling, and chronotropic behavior comparable to endogenous PC. Our results suggest that stem-cell derived PC are a feasible new platform for studies of developmental biology, disease pathogenesis, and screening for novel antiarrhythmic therapies.

Maturing human pluripotent stem cell-derived cardiomyocytes in human engineered cardiac tissues

Engineering functional human cardiac tissue that mimics the native adult morphological and functional phenotype has been a long held objective. In the last 5 years, the field of cardiac tissue engineering has transitioned from cardiac tissues derived from various animal species to the production of the first generation of human engineered cardiac tissues (hECTs), due to recent advances in human stem cell biology. Despite this progress, the hECTs generated to date remain immature relative to the native adult myocardium. In this review, we focus on the maturation challenge in the context of hECTs, the present state of the art, and future perspectives in terms of regenerative medicine, drug discovery, preclinical safety testing and pathophysiological studies.

Cardiovascular Disease Modeling Using Patient-Specific Induced Pluripotent Stem Cells

The generation of induced pluripotent stem cells (iPSCs) has opened up a new scientific frontier in medicine. This technology has made it possible to obtain pluripotent stem cells from individuals with genetic disorders. Because iPSCs carry the identical genetic anomalies related to those disorders, iPSCs are an ideal platform for medical research. The pathophysiological cellular phenotypes of genetically heritable heart diseases such as arrhythmias and cardiomyopathies, have been modeled on cell culture dishes using disease-specific iPSC-derived cardiomyocytes. These model systems can potentially provide new insights into disease mechanisms and drug discoveries. This review focuses on recent progress in cardiovascular disease modeling using iPSCs, and discusses problems and future perspectives concerning their use.

Implementation of quantitative and systems pharmacology in large pharma

Quantitative and systems pharmacology concepts and tools are the foundation of the model-informed drug development paradigm at Merck for integrating knowledge, enabling decisions, and enhancing submissions. Rigorous prioritization of modeling and simulation activities has enabled key drug development decisions and led to a high return on investment through significant cost avoidance. Critical factors for the successful implementation, examples on impact on decision making with associated return of investment, and drivers for continued success are discussed.

New iPSC for old long QT syndrome modeling: putting the evidence into perspective

Induced pluripotent stem cells (iPS cells or iPSCs) are typically derived by transfection of certain stem cell-associated genes into non-pluripotent cells, such as adult fibroblasts (typically adult somatic cells). Various diseases can be modeled through iPSC technology. The important implication of iPSCs to offer an unprecedented opportunity to recapitulate pathologic human tissue formation in vitro has generated great excitement and interest in the whole biomedical research community. Long QT syndrome (LQTS), an inherited heart disease, is characterized by prolonged QT interval on a surface electrocardiogram. LQTS presents with life-threatening cardiac arrhythmias, which can lead to fainting, syncope, and sudden death. The iPSC-derived cardiomyocytes from LQTS patients offer a potentially unlimited source of materials for biomedical study. They can be used to recapitulate complex physiological phenotypes, probe toxicological testing and drug screening, clarify the novel mechanistic insights and may also rectify gene defects at the cellular and molecular level. Despite the emerging challenges, iPSC technology has been increasingly recognized as a valuable and growing toolkit for modeling LQTS over other various models of human diseases.

Predicting drug-induced QT prolongation and torsades de pointes: a review of preclinical endpoint measures

Compound-induced prolongation of the cardiac QT interval is a major concern in drug development and this unit discusses approaches that can predict QT effects prior to undertaking clinical trials. The majority of compounds that prolong the QT interval block the cardiac rapid delayed rectifier potassium current, IKr (hERG). Described in this overview are different ways to measure hERG, from recent advances in automated electrophysiology to the quantification of channel protein trafficking and binding. The contribution of other cardiac ion channels to hERG data interpretation is also discussed. In addition, endpoint measures of the integrated activity of cardiac ion channels at the single-cell, tissue, and whole-animal level, including for example the well-established action potential to the more recent beat-to-beat variability, transmural dispersion of repolarization, and field potential duration, are described in the context of their ability to predict QT prolongation and torsadogenicity in humans.

Design and formulation of functional pluripotent stem cell-derived cardiac microtissues

Access to robust and information-rich human cardiac tissue models would accelerate drug-based strategies for treating heart disease. Despite significant effort, the generation of high-fidelity adult-like human cardiac tissue analogs remains challenging. We used computational modeling of tissue contraction and assembly mechanics in conjunction with microfabricated constraints to guide the design of aligned and functional 3D human pluripotent stem cell (hPSC)-derived cardiac microtissues that we term cardiac microwires (CMWs). Miniaturization of the platform circumvented the need for tissue vascularization and enabled higher-throughput image-based analysis of CMW drug responsiveness. CMW tissue properties could be tuned using electromechanical stimuli and cell composition. Specifically, controlling self-assembly of 3D tissues in aligned collagen, and pacing with point stimulation electrodes, were found to promote cardiac maturation-associated gene expression and in vivo-like electrical signal propagation. Furthermore, screening a range of hPSC-derived cardiac cell ratios identified that 75% NKX2 Homeobox 5 (NKX2-5)+ cardiomyocytes and 25% Cluster of Differentiation 90 OR (CD90)+ nonmyocytes optimized tissue remodeling dynamics and yielded enhanced structural and functional properties. Finally, we demonstrate the utility of the optimized platform in a tachycardic model of arrhythmogenesis, an aspect of cardiac electrophysiology not previously recapitulated in 3D in vitro hPSC-derived cardiac microtissue models. The design criteria identified with our CMW platform should accelerate the development of predictive in vitro assays of human heart tissue function.

A public-private consortium advances cardiac safety evaluation: achievements of the HESI Cardiac Safety Technical Committee

INTRODUCTION

The evaluation of cardiovascular side-effects is a critical element in the development of all new drugs and chemicals. Cardiac safety issues are a major cause of attrition and withdrawal due to adverse drug reactions (ADRs) in pharmaceutical drug development.

METHODS

The evolution of the HESI Technical Committee on Cardiac Safety from 2000-2013 is presented as an example of an effective international consortium of academic, government, and industry scientists working to improve cardiac safety.

RESULTS AND DISCUSSION

The HESI Technical Committee Working Groups facilitated the development of a variety of platforms for resource sharing and communication among experts that led to innovative strategies for improved drug safety. The positive impacts arising from these Working Groups are described in this article.