Predicting discrete-time bifurcations with deep learning.

Many natural and man-made systems are prone to critical transitions-abrupt and potentially devastating changes in dynamics. Deep learning classifiers can provide an early warning signal for critical transitions by learning generic features of bifurcations from large simulated training data sets. So far, classifiers have only been trained to predict continuous-time bifurcations, ignoring rich dynamics unique to discrete-time bifurcations. Here, we train a deep learning classifier to provide an early warning signal for the five local discrete-time bifurcations of codimension-one. We test the classifier on simulation data from discrete-time models used in physiology, economics and ecology, as well as experimental data of spontaneously beating chick-heart aggregates that undergo a period-doubling bifurcation. The classifier shows higher sensitivity and specificity than commonly used early warning signals under a wide range of noise intensities and rates of approach to the bifurcation. It also predicts the correct bifurcation in most cases, with particularly high accuracy for the period-doubling, Neimark-Sacker and fold bifurcations. Deep learning as a tool for bifurcation prediction is still in its nascence and has the potential to transform the way we monitor systems for critical transitions.

Rhythms from Two Competing Periodic Sources Embedded in an Excitable Medium.

In an excitable medium, a stimulus generates a wave that propagates in space until it reaches the boundary or collides with another wave and annihilates. We study the dynamics generated by two periodic sources with different frequencies in excitable cardiac tissue culture using optogenetic techniques. The observed rhythms, which can be modeled using cellular automata and studied analytically, show unexpected regularities related to classic results in number theory. We apply the results to identify cardiac arrhythmias in people that are due to a putative mechanism of two competing pacemakers.

KHz-rate volumetric voltage imaging of the whole Zebrafish heart.

Fast volumetric imaging is essential for understanding the function of excitable tissues such as those found in the brain and heart. Measuring cardiac voltage transients in tissue volumes is challenging, especially at the high spatial and temporal resolutions needed to give insight to cardiac function. We introduce a new imaging modality based on simultaneous illumination of multiple planes in the tissue and parallel detection with multiple cameras, avoiding compromises inherent in any scanning approach. The system enables imaging of voltage transients in situ, allowing us, for the first time to our knowledge, to map voltage activity in the whole heart volume at KHz rates. The high spatiotemporal resolution of our method enabled the observation of novel dynamics of electrical propagation through the zebrafish atrioventricular canal.

Universal mechanisms for self-termination of rapid cardiac rhythm.

Excitable media sustain circulating waves. In the heart, sustained circulating waves can lead to serious impairment or even death. To investigate factors affecting the stability of such waves, we have used optogenetic techniques to stimulate a region at the apex of a mouse heart at a fixed delay after the detection of excitation at the base of the heart. For long delays, rapid circulating rhythms can be sustained, whereas for shorter delays, there are paroxysmal bursts of activity that start and stop spontaneously. By considering the dependence of the action potential and conduction velocity on the preceding recovery time using restitution curves, as well as the reduced excitability (fatigue) due to the rapid excitation, we model prominent features of the dynamics including alternation of the duration of the excited phases and conduction times, as well as termination of the bursts for short delays. We propose that this illustrates universal mechanisms that exist in biological systems for the self-termination of such activities.

High-throughput phenotyping of heteromeric human ether-à-go-go-related gene potassium channel variants can discriminate pathogenic from rare benign variants.

BACKGROUND: KCNH2 encodes the human ether-à-go-go-related gene potassium channel, which passes the rapid delayed rectifier potassium current. Loss-of-function variants in KCNH2 cause long QT syndrome type 2, which is associated with a markedly increased risk of cardiac arrhythmias. The majority of rare KCNH2 variants, however, are likely to be benign. OBJECTIVE: The purpose of this study was to develop a high-throughput assay for discriminating pathogenic from benign KCNH2 variants. METHODS: Nonsynonymous homozygous KCNH2 variants stably expressed in Flp-In human embryonic kidney 293 cell lines were phenotyped using an automated patch-clamp platform and a cell surface enzyme-linked immunosorbent assay. Functional phenotyping of heterozygous KCNH2 variants stably expressed in Flp-In human embryonic kidney 293 cell lines using a bicistronic vector was performed using an automated patch-clamp platform. RESULTS: In homozygous KCNH2 variant cell lines, discrepancies between current density and cell surface expression levels measured using an enzyme-linked immunosorbent assay can be explained by changes in gating properties of the variant channels. For the 30 heterozygous KCNH2 variant cell lines studied, the assay correctly predicted the ClinVar ascribed classification for 17/17 pathogenic/likely pathogenic/benign variants. Of the 13 pore-domain variants studied, 11 had a dominant-negative expression defect while the remaining 2 had enhanced inactivation gating, resulting in a dominant-negative phenotype. CONCLUSION: High-throughput electrophysiological phenotyping of heterozygous KCNH2 variants can accurately distinguish between dominant-negative, haploinsufficient loss-of-function, and benign variants. This assay will help with future classification of KCNH2 variants.

Development, calibration, and validation of a novel human ventricular myocyte model in health, disease, and drug block.

Human-based modelling and simulations are becoming ubiquitous in biomedical science due to their ability to augment experimental and clinical investigations. Cardiac electrophysiology is one of the most advanced areas, with cardiac modelling and simulation being considered for virtual testing of pharmacological therapies and medical devices. Current models present inconsistencies with experimental data, which limit further progress. In this study, we present the design, development, calibration and independent validation of a human-based ventricular model (ToR-ORd) for simulations of electrophysiology and excitation-contraction coupling, from ionic to whole-organ dynamics, including the electrocardiogram. Validation based on substantial multiscale simulations supports the credibility of the ToR-ORd model under healthy and key disease conditions, as well as drug blockade. In addition, the process uncovers new theoretical insights into the biophysical properties of the L-type calcium current, which are critical for sodium and calcium dynamics. These insights enable the reformulation of L-type calcium current, as well as replacement of the hERG current model.

Decades of intensive experimental and clinical research have revealed much about how the human heart works. Though incomplete, this knowledge has been used to construct computer models that represent the activity of this organ as a whole, and of its individual chambers (the atria and ventricles), tissues and cells. Such models have been used to better understand life-threatening irregular heartbeats; they are also beginning to be used to guide decisions about the treatment of patients and the development of new drugs by the pharmaceutical industry. Yet existing computer models of the electrical activity of the human heart are sometimes inconsistent with experimental data. This problem led Tomek et al. to try to create a new model that was consistent with established biophysical knowledge and experimental data for a wide range of conditions including disease and drug action. Tomek et al. designed a strategy that explicitly separated the construction and validation of a model that could recreate the electrical activity of the ventricles in a human heart. This model was able to integrate and explain a wide range of properties of both healthy and diseased hearts, including their response to different drugs. The development of the model also uncovered and resolved theoretical inconsistencies that have been present in almost all models of the heart from the last 25 years. Tomek et al. hope that their new human heart model will enable more basic, translational and clinical research into a range of heart diseases and accelerate the development of new therapies.

Hsp70 and DNAJA2 limit CFTR levels through degradation.

Cystic Fibrosis is caused by mutations in the CFTR anion channel, many of which cause its misfolding and degradation. CFTR folding depends on the Hsc70 and Hsp70 chaperones and their co-chaperone DNAJA1, but Hsc70/Hsp70 is also involved in CFTR degradation. Here, we address how these opposing functions are balanced. DNAJA2 and DNAJA1 were both important for CFTR folding, however overexpressing DNAJA2 but not DNAJA1 enhanced CFTR degradation at the endoplasmic reticulum by Hsc70/Hsp70 and the E3 ubiquitin ligase CHIP. Excess Hsp70 also promoted CFTR degradation, but this occurred through the lysosomal pathway and required CHIP but not complex formation with HOP and Hsp90. Notably, the Hsp70 inhibitor MKT077 enhanced levels of mature CFTR and the most common disease variant ΔF508-CFTR, by slowing turnover and allowing delayed maturation, respectively. MKT077 also boosted the channel activity of ΔF508-CFTR when combined with the corrector compound VX809. Thus, the Hsp70 system is the major determinant of CFTR degradation, and its modulation can partially relieve the misfolding phenotype.

Double-wave reentry in excitable media.

A monolayer of chick embryo cardiac cells grown in an annular geometry supports two simultaneous reentrant excitation waves that circulate as a doublet. We propose a mechanism that can lead to such behavior. The velocity restitution gives the instantaneous velocity of a wave as a function of the time since the passage of the previous wave at a given point in space. Nonmonotonic restitution relationships will lead to situations in which various spacings between circulating waves are possible. In cardiology, the situation in which two waves travel in an anatomically defined circuit is referred to as double-wave reentry. Since double-wave reentry may arise as a consequence of pacing during cardiac arrhythmias, understanding the dynamic features of double-wave reentry may be helpful in understanding the physiological properties of cardiac tissue and in the design of therapy.

Mutation-specific peripheral and ER quality control of hERG channel cell-surface expression.

Impaired functional plasma membrane (PM) expression of the hERG K+-channel is associated with Long-QT syndrome type-2 (LQT2) and increased risk of cardiac arrhythmia. Reduced PM-expression is primarily attributed to retention and degradation of misfolded channels by endoplasmic reticulum (ER) protein quality control (QC) systems. However, as the molecular pathogenesis of LQT2 was defined using severely-misfolded hERG variants with limited PM-expression, the potential contribution of post-ER (peripheral) QC pathways to the disease phenotype remains poorly established. Here, we investigate the cellular processing of mildly-misfolded Per-Arnt-Sim (PAS)-domain mutant hERGs, which display incomplete ER-retention and PM-expression defects at physiological temperature. We show that the attenuated PM-expression of hERG is dictated by mutation-specific contributions from both the ER and peripheral QC systems. At the ER, PAS-mutants experience inefficient conformational maturation coupled with rapid ubiquitin-dependent proteasomal degradation. In post-ER compartments, they are rapidly endocytosed from the PM via a ubiquitin-independent mechanism and rapidly targeted for lysosomal degradation. Conformational destabilization underlies aberrant cellular processing at both ER- and post-ER compartments, since conformational correction by a hERG-specific pharmacochaperone or low-temperatures can restore WT-like trafficking. Our results demonstrate that the post-ER QC alone or jointly with the ER QC determines the loss-of-PM-expression phenotype of a subset of LQT2 mutations.

Aldosterone and Ion Channels.

Since its discovery, aldosterone and ion modulation have been entwined. While scientific investigations throughout the decades have emphasized aldosterone's connection to Na+, K+, and H+ homeostasis, more recent research has demonstrated a relationship between aldosterone and Mg2+, Ca2+, and Cl- homeostasis. The mechanisms connecting aldosterone to ion regulation frequently involve ion channels; the membrane localized proteins containing at least one aqueous pore for ion conduction. In order to precisely control intracellular or intraorganelle ion concentrations, ion channels have evolved highly specific regions within the conduction pore that select ions by charge, size, and/or dehydration energy requirement, meaning aldosterone must be able to modulate multiple ion channels to regulate the many ions described above. The list of ion channels presently connected to aldosterone includes ENaC (Na+), ROMK/BK (K+), TRPV4/5/6 (Ca2+), TRPM7/6 (Mg2+), and ClC-K/CFTR (Cl-), among others. This list is only expected to grow over time, as the promiscuity of aldosterone becomes more understood.

Defining the pattern of initiation of monomorphic ventricular tachycardia using the beat-to-beat intervals recorded on implantable cardioverter defibrillators from the RAFT study: A computer-based algorithm.

Arrhythmia onset pattern may have important implications on morbidity, recurrent implantable cardioverter defibrillator (ICD) shocks, and mortality, given the proposed correlation between initiation pattern and arrhythmia mechanism. Therefore, we developed and tested a computer-based algorithm to differentiate the pattern of initiation based on the beat-to-beat intervals of the ventricular tachycardia (VT) episodes in ICD recordings from the Resynchronization-Defibrillation for Ambulatory Heart Failure Trial (RAFT). Intervals on intracardiac electrograms from ICDs were analyzed backwards starting from the marker of VT detection, comparing each interval with the average tachycardia cycle length. If the morphology of the beat initiating the VT was similar to the morphology of the VT itself, the episode was considered sudden. If the morphology of the beat initiating the VT was not similar to the morphology of the VT itself, the episode was considered non-sudden. The capability of the algorithm to classify the pattern of initiation based only on the beat-to-beat intervals allows for the classification and analysis of large datasets to further investigate the clinical importance of classifying VT initiation. If analysis of the VT initiation proves to be of clinical value, this algorithm could potentially be integrated into ICD software, which would make it easily accessible and potentially helpful in clinical decision-making.

Aldosterone, SGK1, and ion channels in the kidney.

Hyperaldosteronism, a common cause of hypertension, is strongly connected to Na+, K+, and Mg2+ dysregulation. Owing to its steroidal structure, aldosterone is an active transcriptional modifier when bound to the mineralocorticoid receptor (MR) in cells expressing the enzyme 11ß-hydroxysteroid dehydrogenase 2, such as those comprising the aldosterone-sensitive distal nephron (ASDN). One such up-regulated protein, the ubiquitous serum and glucocorticoid regulated kinase 1 (SGK1), has the capacity to modulate the surface expression and function of many classes of renal ion channels, including those that transport Na+ (ENaC), K+ (ROMK/BK), Ca2+ (TRPV4/5/6), Mg2+ (TRPM7/6), and Cl- (ClC-K, CFTR). Here, we discuss the mechanisms by which ASDN expressed channels are up-regulated by SGK1, while highlighting newly discovered pathways connecting aldosterone to nonselective cation channels that are permeable to Mg2+ (TRPM7) or Ca2+ (TRPV4).

Demonstration of cardiac rotor and source mapping techniques in embryonic chick monolayers.

Excitable media, such as the heart, display propagating waves with different geometries including target patterns and rotors (spiral waves). Collision of two waves leads to annihilation of both. We present algorithms for data processing and analysis to identify the core of rotors. In this work, we show that as the spatial sampling resolution decreases it becomes increasingly difficult to identify rotors-there are instances of false negatives and false positives. These observations are relevant to current controversies concerning the role of rotors in the initiation, maintenance, and treatment of cardiac arrhythmias, especially atrial fibrillation. Currently some practitioners target the core of rotors for ablation, but the effectiveness of this procedure has been questioned. In view of the difficulties inherent in the identification of rotors, we conclude that methods to identify rotors need to first be validated prior to assessing the efficacy of ablation.

Characterization of constitutive and acid-induced outwardly rectifying chloride currents in immortalized mouse distal tubular cells.

Thiazides block Na+ reabsorption while enhancing Ca2+ reabsorption in the kidney. As previously demonstrated in immortalized mouse distal convoluted tubule (MDCT) cells, chlorothiazide application induced a robust plasma membrane hyperpolarization, which increased Ca2+ uptake. This essential thiazide-induced hyperpolarization was prevented by the Cl- channel inhibitor 5-Nitro-2-(3-phenylpropylamino) benzoic acid (NPPB), implicating NPPB-sensitive Cl- channels, however the nature of these Cl- channels has been rarely described in the literature. Here we show that MDCT cells express a dominant, outwardly rectifying Cl- current at extracellular pH7.4. This constitutive Cl- current was more permeable to larger anions (Eisenman sequence I; I->Br-≥Cl-) and was substantially inhibited by >100mM [Ca2+]o, which distinguished it from ClC-K2/barttin. Moreover, the constitutive Cl- current was blocked by NPPB, along with other Cl- channel inhibitors (4,4'-diisothiocyanatostilbene-2,2'-disulfonate, DIDS; flufenamic acid, FFA). Subjecting the MDCT cells to an acidic extracellular solution (pH<5.5) induced a substantially larger outwardly rectifying NPPB-sensitive Cl- current. This acid-induced Cl- current was also anion permeable (I->Br->Cl-), but was distinguished from the constitutive Cl- current by its rectification characteristics, ion sensitivities, and response to FFA. In addition, we have identified similar outwardly rectifying and acid-sensitive currents in immortalized cells from the inner medullary collecting duct (mIMCD-3 cells). Expression of an acid-induced Cl- current would be particularly relevant in the acidic IMCD (pH<5.5). To our knowledge, the properties of these Cl- currents are unique and provide the mechanisms to account for the Cl- efflux previously speculated to be present in MDCT cells.

Varieties of reentrant dynamics.

Experiments were carried out in monolayer tissue cultures of embryonic chick heart cells imaged using a calcium sensitive fluorescent dye. The cells were grown in annular geometries and in annular geometries with an isthmus connecting antipodal region of the annulus. We observed a large number of spatially different patterns of propagation consisting of one or more circulating waves. As well, we also observed rhythms in which rotors embedded in the annuli generated propagating pulses. These results demonstrate that many different patterns of excitation can be present in cardiac tissue with simple geometries.

Pattern of initiation of monomorphic ventricular tachycardia and implications on tachycardia mechanism.

The incidence of sudden cardiac death, predominantly caused by ventricular tachycardia and ventricular fibrillation, is high in patients with congestive heart failure. Implantable cardiac defibrillators have improved survival in this population but defibrillator shocks can lead to low quality of life and heart failure progression. The current management of recurrent ventricular tachycardia includes ablation and anti-arrhythmic drugs and both are associated with high recurrence rates. Better understanding the mechanism of ventricular tachycardia allowing individualization of treatment may improve outcomes. Re-entry is currently accepted as the mechanism of the majority of monomorphic ventricular tachycardias in patients with congestive heart failure, being responsible for more than 90% of the ventricular tachycardia in patients with ischemic cardiomyopathy. On the other hand, some studies show a greater participation of focal arrhythmias in the genesis of ventricular tachycardia in this population. The pattern of initiation of ventricular tachycardia is divided into sudden, when the first beat of the tachycardia is morphologically similar to the rest of the tachycardia, and non-sudden, when its morphology is dissimilar. An association between the pattern of the initiation and the mechanism of ventricular tachycardia has been proposed. The pattern of initiation of ventricular tachycardia is a readily available from data stored in current generation implantable cardiac defibrillators. The association with tachycardia mechanism may allow individualization of the therapy, however evidence is lacking and further research is required.

Bag1 Co-chaperone Promotes TRC8 E3 Ligase-dependent Degradation of Misfolded Human Ether a Go-Go-related Gene (hERG) Potassium Channels.

Cardiac long QT syndrome type 2 is caused by mutations in the human ether a go-go-related gene (hERG) potassium channel, many of which cause misfolding and degradation at the endoplasmic reticulum instead of normal trafficking to the cell surface. The Hsc70/Hsp70 chaperones assist the folding of the hERG cytosolic domains. Here, we demonstrate that the Hsp70 nucleotide exchange factor Bag1 promotes hERG degradation by the ubiquitin-proteasome system at the endoplasmic reticulum to regulate hERG levels and channel activity. Dissociation of hERG complexes containing Hsp70 and the E3 ubiquitin ligase CHIP requires the interaction of Bag1 with Hsp70, but this does not involve the Bag1 ubiquitin-like domain. The interaction with Bag1 then shifts hERG degradation to the membrane-anchored E3 ligase TRC8 and its E2-conjugating enzyme Ube2g2, as determined by siRNA screening. TRC8 interacts through the transmembrane region with hERG and decreases hERG functional expression. TRC8 also mediates degradation of the misfolded hERG-G601S disease mutant, but pharmacological stabilization of the mutant structure prevents degradation. Our results identify TRC8 as a previously unknown Hsp70-independent quality control E3 ligase for hERG.

Aldosterone Upregulates Transient Receptor Potential Melastatin 7 (TRPM7).

Transient receptor potential melastatin 7 (TRPM7) is a ubiquitously expressed Mg(2+)-permeable ion channel fused to a C-terminal α-kinase domain. Recently, aldosterone was shown to increase intracellular Mg(2+) levels and alter inflammatory signaling in TRPM7-expressing HEK293 cells. This study was undertaken to assess whether these effects were related to an aldosterone-mediated increase of TRPM7 current and/or plasma membrane localization. Using HEK293 cells stably expressing WT-TRPM7, we found that 18-h application of aldosterone significantly increased TRPM7 current and TRPM7 plasma membrane protein expression by 48% and 34%, respectively. The aldosterone-mediated increase of TRPM7 current was inhibited by eplerenone, a mineralocorticoid receptor (MR) blocker, and GSK-650394, an inhibitor of the serum- and glucocorticoid-regulated kinase 1 (SGK1). SGK1 blockade also prevented the aldosterone-induced increase of TRPM7 plasma membrane protein. It was further determined that K1648R-TRPM7, the phosphotransferase-inactive TRPM7 mutant, was unresponsive to aldosterone. Therefore, chronic aldosterone treatment increases the plasma membrane expression of TRPM7, which is associated with an increase of TRPM7 current. This process occurs via an MR-dependent, genomic signaling cascade involving SGK1 and a functioning TRPM7 α-kinase domain. We suggest that this mechanism may be of general relevance when interpreting the effects of aldosterone because the MR receptor is found in multiple tissues, and TRPM7 and SGK1 are ubiquitously expressed.