Computational modeling of cardiac optogenetics : Methodology overview & review of fi ndings from simulations $
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paper_title: Tachycardia in Post-Infarction Hearts: Insights from 3D Image-Based Ventricular Models

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Ventricular tachycardia, a life-threatening regular and repetitive fast heart rhythm, frequently occurs in the setting of myocardial infarction. Recently, the peri-infarct zones surrounding the necrotic scar (termed gray zones) have been shown to correlate with ventricular tachycardia inducibility. However, it remains unknown how the latter is determined by gray zone distribution and size. The goal of this study is to examine how tachycardia circuits are maintained in the infarcted heart and to explore the relationship between the tachycardia organizing centers and the infarct gray zone size and degree of heterogeneity. To achieve the goals of the study, we employ a sophisticated high-resolution electrophysiological model of the infarcted canine ventricles reconstructed from imaging data, representing both scar and gray zone. The baseline canine ventricular model was also used to generate additional ventricular models with different gray zone sizes, as well as models in which the gray zone was represented as different heterogeneous combinations of viable tissue and necrotic scar. The results of the tachycardia induction simulations with a number of high-resolution canine ventricular models (22 altogether) demonstrated that the gray zone was the critical factor resulting in arrhythmia induction and maintenance. In all models with inducible arrhythmia, the scroll-wave filaments were contained entirely within the gray zone, regardless of its size or the level of heterogeneity of its composition. The gray zone was thus found to be the arrhythmogenic substrate that promoted wavebreak and reentry formation. We found that the scroll-wave filament locations were insensitive to the structural composition of the gray zone and were determined predominantly by the gray zone morphology and size. The findings of this study have important implications for the advancement of improved criteria for stratifying arrhythmia risk in post-infarction patients and for the development of new approaches for determining the ablation targets of infarct-related tachycardia.
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paper_title: Stimulating Cardiac Muscle by Light: Cardiac Optogenetics by Cell Delivery

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Background —After the recent cloning of light-sensitive ion channels and their expression in mammalian cells, a new field, optogenetics, emerged in neuroscience, allowing for precise perturbations of neural circuits by light. However, functionality of optogenetic tools has not been fully explored outside neuroscience; and a non-viral, non-embryogenesis based strategy for optogenetics has not been shown before. ::: ::: Methods and Results —We demonstrate the utility of optogenetics to cardiac muscle by a tandem cell unit (TCU) strategy, where non-excitable cells carry exogenous light-sensitive ion channels, and when electrically coupled to cardiomyocytes, produce optically-excitable heart tissue. A stable channelrhodopsin2 (ChR2) expressing cell line was developed, characterized and used as a cell delivery system. The TCU strategy was validated in vitro in cell pairs with adult canine myocytes (for a wide range of coupling strengths) and in cardiac syncytium with neonatal rat cardiomyocytes. For the first time, we combined optical excitation and optical imaging to capture light-triggered muscle contractions and high-resolution propagation maps of light-triggered electrical waves, found to be quantitatively indistinguishable from electrically-triggered waves. ::: ::: Conclusions —Our results demonstrate feasibility to control excitation and contraction in cardiac muscle by light using the TCU approach. Optical pacing in this case uses less energy, offers superior spatiotemporal control, remote access and can serve not only as an elegant tool in arrhythmia research, but may form the basis for a new generation of light-driven cardiac pacemakers and muscle actuators. The TCU strategy is extendable to (non-viral) stem cell therapy and is directly relevant to in vivo applications.
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paper_title: A comprehensive multiscale framework for simulating optogenetics in the heart

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Optogenetics has emerged as an alternative method for electrical control of the heart, where illumination is used to elicit a bioelectric response in tissue modified to express photosensitive proteins (opsins). This technology promises to enable evocation of spatiotemporally precise responses in targeted cells or tissues, thus creating new possibilities for safe and effective therapeutic approaches to ameliorate cardiac function. Here we present a comprehensive framework for multiscale modelling of cardiac optogenetics, allowing both mechanistic examination of optical control and exploration of potential therapeutic applications. The framework incorporates accurate representations of opsin channel kinetics and delivery modes, spatial distribution of photosensitive cells, and tissue illumination constraints, making possible the prediction of emergent behaviour resulting from interactions at sub-organ scales. We apply this framework to explore how optogenetic delivery characteristics determine energy requirements for optical stimulation and to identify cardiac structures that are potential pacemaking targets with low optical excitation thresholds.
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paper_title: Methodology for image-based reconstruction of ventricular geometry for patient-specific modeling of cardiac electrophysiology.

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Patient-specific modeling of ventricular electrophysiology requires an interpolated reconstruction of the 3-dimensional (3D) geometry of the patient ventricles from the low-resolution (Lo-res) clinical images. The goal of this study was to implement a processing pipeline for obtaining the interpolated reconstruction, and thoroughly evaluate the efficacy of this pipeline in comparison with alternative methods. The pipeline implemented here involves contouring the epi- and endocardial boundaries in Lo-res images, interpolating the contours using the variational implicit functions method, and merging the interpolation results to obtain the ventricular reconstruction. Five alternative interpolation methods, namely linear, cubic spline, spherical harmonics, cylindrical harmonics, and shape-based interpolation were implemented for comparison. In the thorough evaluation of the processing pipeline, Hi-res magnetic resonance (MR), computed tomography (CT), and diffusion tensor (DT) MR images from numerous hearts were used. Reconstructions obtained from the Hi-res images were compared with the reconstructions computed by each of the interpolation methods from a sparse sample of the Hi-res contours, which mimicked Lo-res clinical images. Qualitative and quantitative comparison of these ventricular geometry reconstructions showed that the variational implicit functions approach performed better than others. Additionally, the outcomes of electrophysiological simulations (sinus rhythm activation maps and pseudo-ECGs) conducted using models based on the various reconstructions were compared. These electrophysiological simulations demonstrated that our implementation of the variational implicit functions-based method had the best accuracy.
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paper_title: Channelrhodopsin-2, a directly light-gated cation-selective membrane channel

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Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 (ChR1), a recently identified light-gated proton channel from the green alga Chlamydomonas reinhardtii. ChR1 and ChR2, a related microbial-type rhodopsin from C. reinhardtii, were shown to be involved in generation of photocurrents of this green alga. We demonstrate by functional expression, both in oocytes of Xenopus laevis and mammalian cells, that ChR2 is a directly light-switched cation-selective ion channel. This channel opens rapidly after absorption of a photon to generate a large permeability for monovalent and divalent cations. ChR2 desensitizes in continuous light to a smaller steady-state conductance. Recovery from desensitization is accelerated by extracellular H+ and negative membrane potential, whereas closing of the ChR2 ion channel is decelerated by intracellular H+. ChR2 is expressed mainly in C. reinhardtii under low-light conditions, suggesting involvement in photoreception in dark-adapted cells. The predicted seven-transmembrane alpha helices of ChR2 are characteristic for G protein-coupled receptors but reflect a different motif for a cation-selective ion channel. Finally, we demonstrate that ChR2 may be used to depolarize small or large cells, simply by illumination.
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paper_title: Length-dependent tension in the failing heart and the efficacy of cardiac resynchronization therapy

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Aims Cardiac resynchronization therapy (CRT) has emerged as one of the few effective and safe treatments for heart failure. However, identifying patients that will benefit from CRT remains controversial. The dependence of CRT efficacy on organ and cellular scale mechanisms was investigated in a patient-specific computer model to identify novel patient selection criteria. ::: ::: Methods and results A biophysically based patient-specific coupled electromechanics heart model has been developed which links the cellular and sub-cellular mechanisms which regulate cardiac function to the whole organ function observed clinically before and after CRT. A sensitivity analysis of the model identified lack of length dependence of tension regulation within the sarcomere as a significant contributor to the efficacy of CRT. Further simulation analysis demonstrated that in the whole heart, length-dependent tension development is key not only for the beat-to-beat regulation of stroke volume (Frank–Starling mechanism), but also the homogenization of tension development and strain. ::: ::: Conclusions In individuals with effective Frank–Starling mechanism, the length dependence of tension facilitates the homogenization of stress and strain. This can result in synchronous contraction despite asynchronous electrical activation. In these individuals, synchronizing electrical activation through CRT may have minimal benefit.
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paper_title: Millisecond-timescale, genetically targeted optical control of neural activity

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Temporally precise, noninvasive control of activity in well-defined neuronal populations is a long-sought goal of systems neuroscience. We adapted for this purpose the naturally occurring algal protein Channelrhodopsin-2, a rapidly gated light-sensitive cation channel, by using lentiviral gene delivery in combination with high-speed optical switching to photostimulate mammalian neurons. We demonstrate reliable, millisecond-timescale control of neuronal spiking, as well as control of excitatory and inhibitory synaptic transmission. This technology allows the use of light to alter neural processing at the level of single spikes and synaptic events, yielding a widely applicable tool for neuroscientists and biomedical engineers.
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paper_title: Molecular and Cellular Approaches for Diversifying and Extending Optogenetics

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Optogenetic technologies employ light to control biological processes within targeted cells in vivo with high temporal precision. Here, we show that application of molecular trafficking principles can expand the optogenetic repertoire along several long-sought dimensions. Subcellular and transcellular trafficking strategies now permit (1) optical regulation at the far-red/infrared border and extension of optogenetic control across the entire visible spectrum, (2) increased potency of optical inhibition without increased light power requirement (nanoampere-scale chloride-mediated photocurrents that maintain the light sensitivity and reversible, step-like kinetic stability of earlier tools), and (3) generalizable strategies for targeting cells based not only on genetic identity, but also on morphology and tissue topology, to allow versatile targeting when promoters are not known or in genetically intractable organisms. Together, these results illustrate use of cell-biological principles to enable expansion of the versatile fast optogenetic technologies suitable for intact-systems biology and behavior.
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paper_title: "Beauty is a light in the heart": the transformative potential of optogenetics for clinical applications in cardiovascular medicine.

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Optogenetics is an exciting new technology in which viral gene or cell delivery is used to inscribe light sensitivity in excitable tissue to enable optical control of bioelectric behavior. Initial progress in the fledgling domain of cardiac optogenetics has included in vitro expression of various light-sensitive proteins in cell monolayers and transgenic animals to demonstrate an array of potentially useful applications, including light-based pacing, silencing of spontaneous activity, and spiral wave termination. In parallel to these developments, the cardiac modeling community has developed a versatile computational framework capable of realistically simulating optogenetics in biophysically detailed, patient-specific representations of the human heart, enabling the exploration of potential clinical applications in a predictive virtual platform. Toward the ultimate goal of assessing the feasibility and potential impact of optogenetics-based therapies in cardiovascular medicine, this review provides (1) a detailed synopsis of in vivo, in vitro, and in silico developments in the field and (2) a critical assessment of how existing clinical technology for gene/cell delivery and intra-cardiac illumination could be harnessed to achieve such lofty goals as light-based arrhythmia termination.
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paper_title: Modulation of cardiac tissue electrophysiological properties with light-sensitive proteins.

paper_content:

AIMS ::: Optogenetics approaches, utilizing light-sensitive proteins, have emerged as unique experimental paradigms to modulate neuronal excitability. We aimed to evaluate whether a similar strategy could be used to control cardiac-tissue excitability. ::: ::: ::: METHODS AND RESULTS ::: A combined cell and gene therapy strategy was developed in which fibroblasts were transfected to express the light-activated depolarizing channel Channelrhodopsin-2 (ChR2). Patch-clamp studies confirmed the development of a robust inward current in the engineered fibroblasts following monochromatic blue-light exposure. The engineered cells were co-cultured with neonatal rat cardiomyocytes (or human embryonic stem cell-derived cardiomyocytes) and studied using a multielectrode array mapping technique. These studies revealed the ability of the ChR2-fibroblasts to electrically couple and pace the cardiomyocyte cultures at varying frequencies in response to blue-light flashes. Activation mapping pinpointed the source of this electrical activity to the engineered cells. Similarly, diffuse seeding of the ChR2-fibroblasts allowed multisite optogenetics pacing of the co-cultures, significantly shortening their electrical activation time and synchronizing contraction. Next, optogenetics pacing in an in vitro model of conduction block allowed the resynchronization of the tissue's electrical activity. Finally, the ChR2-fibroblasts were transfected to also express the light-sensitive hyperpolarizing proton pump Archaerhodopsin-T (Arch-T). Seeding of the ChR2/ArchT-fibroblasts allowed to either optogentically pace the cultures (in response to blue-light flashes) or completely suppress the cultures' electrical activity (following continuous illumination with 624 nm monochromatic light, activating ArchT). ::: ::: ::: CONCLUSIONS ::: The results of this proof-of-concept study highlight the unique potential of optogenetics for future biological pacemaking and resynchronization therapy applications and for the development of novel anti-arrhythmic strategies.
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paper_title: Optogenetic control of heart muscle in vitro and in vivo

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Stimulation of the light-activated cation channel channelrhodopsin-2 can depolarize heart muscle in vitro and in vivo, resulting in precise localized stimulation and constant prolonged depolarization of genetically targeted cardiomyocytes and cardiac tissue.
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paper_title: Image-based left ventricular shape analysis for sudden cardiac death risk stratification.

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BACKGROUND ::: Low left ventricular ejection fraction (LVEF), the main criterion used in the current clinical practice to stratify sudden cardiac death (SCD) risk, has low sensitivity and specificity. ::: ::: ::: OBJECTIVE ::: To uncover indices of left ventricular (LV) shape that differ between patients with a high risk of SCD and those with a low risk. ::: ::: ::: METHODS ::: By using clinical cardiac magnetic resonance imaging and computational anatomy tools, a novel computational framework to compare 3-dimensional LV endocardial surface curvedness, wall thickness, and relative wall thickness between patient groups was implemented. The framework was applied to cardiac magnetic resonance data of 61 patients with ischemic cardiomyopathy who were selected for prophylactic implantable cardioverter-defibrillator treatment on the basis of reduced LVEF. The patients were classified by outcome: group 0 had no events; group 1, arrhythmic events; and group 2, heart failure events. Segmental differences in LV shape were assessed. ::: ::: ::: RESULTS ::: Global LV volumes and mass were similar among groups. Compared with patients with no events, patients in groups 1 and 2 had lower mean shape metrics in all coronary artery regions, with statistical significance in 9 comparisons, reflecting wall thinning and stretching/flattening. ::: ::: ::: CONCLUSION ::: In patients with ischemic cardiomyopathy and low LVEF, there exist quantifiable differences in 3-dimensional endocardial surface curvedness, LV wall thickness, and LV relative wall thickness between those with no clinical events and those with arrhythmic or heart failure outcomes, reflecting adverse LV remodeling. This retrospective study is a proof of concept to demonstrate that regional LV remodeling indices have the potential to improve the personalized risk assessment for SCD.
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paper_title: Cardiac applications of optogenetics.

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In complex multicellular systems, such as the brain or the heart, the ability to selectively perturb and observe the response of individual components at the cellular level and with millisecond resolution in time, is essential for mechanistic understanding of function. Optogenetics uses genetic encoding of light sensitivity (by the expression of microbial opsins) to provide such capabilities for manipulation, recording, and control by light with cell specificity and high spatiotemporal resolution. As an optical approach, it is inherently scalable for remote and parallel interrogation of biological function at the tissue level; with implantable miniaturized devices, the technique is uniquely suitable for in vivo tracking of function, as illustrated by numerous applications in the brain. Its expansion into the cardiac area has been slow. Here, using examples from published research and original data, we focus on optogenetics applications to cardiac electrophysiology, specifically dealing with the ability to manipulate membrane voltage by light with implications for cardiac pacing, cardioversion, cell communication, and arrhythmia research, in general. We discuss gene and cell delivery methods of inscribing light sensitivity in cardiac tissue, functionality of the light-sensitive ion channels within different types of cardiac cells, utility in probing electrical coupling between different cell types, approaches and design solutions to all-optical electrophysiology by the combination of optogenetic sensors and actuators, and specific challenges in moving towards in vivo cardiac optogenetics.
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paper_title: Multiple-Color Optical Activation, Silencing, and Desynchronization of Neural Activity, with Single-Spike Temporal Resolution

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The quest to determine how precise neural activity patterns mediate computation, behavior, and pathology would be greatly aided by a set of tools for reliably activating and inactivating genetically targeted neurons, in a temporally precise and rapidly reversible fashion. Having earlier adapted a light-activated cation channel, channelrhodopsin-2 (ChR2), for allowing neurons to be stimulated by blue light, we searched for a complementary tool that would enable optical neuronal inhibition, driven by light of a second color. Here we report that targeting the codon-optimized form of the light-driven chloride pump halorhodopsin from the archaebacterium Natronomas pharaonis (hereafter abbreviated Halo) to genetically-specified neurons enables them to be silenced reliably, and reversibly, by millisecond-timescale pulses of yellow light. We show that trains of yellow and blue light pulses can drive high-fidelity sequences of hyperpolarizations and depolarizations in neurons simultaneously expressing yellow light-driven Halo and blue light-driven ChR2, allowing for the first time manipulations of neural synchrony without perturbation of other parameters such as spiking rates. The Halo/ChR2 system thus constitutes a powerful toolbox for multichannel photoinhibition and photostimulation of virally or transgenically targeted neural circuits without need for exogenous chemicals, enabling systematic analysis and engineering of the brain, and quantitative bioengineering of excitable cells.
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paper_title: Channelrhodopsin-2 and optical control of excitable cells

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Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrhodopsin-2 offers a new and promising solution by permitting minimally invasive, genetically targeted and temporally precise photostimulation. Here we explore technological issues relevant to the temporal precision, spatial targeting and physiological implementation of ChR2, in the context of other photostimulation approaches to optical control of excitable cells.
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paper_title: Cardiac optogenetics

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Optogenetics is an emerging technology for optical interrogation and control of biological function with high specificity and high spatiotemporal resolution. Mammalian cells and tissues can be sensitized to respond to light by a relatively simple and well-tolerated genetic modification using microbial opsins (light-gated ion channels and pumps). These can achieve fast and specific excitatory or inhibitory response, offering distinct advantages over traditional pharmacological or electrical means of perturbation. Since the first demonstrations of utility in mammalian cells (neurons) in 2005, optogenetics has spurred immense research activity and has inspired numerous applications for dissection of neural circuitry and understanding of brain function in health and disease, applications ranging from in vitro to work in behaving animals. Only recently (since 2010), the field has extended to cardiac applications with less than a dozen publications to date. In consideration of the early phase of work on cardiac optogenetics and the impact of the technique in understanding another excitable tissue, the brain, this review is largely a perspective of possibilities in the heart. It covers the basic principles of operation of light-sensitive ion channels and pumps, the available tools and ongoing efforts in optimizing them, overview of neuroscience use, as well as cardiac-specific questions of implementation and ideas for best use of this emerging technology in the heart.
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paper_title: High-performance genetically targetable optical neural silencing by light-driven proton pumps

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If the activity of genetically specified neurons is silenced in a temporally precise fashion, the roles of different cell classes in neural processes can be studied. Members of the class of light-driven outward proton pumps are now shown to mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 (Arch) enables near 100% silencing of neurons in the awake brain when virally expressed in the mouse cortex and illuminated with yellow light.
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paper_title: See the light: can optogenetics restore healthy heartbeats? And, if it can, is it really worth the effort?

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Cardiac optogenetics is an exciting new methodology in which light-sensitive ion channels are expressed in heart tissue to enable optical control of bioelectricity. This technology has the potential to open new avenues for safely and effectively treating rhythm disorders in the heart with gentle beams of light. Recently, we developed a comprehensive framework for modeling cardiac optogenetics. Simulations conducted in this platform will provide insights to guide in vitro investigation and steer the development of therapeutic applications - these are the first steps toward clinical translation. In this editorial, we review literature relevant to light-sensitive protein delivery and intracardiac illumination to provide a holistic feasibility assessment for optogenetics-based arrhythmia termination therapy. We then draw on examples from computational work to show that the optical control paradigm has undeniable advantages that cannot be attained with conventional electrotherapy. Hence, we argue that cardiac optogenetics is more than a flashy substitute for current approaches.
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paper_title: Feasibility of image-based simulation to estimate ablation target in human ventricular arrhythmia.

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BACKGROUND ::: Previous studies suggest that magnetic resonance imaging with late gadolinium enhancement (LGE) may identify slowly conducting tissues in scar-related ventricular tachycardia (VT). ::: ::: ::: OBJECTIVE ::: To test the feasibility of image-based simulation based on LGE to estimate ablation targets in VT. ::: ::: ::: METHODS ::: We conducted a retrospective study in 13 patients who had preablation magnetic resonance imaging for scar-related VT ablation. We used image-based simulation to induce VT and estimate target regions according to the simulated VT circuit. The estimated target regions were coregistered with the LGE scar map and the ablation sites from the electroanatomical map in the standard ablation approach. ::: ::: ::: RESULTS ::: In image-based simulation, VT was inducible in 12 (92.3%) patients. All VTs showed macroreentrant propagation patterns, and the narrowest width of estimated target region that an ablation line should span to prevent VT recurrence was 5.0 ± 3.4 mm. Of 11 patients who underwent ablation, the results of image-based simulation and the standard approach were consistent in 9 (82%) patients, where ablation within the estimated target region was associated with acute success (n = 8) and ablation outside the estimated target region was associated with failure (n = 1). In 1 (9%) case, the results of image-based simulation and the standard approach were inconsistent, where ablation outside the estimated target region was associated with acute success. ::: ::: ::: CONCLUSIONS ::: The image-based simulation can be used to estimate potential ablation targets of scar-related VT. The image-based simulation may be a powerful noninvasive tool for preprocedural planning of ablation procedures to potentially reduce the procedure time and complication rates.
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paper_title: Image-based models of cardiac structure with applications in arrhythmia and defibrillation studies

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Abstract The objective of this article is to present a set of methods for constructing realistic computational models of cardiac structure from high-resolution structural and diffusion tensor magnetic resonance images and to demonstrate the applicability of the models in simulation studies. The structural image is segmented to identify various regions such as normal myocardium, ventricles, and infarct. A finite element mesh is generated from the processed structural data, and fiber orientations are assigned to the elements. The Purkinje system, when visible, is modeled using linear elements that interconnect a set of manually identified points. The methods were applied to construct 2 different models; and 2 simulation studies, which demonstrate the applicability of the models in the analysis of arrhythmia and defibrillation, were performed. The models represent cardiac structure with unprecedented detail for simulation studies.
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paper_title: An accurate, fast and robust method to generate patient-specific cubic Hermite meshes

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Abstract In-silico continuum simulations of organ and tissue scale physiology often require a discretisation or mesh of the solution domain. Cubic Hermite meshes provide a smooth representation of anatomy that is well-suited for simulating large deformation mechanics. Models of organ mechanics and deformation have demonstrated significant potential for clinical application. However, the production of a personalised mesh from patient’s anatomy using medical images remains a major bottleneck in simulation workflows. To address this issue, we have developed an accurate, fast and automatic method for deriving patient-specific cubic Hermite meshes. The proposed solution customises a predefined template with a fast binary image registration step and a novel cubic Hermite mesh warping constructed using a variational technique. Image registration is used to retrieve the mapping field between the template mesh and the patient images. The variational warping technique then finds a smooth and accurate projection of this field into the basis functions of the mesh. Applying this methodology, cubic Hermite meshes are fitted to the binary description of shape with sub-voxel accuracy and within a few minutes, which is a significant advance over the existing state of the art methods. To demonstrate its clinical utility, a generic cubic Hermite heart biventricular model is personalised to the anatomy of four patients, and the resulting mechanical stability of these customised meshes is successfully demonstrated.
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paper_title: Multiple photocycles of channelrhodopsin.

paper_content:

Two rhodopsins with intrinsic ion conductance have been identified recently in Chlamydomonas reinhardtii. They were named "channelrhodopsins" ChR1 and ChR2. Both were expressed in Xenopus laevis oocytes, and their properties were studied qualitatively by two electrode voltage clamp techniques. ChR1 is specific for H+, whereas ChR2 conducts Na+, K+, Ca2+, and guanidinium. ChR2 responds to the onset of light with a peak conductance, followed by a smaller steady-state conductance. Upon a second stimulation, the peak is smaller and recovers to full size faster at high external pH. ChR1 was reported to respond with a steady-state conductance only but is demonstrated here to have a peak conductance at high light intensities too. We analyzed quantitatively the light-induced conductance of ChR1 and developed a reaction scheme that describes the photocurrent kinetics at various light conditions. ChR1 exists in two dark states, D1 and D2, that photoisomerize to the conducting states M1 and M2, respectively. Dark-adapted ChR1 is completely arrested in D1. M1 converts into D1 within milliseconds but, in addition, equilibrates with the second conducting state M2 that decays to the second dark state D2. Thus, light-adapted ChR1 represents a mixture of D1 and D2. D2 thermally reconverts to D1 in minutes, i.e., much slower than any reaction of the two photocycles.
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paper_title: ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation

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Channelrhodopsins (ChRs) are used to optogenetically depolarize neurons. We engineered a variant of ChR, denoted red-activatable ChR (ReaChR), that is optimally excited with orange to red light (λ ∼590-630 nm) and offers improved membrane trafficking, higher photocurrents and faster kinetics compared to existing red-shifted ChRs. Red light is less scattered by tissue and is absorbed less by blood than the blue to green wavelengths that are required by other ChR variants. We used ReaChR expressed in the vibrissa motor cortex to drive spiking and vibrissa motion in awake mice when excited with red light through intact skull. Precise vibrissa movements were evoked by expressing ReaChR in the facial motor nucleus in the brainstem and illumination with red light through the external auditory canal. Thus, ReaChR enables transcranial optical activation of neurons in deep brain structures without the need to surgically thin the skull, form a transcranial window or implant optical fibers.
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paper_title: Genetically encoded molecular tools for light-driven silencing of targeted neurons

paper_content:

Abstract The ability to silence, in a temporally precise fashion, the electrical activity of specific neurons embedded within intact brain tissue, is important for understanding the role that those neurons play in behaviors, brain disorders, and neural computations. “Optogenetic” silencers, genetically encoded molecules that, when expressed in targeted cells within neural networks, enable their electrical activity to be quieted in response to pulses of light, are enabling these kinds of causal circuit analyses studies. Two major classes of optogenetic silencer are in broad use in species ranging from worm to monkey: light-driven inward chloride pumps, or halorhodopsins, and light-driven outward proton pumps, such as archaerhodopsins and fungal light-driven proton pumps. Both classes of molecule, when expressed in neurons via viral or other transgenic means, enable the targeted neurons to be hyperpolarized by light. We here review the current status of these sets of molecules, and discuss how they are being discovered and engineered. We also discuss their expression properties, ionic properties, spectral characteristics, and kinetics. Such tools may not only find many uses in the quieting of electrical activity for basic science studies but may also, in the future, find clinical uses for their ability to safely and transiently shut down cellular electrical activity in a precise fashion.
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paper_title: Channelrhodopsin-2, a directly light-gated cation-selective membrane channel

paper_content:

Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 (ChR1), a recently identified light-gated proton channel from the green alga Chlamydomonas reinhardtii. ChR1 and ChR2, a related microbial-type rhodopsin from C. reinhardtii, were shown to be involved in generation of photocurrents of this green alga. We demonstrate by functional expression, both in oocytes of Xenopus laevis and mammalian cells, that ChR2 is a directly light-switched cation-selective ion channel. This channel opens rapidly after absorption of a photon to generate a large permeability for monovalent and divalent cations. ChR2 desensitizes in continuous light to a smaller steady-state conductance. Recovery from desensitization is accelerated by extracellular H+ and negative membrane potential, whereas closing of the ChR2 ion channel is decelerated by intracellular H+. ChR2 is expressed mainly in C. reinhardtii under low-light conditions, suggesting involvement in photoreception in dark-adapted cells. The predicted seven-transmembrane alpha helices of ChR2 are characteristic for G protein-coupled receptors but reflect a different motif for a cation-selective ion channel. Finally, we demonstrate that ChR2 may be used to depolarize small or large cells, simply by illumination.
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paper_title: Optical mapping of optogenetically shaped cardiac action potentials

paper_content:

Light-mediated silencing and stimulation of cardiac excitability, an important complement to electrical stimulation, promises important discoveries and therapies. To date, cardiac optogenetics has been studied with patch-clamp, multielectrode arrays, video microscopy, and an all-optical system measuring calcium transients. The future lies in achieving simultaneous optical acquisition of excitability signals and optogenetic control, both with high spatio-temporal resolution. Here, we make progress by combining optical mapping of action potentials with concurrent activation of channelrhodopsin-2 (ChR2) or halorhodopsin (eNpHR3.0), via an all-optical system applied to monolayers of neonatal rat ventricular myocytes (NRVM). Additionally, we explore the capability of ChR2 and eNpHR3.0 to shape action-potential waveforms, potentially aiding the study of short/long QT syndromes that result from abnormal changes in action potential duration (APD). These results show the promise of an all-optical system to acquire action potentials with precise temporal optogenetics control, achieving a long-sought flexibility beyond the means of conventional electrical stimulation.
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paper_title: Modulation of cardiac tissue electrophysiological properties with light-sensitive proteins.

paper_content:

AIMS ::: Optogenetics approaches, utilizing light-sensitive proteins, have emerged as unique experimental paradigms to modulate neuronal excitability. We aimed to evaluate whether a similar strategy could be used to control cardiac-tissue excitability. ::: ::: ::: METHODS AND RESULTS ::: A combined cell and gene therapy strategy was developed in which fibroblasts were transfected to express the light-activated depolarizing channel Channelrhodopsin-2 (ChR2). Patch-clamp studies confirmed the development of a robust inward current in the engineered fibroblasts following monochromatic blue-light exposure. The engineered cells were co-cultured with neonatal rat cardiomyocytes (or human embryonic stem cell-derived cardiomyocytes) and studied using a multielectrode array mapping technique. These studies revealed the ability of the ChR2-fibroblasts to electrically couple and pace the cardiomyocyte cultures at varying frequencies in response to blue-light flashes. Activation mapping pinpointed the source of this electrical activity to the engineered cells. Similarly, diffuse seeding of the ChR2-fibroblasts allowed multisite optogenetics pacing of the co-cultures, significantly shortening their electrical activation time and synchronizing contraction. Next, optogenetics pacing in an in vitro model of conduction block allowed the resynchronization of the tissue's electrical activity. Finally, the ChR2-fibroblasts were transfected to also express the light-sensitive hyperpolarizing proton pump Archaerhodopsin-T (Arch-T). Seeding of the ChR2/ArchT-fibroblasts allowed to either optogentically pace the cultures (in response to blue-light flashes) or completely suppress the cultures' electrical activity (following continuous illumination with 624 nm monochromatic light, activating ArchT). ::: ::: ::: CONCLUSIONS ::: The results of this proof-of-concept study highlight the unique potential of optogenetics for future biological pacemaking and resynchronization therapy applications and for the development of novel anti-arrhythmic strategies.
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paper_title: Photocycles of Channelrhodopsin-2

paper_content:

Recent developments have used light-activated channels or transporters to modulate neuronal activity. One such genetically-encoded modulator of activity, channelrhodopsin-2 (ChR2), depolarizes neurons in response to blue light. In this work, we first conducted electrophysiological studies of the photokinetics of hippocampal cells expressing ChR2, for various light stimulations. These and other experimental results were then used for systematic investigation of the previously proposed three-state and four-state models of the ChR2 photocycle. We show the limitations of the previously suggested three-state models and identify a four-state model that accurately follows the ChR2 photocurrents. We find that ChR2 currents decay biexponentially, a fact that can be explained by the four-state model. The model is composed of two closed (C1 and C2) and two open (O1 and O2) states, and our simulation results suggest that they might represent the dark-adapted (C1-O1) and light-adapted (C2-O2) branches. The crucial insight provided by the analysis of the new model is that it reveals an adaptation mechanism of the ChR2 molecule. Hence very simple organisms expressing ChR2 can use this form of light adaptation.
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paper_title: Independent optical excitation of distinct neural populations

paper_content:

Sequencing the transcriptomes of more than 100 species of alga yields new channelrhodopsins with promising properties for optogenetics. A far red–shifted channelrhodopsin, Chrimson, opens up new behavioral capabilities in Drosophila, and alongside a fast yet light-sensitive blue channelrhodopsin, Chronos, enables independent excitation of two neuronal populations in brain slices.
---
paper_title: Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation

paper_content:

Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation
---
paper_title: Light-induced termination of spiral wave arrhythmias by optogenetic engineering of atrial cardiomyocytes

paper_content:

Aims Atrial fibrillation (AF) is the most common cardiac arrhythmia and often involves reentrant electrical activation (e.g. spiral waves). Drug therapy for AF can have serious side effects including proarrhythmia, while electrical shock therapy is associated with discomfort and tissue damage. Hypothetically, forced expression and subsequent activation of light-gated cation channels in cardiomyocytes might deliver a depolarizing force sufficient for defibrillation, thereby circumventing the aforementioned drawbacks. We therefore investigated the feasibility of light-induced spiral wave termination through cardiac optogenetics. ::: ::: Methods and results Neonatal rat atrial cardiomyocyte monolayers were transduced with lentiviral vectors encoding light-activated Ca2+-translocating channelrhodopsin (CatCh; LV.CatCh∼eYFP↑) or eYFP (LV.eYFP↑) as control, and burst-paced to induce spiral waves rotating around functional cores. Effects of CatCh activation on reentry were investigated by optical and multi-electrode array (MEA) mapping. Western blot analyses and immunocytology confirmed transgene expression. Brief blue light pulses (10 ms/470 nm) triggered action potentials only in LV.CatCh∼eYFP↑-transduced cultures, confirming functional CatCh-mediated current. Prolonged light pulses (500 ms) resulted in reentry termination in 100% of LV.CatCh∼eYFP↑-transduced cultures ( n = 31) vs. 0% of LV.eYFP↑-transduced cultures ( n = 11). Here, CatCh activation caused uniform depolarization, thereby decreasing overall excitability (MEA peak-to-peak amplitude decreased 251.3 ± 217.1 vs. 9.2 ± 9.5 μV in controls). Consequently, functional coresize increased and phase singularities (PSs) drifted, leading to reentry termination by PS–PS or PS–boundary collisions. ::: ::: Conclusion This study shows that spiral waves in atrial cardiomyocyte monolayers can be terminated effectively by a light-induced depolarizing current, produced by the arrhythmogenic substrate itself, upon optogenetic engineering. These results provide proof-of-concept for shockless defibrillation.
---
paper_title: Multiple-Color Optical Activation, Silencing, and Desynchronization of Neural Activity, with Single-Spike Temporal Resolution

paper_content:

The quest to determine how precise neural activity patterns mediate computation, behavior, and pathology would be greatly aided by a set of tools for reliably activating and inactivating genetically targeted neurons, in a temporally precise and rapidly reversible fashion. Having earlier adapted a light-activated cation channel, channelrhodopsin-2 (ChR2), for allowing neurons to be stimulated by blue light, we searched for a complementary tool that would enable optical neuronal inhibition, driven by light of a second color. Here we report that targeting the codon-optimized form of the light-driven chloride pump halorhodopsin from the archaebacterium Natronomas pharaonis (hereafter abbreviated Halo) to genetically-specified neurons enables them to be silenced reliably, and reversibly, by millisecond-timescale pulses of yellow light. We show that trains of yellow and blue light pulses can drive high-fidelity sequences of hyperpolarizations and depolarizations in neurons simultaneously expressing yellow light-driven Halo and blue light-driven ChR2, allowing for the first time manipulations of neural synchrony without perturbation of other parameters such as spiking rates. The Halo/ChR2 system thus constitutes a powerful toolbox for multichannel photoinhibition and photostimulation of virally or transgenically targeted neural circuits without need for exogenous chemicals, enabling systematic analysis and engineering of the brain, and quantitative bioengineering of excitable cells.
---
paper_title: Ultra light-sensitive and fast neuronal activation with the Ca2+-permeable channelrhodopsin CatCh

paper_content:

In this Technical Report, Kleinlogel and colleagues created and characterized a new channelrhodopsin-2 mutant with an enhanced permeability to calcium. Dubbed CatCh (calcium translocating channelrhodopsin), this new variant's enhanced calcium permeability mediates an accelerated response time and voltage response that is ~70-fold more light sensitive than that of wild-type channelrhodopsin-2.
---
paper_title: Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

paper_content:

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
---
paper_title: Spectral characteristics of the photocycle of channelrhodopsin-2 and its implication for channel function.

paper_content:

In 2003, channelrhodopsin-2 (ChR2) from Chlamydomonas reinhardtii was discovered to be a light-gated cation channel, and since that time the channel became an excellent tool to control by light neuronal cells in culture as well as in living animals with high temporal and spatial resolution in a noninvasive manner. However, little is known about the spectral properties and their relation to the channel function. We have expressed ChR2 in the yeast Pichia pastoris and purified the protein. Flash-photolysis data were combined with patch-clamp studies to elucidate the photocycle. The protein absorbs maximally at approximately 480 nm before light excitation and shows flash-induced absorbance changes with at least two different photointermediates. Four relaxation processes can be extracted from the time course that we have analysed in a linear model for the photocycle leading to the kinetic intermediates P(1) to P(4). A short-lived photointermediate at 400 nm, suggesting a deprotonation of the retinal Schiff base, is followed by a red-shifted (520 nm) species with a millisecond lifetime. The first three kinetic intermediates in the photocycle, P(1) to P(3), are described mainly by the red-shifted 520-nm species. The 400-nm species contributes to a smaller extent to P(1) and P(2). The fourth one, P(4), is spectroscopically almost identical with the ground state and lasts into the seconds time region. We compared the spectroscopic data to current measurements under whole-cell patch-clamp conditions on HEK 293 cells. The lifetimes of the spectroscopically and electrophysiologically determined intermediates are in excellent agreement. The intermediates P(2) and P(3) (absorbing at 520 nm) are identified as the cation permeating states of the channel. Under stationary light, a modulation of the photocurrent by green light (540 nm) was observed. We conclude that the red-shifted spectral species represents the open channel state, and the thermal relaxation of this intermediate, the transition from P(3) to P(4), is coupled to channel closing.
---
paper_title: Computational models of optogenetic tools for controlling neural circuits with light

paper_content:

Optogenetics is a new neurotechnology innovation based on the creation of light sensitivity of neurons using gene technologies and remote light activation. Optogenetics allows for the first time straightforward targeted neural stimulation with practically no interference between multiple stimulation points since either light beam can be finely confined or the expression of light sensitive ion channels and pumps can be genetically targeted. Here we present a generalised computational modeling technique for various types of optogenetic mechanisms, which was implemented in the NEURON simulation environment. It was demonstrated on the example of a two classical mechanisms for cells optical activation and silencing: channelrhodopsin-2 (ChR2) and halorhodopsin (NpHR).We theoretically investigate the dynamics of the neural response of a layer 5 cortical pyramidal neuron (L5) to four different types of illuminations: 1) wide-field whole cell illumination 2) wide-field apical dendritic illumination 3) focal somatic illumination and 4) focal axon initial segment (AIS) illumination. We show that whole-cell illumination of halorhodopsin most effectively hyperpolarizes the neuron and is able to silence the cell even when driving input is present. However, when channelrhodopsin-2 and halorhodopsin are concurrently active, the relative location of each illumination determines whether the response is modulated with a balance towards depolarization. The methodology developed in this study will be significant to interpret and design optogenetic experiments and in the field of neuroengineering in general.
---
paper_title: Alternans and spiral breakup in human ventricular tissue model

paper_content:

Ventricular fibrillation (VF) is one of the main causes of death in the Western world. According to one hypothesis, the chaotic excitation dynamics during VF are the result of dynamical instabilities in action potential duration (APD) the occurrence of which requires that the slope of the APD restitution curve exceeds 1. Other factors such as electrotonic coupling and cardiac memory also determine whether these instabilities can develop. In this paper we study the conditions for alternans and spiral breakup in human cardiac tissue. Therefore, we develop a new version of our human ventricular cell model, which is based on recent experimental measurements of human APD restitution and includes a more extensive description of intracellular calcium dynamics. We apply this model to study the conditions for electrical instability in single cells, for reentrant waves in a ring of cells, and for reentry in two-dimensional sheets of ventricular tissue. We show that an important determinant for the onset of instability is the recovery dynamics of the fast sodium current. Slower sodium current recovery leads to longer periods of spiral wave rotation and more gradual conduction velocity restitution, both of which suppress restitution-mediated instability. As a result, maximum restitution slopes considerably exceeding 1 (up to 1.5) may be necessary for electrical instability to occur. Although slopes necessary for the onset of instabilities found in our study exceed 1, they are within the range of experimentally measured slopes. Therefore, we conclude that steep APD restitution-mediated instability is a potential mechanism for VF in the human heart.
---
paper_title: Stimulating Cardiac Muscle by Light: Cardiac Optogenetics by Cell Delivery

paper_content:

Background —After the recent cloning of light-sensitive ion channels and their expression in mammalian cells, a new field, optogenetics, emerged in neuroscience, allowing for precise perturbations of neural circuits by light. However, functionality of optogenetic tools has not been fully explored outside neuroscience; and a non-viral, non-embryogenesis based strategy for optogenetics has not been shown before. ::: ::: Methods and Results —We demonstrate the utility of optogenetics to cardiac muscle by a tandem cell unit (TCU) strategy, where non-excitable cells carry exogenous light-sensitive ion channels, and when electrically coupled to cardiomyocytes, produce optically-excitable heart tissue. A stable channelrhodopsin2 (ChR2) expressing cell line was developed, characterized and used as a cell delivery system. The TCU strategy was validated in vitro in cell pairs with adult canine myocytes (for a wide range of coupling strengths) and in cardiac syncytium with neonatal rat cardiomyocytes. For the first time, we combined optical excitation and optical imaging to capture light-triggered muscle contractions and high-resolution propagation maps of light-triggered electrical waves, found to be quantitatively indistinguishable from electrically-triggered waves. ::: ::: Conclusions —Our results demonstrate feasibility to control excitation and contraction in cardiac muscle by light using the TCU approach. Optical pacing in this case uses less energy, offers superior spatiotemporal control, remote access and can serve not only as an elegant tool in arrhythmia research, but may form the basis for a new generation of light-driven cardiac pacemakers and muscle actuators. The TCU strategy is extendable to (non-viral) stem cell therapy and is directly relevant to in vivo applications.
---
paper_title: A comprehensive multiscale framework for simulating optogenetics in the heart

paper_content:

Optogenetics has emerged as an alternative method for electrical control of the heart, where illumination is used to elicit a bioelectric response in tissue modified to express photosensitive proteins (opsins). This technology promises to enable evocation of spatiotemporally precise responses in targeted cells or tissues, thus creating new possibilities for safe and effective therapeutic approaches to ameliorate cardiac function. Here we present a comprehensive framework for multiscale modelling of cardiac optogenetics, allowing both mechanistic examination of optical control and exploration of potential therapeutic applications. The framework incorporates accurate representations of opsin channel kinetics and delivery modes, spatial distribution of photosensitive cells, and tissue illumination constraints, making possible the prediction of emergent behaviour resulting from interactions at sub-organ scales. We apply this framework to explore how optogenetic delivery characteristics determine energy requirements for optical stimulation and to identify cardiac structures that are potential pacemaking targets with low optical excitation thresholds.
---
paper_title: Optical mapping of optogenetically shaped cardiac action potentials

paper_content:

Light-mediated silencing and stimulation of cardiac excitability, an important complement to electrical stimulation, promises important discoveries and therapies. To date, cardiac optogenetics has been studied with patch-clamp, multielectrode arrays, video microscopy, and an all-optical system measuring calcium transients. The future lies in achieving simultaneous optical acquisition of excitability signals and optogenetic control, both with high spatio-temporal resolution. Here, we make progress by combining optical mapping of action potentials with concurrent activation of channelrhodopsin-2 (ChR2) or halorhodopsin (eNpHR3.0), via an all-optical system applied to monolayers of neonatal rat ventricular myocytes (NRVM). Additionally, we explore the capability of ChR2 and eNpHR3.0 to shape action-potential waveforms, potentially aiding the study of short/long QT syndromes that result from abnormal changes in action potential duration (APD). These results show the promise of an all-optical system to acquire action potentials with precise temporal optogenetics control, achieving a long-sought flexibility beyond the means of conventional electrical stimulation.
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paper_title: Modulation of cardiac tissue electrophysiological properties with light-sensitive proteins.

paper_content:

AIMS ::: Optogenetics approaches, utilizing light-sensitive proteins, have emerged as unique experimental paradigms to modulate neuronal excitability. We aimed to evaluate whether a similar strategy could be used to control cardiac-tissue excitability. ::: ::: ::: METHODS AND RESULTS ::: A combined cell and gene therapy strategy was developed in which fibroblasts were transfected to express the light-activated depolarizing channel Channelrhodopsin-2 (ChR2). Patch-clamp studies confirmed the development of a robust inward current in the engineered fibroblasts following monochromatic blue-light exposure. The engineered cells were co-cultured with neonatal rat cardiomyocytes (or human embryonic stem cell-derived cardiomyocytes) and studied using a multielectrode array mapping technique. These studies revealed the ability of the ChR2-fibroblasts to electrically couple and pace the cardiomyocyte cultures at varying frequencies in response to blue-light flashes. Activation mapping pinpointed the source of this electrical activity to the engineered cells. Similarly, diffuse seeding of the ChR2-fibroblasts allowed multisite optogenetics pacing of the co-cultures, significantly shortening their electrical activation time and synchronizing contraction. Next, optogenetics pacing in an in vitro model of conduction block allowed the resynchronization of the tissue's electrical activity. Finally, the ChR2-fibroblasts were transfected to also express the light-sensitive hyperpolarizing proton pump Archaerhodopsin-T (Arch-T). Seeding of the ChR2/ArchT-fibroblasts allowed to either optogentically pace the cultures (in response to blue-light flashes) or completely suppress the cultures' electrical activity (following continuous illumination with 624 nm monochromatic light, activating ArchT). ::: ::: ::: CONCLUSIONS ::: The results of this proof-of-concept study highlight the unique potential of optogenetics for future biological pacemaking and resynchronization therapy applications and for the development of novel anti-arrhythmic strategies.
---
paper_title: Optogenetic control of heart muscle in vitro and in vivo

paper_content:

Stimulation of the light-activated cation channel channelrhodopsin-2 can depolarize heart muscle in vitro and in vivo, resulting in precise localized stimulation and constant prolonged depolarization of genetically targeted cardiomyocytes and cardiac tissue.
---
paper_title: Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation

paper_content:

Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation
---
paper_title: Light-induced termination of spiral wave arrhythmias by optogenetic engineering of atrial cardiomyocytes

paper_content:

Aims Atrial fibrillation (AF) is the most common cardiac arrhythmia and often involves reentrant electrical activation (e.g. spiral waves). Drug therapy for AF can have serious side effects including proarrhythmia, while electrical shock therapy is associated with discomfort and tissue damage. Hypothetically, forced expression and subsequent activation of light-gated cation channels in cardiomyocytes might deliver a depolarizing force sufficient for defibrillation, thereby circumventing the aforementioned drawbacks. We therefore investigated the feasibility of light-induced spiral wave termination through cardiac optogenetics. ::: ::: Methods and results Neonatal rat atrial cardiomyocyte monolayers were transduced with lentiviral vectors encoding light-activated Ca2+-translocating channelrhodopsin (CatCh; LV.CatCh∼eYFP↑) or eYFP (LV.eYFP↑) as control, and burst-paced to induce spiral waves rotating around functional cores. Effects of CatCh activation on reentry were investigated by optical and multi-electrode array (MEA) mapping. Western blot analyses and immunocytology confirmed transgene expression. Brief blue light pulses (10 ms/470 nm) triggered action potentials only in LV.CatCh∼eYFP↑-transduced cultures, confirming functional CatCh-mediated current. Prolonged light pulses (500 ms) resulted in reentry termination in 100% of LV.CatCh∼eYFP↑-transduced cultures ( n = 31) vs. 0% of LV.eYFP↑-transduced cultures ( n = 11). Here, CatCh activation caused uniform depolarization, thereby decreasing overall excitability (MEA peak-to-peak amplitude decreased 251.3 ± 217.1 vs. 9.2 ± 9.5 μV in controls). Consequently, functional coresize increased and phase singularities (PSs) drifted, leading to reentry termination by PS–PS or PS–boundary collisions. ::: ::: Conclusion This study shows that spiral waves in atrial cardiomyocyte monolayers can be terminated effectively by a light-induced depolarizing current, produced by the arrhythmogenic substrate itself, upon optogenetic engineering. These results provide proof-of-concept for shockless defibrillation.
---
paper_title: Optogenetic activation of Gq signalling modulates pacemaker activity of cardiomyocytes

paper_content:

Aims Investigation of Gq signalling with pharmacological agonists of Gq-coupled receptors lacks spatio-temporal precision. The aim of this study was to establish melanopsin, a light-sensitive Gq-coupled receptor, as a new tool for the investigation of spatial and temporal effects of Gq stimulation on pacemaking in cardiomyocytes at an early developmental stage. ::: ::: Methods and results A vector for ubiquitous expression of melanopsin was tested in HEK293FT cells, which showed light-induced production of inositol-1,4,5-trisphosphate and elevation of intracellular Ca2+ concentration. Mouse embryonic stem cells were stably transfected with this plasmid and differentiated into spontaneously beating embryoid bodies (EBs). Cardiomyocytes within EBs showed melanopsin expression and illumination (60 s, 308.5 nW/mm2, 470 nm) of EBs increased beating rate within 10.2 ± 1.7 s to 317.1 ± 16.3% of baseline frequency. Illumination as short as 5 s was sufficient for generating the maximal frequency response. After termination of illumination, baseline frequency was reached with a decay constant of 27.1 ± 2.5 s. The light-induced acceleration of beating frequency showed a sigmoid dependence on light intensity with a half maximal effective light intensity of 41.7 nW/mm2. Interestingly, EBs showed a high rate of irregular contractions after termination of high-intensity illumination. Local Gq activation by illumination of a small region in a functional syncytium of cardiomyocytes led to pacemaker activity within the illuminated area. ::: ::: Conclusions Light-induced Gq activation in melanopsin-expressing cardiomyocytes increases beating rate and generates local pacemaker activity. We propose that melanopsin is a powerful optogenetic tool for the investigation of spatial and temporal aspects of Gq signalling in cardiovascular research.
---
paper_title: Light induced stimulation and delay of cardiac activity.

paper_content:

This article shows the combination of light activatable ion channels and microelectrode array (MEA) technology for bidirectionally interfacing cells. HL-1 cultures, a mouse derived cardiomyocyte-like cell line, transfected with channelrhodopsin were stimulated with a microscope coupled 473 nm laser and recorded with custom built 64 electrode MEAs. Channelrhodopsin induced depolarization of the cell can evoke action potentials (APs) in single cells. Spreading of the AP over the cell layer can then be measured with good spatiotemporal resolution using MEA recordings. The possibility for light induced pacemaker switching in cultures was shown. Furthermore, the suppression of APs can also be achieved with the laser. Possible applications include cell analysis, e.g. pacemaker interference or induced pacemaker switching, and medical applications such as a combined cardiac pacemaker and defibrillator triggered by light. Since current prosthesis research focuses on bidirectionality, this system may be applied to any electrogenic cell, including neurons or muscles, to advance this field.
---
paper_title: Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

paper_content:

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
---
paper_title: Computational models of optogenetic tools for controlling neural circuits with light

paper_content:

Optogenetics is a new neurotechnology innovation based on the creation of light sensitivity of neurons using gene technologies and remote light activation. Optogenetics allows for the first time straightforward targeted neural stimulation with practically no interference between multiple stimulation points since either light beam can be finely confined or the expression of light sensitive ion channels and pumps can be genetically targeted. Here we present a generalised computational modeling technique for various types of optogenetic mechanisms, which was implemented in the NEURON simulation environment. It was demonstrated on the example of a two classical mechanisms for cells optical activation and silencing: channelrhodopsin-2 (ChR2) and halorhodopsin (NpHR).We theoretically investigate the dynamics of the neural response of a layer 5 cortical pyramidal neuron (L5) to four different types of illuminations: 1) wide-field whole cell illumination 2) wide-field apical dendritic illumination 3) focal somatic illumination and 4) focal axon initial segment (AIS) illumination. We show that whole-cell illumination of halorhodopsin most effectively hyperpolarizes the neuron and is able to silence the cell even when driving input is present. However, when channelrhodopsin-2 and halorhodopsin are concurrently active, the relative location of each illumination determines whether the response is modulated with a balance towards depolarization. The methodology developed in this study will be significant to interpret and design optogenetic experiments and in the field of neuroengineering in general.
---
paper_title: Multiscale Computational Models for Optogenetic Control of Cardiac Function

paper_content:

The ability to stimulate mammalian cells with light has significantly changed our understanding of electrically excitable tissues in health and disease, paving the way toward various novel therapeutic applications. Here, we demonstrate the potential of optogenetic control in cardiac cells using a hybrid experimental/computational technique. Experimentally, we introduced channelrhodopsin-2 into undifferentiated human embryonic stem cells via a lentiviral vector, and sorted and expanded the genetically engineered cells. Via directed differentiation, we created channelrhodopsin-expressing cardiomyocytes, which we subjected to optical stimulation. To quantify the impact of photostimulation, we assessed electrical, biochemical, and mechanical signals using patch-clamping, multielectrode array recordings, and video microscopy. Computationally, we introduced channelrhodopsin-2 into a classic autorhythmic cardiac cell model via an additional photocurrent governed by a light-sensitive gating variable. Upon optical stimulation, the channel opens and allows sodium ions to enter the cell, inducing a fast upstroke of the transmembrane potential. We calibrated the channelrhodopsin-expressing cell model using single action potential readings for different photostimulation amplitudes, pulse widths, and frequencies. To illustrate the potential of the proposed approach, we virtually injected channelrhodopsin-expressing cells into different locations of a human heart, and explored its activation sequences upon optical stimulation. Our experimentally calibrated computational toolbox allows us to virtually probe landscapes of process parameters, and identify optimal photostimulation sequences toward pacing hearts with light.
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paper_title: Cardiac applications of optogenetics.

paper_content:

In complex multicellular systems, such as the brain or the heart, the ability to selectively perturb and observe the response of individual components at the cellular level and with millisecond resolution in time, is essential for mechanistic understanding of function. Optogenetics uses genetic encoding of light sensitivity (by the expression of microbial opsins) to provide such capabilities for manipulation, recording, and control by light with cell specificity and high spatiotemporal resolution. As an optical approach, it is inherently scalable for remote and parallel interrogation of biological function at the tissue level; with implantable miniaturized devices, the technique is uniquely suitable for in vivo tracking of function, as illustrated by numerous applications in the brain. Its expansion into the cardiac area has been slow. Here, using examples from published research and original data, we focus on optogenetics applications to cardiac electrophysiology, specifically dealing with the ability to manipulate membrane voltage by light with implications for cardiac pacing, cardioversion, cell communication, and arrhythmia research, in general. We discuss gene and cell delivery methods of inscribing light sensitivity in cardiac tissue, functionality of the light-sensitive ion channels within different types of cardiac cells, utility in probing electrical coupling between different cell types, approaches and design solutions to all-optical electrophysiology by the combination of optogenetic sensors and actuators, and specific challenges in moving towards in vivo cardiac optogenetics.
---
paper_title: Stimulating Cardiac Muscle by Light: Cardiac Optogenetics by Cell Delivery

paper_content:

Background —After the recent cloning of light-sensitive ion channels and their expression in mammalian cells, a new field, optogenetics, emerged in neuroscience, allowing for precise perturbations of neural circuits by light. However, functionality of optogenetic tools has not been fully explored outside neuroscience; and a non-viral, non-embryogenesis based strategy for optogenetics has not been shown before. ::: ::: Methods and Results —We demonstrate the utility of optogenetics to cardiac muscle by a tandem cell unit (TCU) strategy, where non-excitable cells carry exogenous light-sensitive ion channels, and when electrically coupled to cardiomyocytes, produce optically-excitable heart tissue. A stable channelrhodopsin2 (ChR2) expressing cell line was developed, characterized and used as a cell delivery system. The TCU strategy was validated in vitro in cell pairs with adult canine myocytes (for a wide range of coupling strengths) and in cardiac syncytium with neonatal rat cardiomyocytes. For the first time, we combined optical excitation and optical imaging to capture light-triggered muscle contractions and high-resolution propagation maps of light-triggered electrical waves, found to be quantitatively indistinguishable from electrically-triggered waves. ::: ::: Conclusions —Our results demonstrate feasibility to control excitation and contraction in cardiac muscle by light using the TCU approach. Optical pacing in this case uses less energy, offers superior spatiotemporal control, remote access and can serve not only as an elegant tool in arrhythmia research, but may form the basis for a new generation of light-driven cardiac pacemakers and muscle actuators. The TCU strategy is extendable to (non-viral) stem cell therapy and is directly relevant to in vivo applications.
---
paper_title: Methodology for patient-specific modeling of atrial fibrosis as a substrate for atrial fibrillation.

paper_content:

Personalized computational cardiac models are emerging as an important tool for studying cardiac arrhythmia mechanisms, and have the potential to become powerful instruments for guiding clinical anti-arrhythmia therapy. In this article, we present the methodology for constructing a patient-specific model of atrial fibrosis as a substrate for atrial fibrillation. The model is constructed from high-resolution late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) images acquired in vivo from a patient suffering from persistent atrial fibrillation, accurately capturing both the patient's atrial geometry and the distribution of the fibrotic regions in the atria. Atrial fiber orientation is estimated using a novel image-based method, and fibrosis is represented in the patient-specific fibrotic regions as incorporating collagenous septa, gap junction remodeling, and myofibroblast proliferation. A proof-of-concept simulation result of reentrant circuits underlying atrial fibrillation in the model of the patient's fibrotic atrium is presented to demonstrate the completion of methodology development.
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paper_title: Mechanistic inquiry into the role of tissue remodeling in fibrotic lesions in human atrial fibrillation.

paper_content:

Atrial fibrillation (AF), the most common arrhythmia in humans, is initiated when triggered activity from the pulmonary veins propagates into atrial tissue and degrades into reentrant activity. Although experimental and clinical findings show a correlation between atrial fibrosis and AF, the causal relationship between the two remains elusive. This study used an array of 3D computational models with different representations of fibrosis based on a patient-specific atrial geometry with accurate fibrotic distribution to determine the mechanisms by which fibrosis underlies the degradation of a pulmonary vein ectopic beat into AF. Fibrotic lesions in models were represented with combinations of: gap junction remodeling; collagen deposition; and myofibroblast proliferation with electrotonic or paracrine effects on neighboring myocytes. The study found that the occurrence of gap junction remodeling and the subsequent conduction slowing in the fibrotic lesions was a necessary but not sufficient condition for AF development, whereas myofibroblast proliferation and the subsequent electrophysiological effect on neighboring myocytes within the fibrotic lesions was the sufficient condition necessary for reentry formation. Collagen did not alter the arrhythmogenic outcome resulting from the other fibrosis components. Reentrant circuits formed throughout the noncontiguous fibrotic lesions, without anchoring to a specific fibrotic lesion.
---
paper_title: A comprehensive multiscale framework for simulating optogenetics in the heart

paper_content:

Optogenetics has emerged as an alternative method for electrical control of the heart, where illumination is used to elicit a bioelectric response in tissue modified to express photosensitive proteins (opsins). This technology promises to enable evocation of spatiotemporally precise responses in targeted cells or tissues, thus creating new possibilities for safe and effective therapeutic approaches to ameliorate cardiac function. Here we present a comprehensive framework for multiscale modelling of cardiac optogenetics, allowing both mechanistic examination of optical control and exploration of potential therapeutic applications. The framework incorporates accurate representations of opsin channel kinetics and delivery modes, spatial distribution of photosensitive cells, and tissue illumination constraints, making possible the prediction of emergent behaviour resulting from interactions at sub-organ scales. We apply this framework to explore how optogenetic delivery characteristics determine energy requirements for optical stimulation and to identify cardiac structures that are potential pacemaking targets with low optical excitation thresholds.
---
paper_title: NOTES ON CONTINUOUS STOCHASTIC PHENOMENA

paper_content:

The study of stochastic processes has naturally led to the consideration of stochastic phenomena which are distributed in space of two or more dimensions. Such investigations are, for instance, of practical interest in connexion with problems concerning the distribution of soil fertility over a field or the relations between the velocities at different points in a turbulent fluid. A review of such work with many references has recently been given by Ghosh (1949) (see also Matern, 1947). In the present note I consider two problems arising in the twoand three-dimensional cases.
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paper_title: Interactions between cardiac fibrosis spatial pattern and ionic remodeling on electrical wave propagation

paper_content:

Cardiac fibrosis is an important form of pathological tissue remodeling. Fibrosis can electrically-uncouple neighboring excitable cardiomyocytes thus acting as an obstacle to electrical propagation. In this study, we investigated the effects of fibrosis spatial pattern on electrical propagation in control, decreased maximum sodium conductance, and increased intracellular resistivity conditions. Simulations were performed with a monodomain approach and a realistic canine ionic model. We found that the propagation failure is highly dependent on the spatial pattern of fibrosis for all conditions studied with maximum sensitivity for patterns with combination of small and large clusters. However, the effect is particularly sensitive to reduced sodium current condition where conduction block occurred at lower fibrosis density.
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paper_title: Finding Fluorescent Needles in the Cardiac Haystack: Tracking Human Mesenchymal Stem Cells Labeled with Quantum Dots for Quantitative In Vivo Three-Dimensional Fluorescence Analysis

paper_content:

Stem cells show promise for repair of damaged cardiac tissue. Little is known with certainty, however, about the distribution of these cells once introduced in vivo. Previous attempts at tracking delivered stem cells have been hampered by the autofluorescence of host tissue and limitations of existing labeling techniques. We have developed a novel loading approach to stably label human mesenchymal stem cells with quantum dot (QD) nanoparticles. We report the optimization and validation of this long-term tracking technique and highlight several important biological applications by delivering labeled cells to the mammalian heart. The bright QD crystals illuminate exogenous stem cells in histologic sections for at least 8 weeks following delivery and permit, for the first time, the complete three-dimensional reconstruction of the locations of all stem cells following injection into the heart. Disclosure of potential conflicts of interest is found at the end of this article.
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paper_title: A single direct injection into the left ventricular wall of an adeno-associated virus 9 (AAV9) vector expressing extracellular superoxide dismutase from the cardiac troponin-T promoter protects mice against myocardial infarction

paper_content:

BACKGROUND ::: Localized administration of a highly efficient gene delivery system in combination with a cardiac-selective promoter may provide a favorable biosafety profile in clinical applications such as coronary artery bypass graft surgery, where regions of myocardium can be readily injected to protect them against the potential threat of future ischemic events. ::: ::: ::: METHODS ::: Adeno-associated virus (AAV) vectors expressing luciferase or enhanced green fluorescent protein (eGFP) packaged into AAV serotypes 1, 2, 6, 8 and 9 were injected into the left ventricular (LV) wall of adult mice to determine the time course, magnitude and distribution of gene expression. An AAV9 vector expressing extracellular superoxide dismutase (EcSOD) from the cardiac troponin T (cTnT) promoter was then directly injected into the LV wall of adult mice. Myocardial infarction was induced 4 weeks after injection and infarct size was determined by triphenyltetrazolium chloride and phthalo blue staining. ::: ::: ::: RESULTS ::: Serotypes AAV 9, 8, 1 and 6 provided early onset of gene expression in the heart with minimal extra-cardiac gene expression. AAV9 provided the highest magnitude of gene expression. Immunostaining for eGFP showed expression spanning the anterior to posterior walls from the mid ventricle to the apex. A single direct injection of the AAV9 vector bearing EcSOD ( n = 5) decreased the mean infarct size by 50% compared to the eGFP control group (n = 8) (44 ± 7% versus 22 ± 5%; p = 0.04). ::: ::: ::: CONCLUSIONS ::: AAV serotype 9 is highly efficient for cardiac gene delivery, as evidenced by early onset and high-level gene expression. AAV9-mediated, cardiac selective overexpression of EcSOD from the cTnT promoter significantly reduced infarct size in mice.
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paper_title: Robust cardiomyocyte-specific gene expression following systemic injection of AAV: in vivo gene delivery follows a Poisson distribution

paper_content:

Robust cardiomyocyte-specific gene expression following systemic injection of AAV: in vivo gene delivery follows a Poisson distribution
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paper_title: A comprehensive multiscale framework for simulating optogenetics in the heart

paper_content:

Optogenetics has emerged as an alternative method for electrical control of the heart, where illumination is used to elicit a bioelectric response in tissue modified to express photosensitive proteins (opsins). This technology promises to enable evocation of spatiotemporally precise responses in targeted cells or tissues, thus creating new possibilities for safe and effective therapeutic approaches to ameliorate cardiac function. Here we present a comprehensive framework for multiscale modelling of cardiac optogenetics, allowing both mechanistic examination of optical control and exploration of potential therapeutic applications. The framework incorporates accurate representations of opsin channel kinetics and delivery modes, spatial distribution of photosensitive cells, and tissue illumination constraints, making possible the prediction of emergent behaviour resulting from interactions at sub-organ scales. We apply this framework to explore how optogenetic delivery characteristics determine energy requirements for optical stimulation and to identify cardiac structures that are potential pacemaking targets with low optical excitation thresholds.
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paper_title: Toward microendoscopy-inspired cardiac optogenetics in vivo: technical overview and perspective

paper_content:

The ability to perform precise, spatially localized actuation and measurements of electrical activity in the heart is crucial in understanding cardiac electrophysiology and devising new therapeutic solutions for control of cardiac arrhythmias. Current cardiac imaging techniques (i.e. optical mapping) employ voltage- or calcium-sensitive fluorescent dyes to visualize the electrical signal propagation through cardiac syncytium in vitro or in situ with very high-spatiotemporal resolution. The extension of optogenetics into the cardiac field, where cardiac tissue is genetically altered to express light-sensitive ion channels allowing electrical activity to be elicited or suppressed in a precise cell-specific way, has opened the possibility for all-optical interrogation of cardiac electrophysiology. In vivo application of cardiac optogenetics faces multiple challenges and necessitates suitable optical systems employing fiber optics to actuate and sense electrical signals. In this technical perspective, we present a compendium of clinically relevant access routes to different parts of the cardiac electrical conduction system based on currently employed catheter imaging systems and determine the quantitative size constraints for endoscopic cardiac optogenetics. We discuss the relevant technical advancements in microendoscopy, cardiac imaging, and optogenetics and outline the strategies for combining them to create a portable, miniaturized fiber-based system for all-optical interrogation of cardiac electrophysiology in vivo.
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paper_title: Cardiac Electromechanical Models: From Cell to Organ

paper_content:

The heart is a multiphysics and multiscale system that has driven the development of the most sophisticated mathematical models at the frontiers of computation physiology and medicine. This review focuses on electromechanical (EM) models of the heart from the molecular level of myofilaments to anatomical models of the organ. Because of the coupling in terms of function and emergent behaviors at each level of biological hierarchy, separation of behaviors at a given scale is difficult. Here, a separation is drawn at the cell level so that the first half addresses subcellular/single cell models and the second half addresses organ models. At the subcelluar level, myofilament models represent actin-myosin interaction and Ca-based activation. Myofilament models and their refinements represent an overview of the development in the field. The discussion of specific models emphasizes the roles of cooperative mechanisms and sarcomere length dependence of contraction force, considered the cellular basis of the Frank-Starling law. A model of electrophysiology and Ca handling can be coupled to a myofilament model to produce an EM cell model, and representative examples are summarized to provide an overview of the progression of field. The second half of the review covers organ-level models that require solution of the electrical component as a reaction-diffusion system and the mechanical component, in which active tension generated by the myocytes produces deformation of the organ as described by the equations of continuum mechanics. As outlined in the review, different organ-level models have chosen to use different ionic and myofilament models depending on the specific application; this choice has been largely dictated by compromises between model complexity and computational tractability. The review also addresses application areas of EM models such as cardiac resynchronization therapy and the role of mechano-electric coupling in arrhythmias and defibrillation.
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paper_title: "Beauty is a light in the heart": the transformative potential of optogenetics for clinical applications in cardiovascular medicine.

paper_content:

Optogenetics is an exciting new technology in which viral gene or cell delivery is used to inscribe light sensitivity in excitable tissue to enable optical control of bioelectric behavior. Initial progress in the fledgling domain of cardiac optogenetics has included in vitro expression of various light-sensitive proteins in cell monolayers and transgenic animals to demonstrate an array of potentially useful applications, including light-based pacing, silencing of spontaneous activity, and spiral wave termination. In parallel to these developments, the cardiac modeling community has developed a versatile computational framework capable of realistically simulating optogenetics in biophysically detailed, patient-specific representations of the human heart, enabling the exploration of potential clinical applications in a predictive virtual platform. Toward the ultimate goal of assessing the feasibility and potential impact of optogenetics-based therapies in cardiovascular medicine, this review provides (1) a detailed synopsis of in vivo, in vitro, and in silico developments in the field and (2) a critical assessment of how existing clinical technology for gene/cell delivery and intra-cardiac illumination could be harnessed to achieve such lofty goals as light-based arrhythmia termination.
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paper_title: Visualizing excitation waves inside cardiac muscle using transillumination.

paper_content:

Voltage-sensitive fluorescent dyes have become powerful tools for the visualization of excitation propagation in the heart. However, until recently they were used exclusively for surface recordings. Here we demonstrate the possibility of visualizing the electrical activity from inside cardiac muscle via fluorescence measurements in the transillumination mode (in which the light source and photodetector are on opposite sides of the preparation). This mode enables the detection of light escaping from layers deep within the tissue. Experiments were conducted in perfused (8 mm thick) slabs of sheep right ventricular wall stained with the voltage-sensitive dye di-4-ANEPPS. Although the amplitude and signal-to-noise ratio recorded in the transillumination mode were significantly smaller than those recorded in the epi-illumination mode, they were sufficient to reliably determine the activation sequence. Penetration depths (spatial decay constants) derived from measurements of light attenuation in cardiac muscle were 0.8 mm for excitation (520 +/- 30 nm) and 1.3 mm for emission wavelengths (640 +/- 50 nm). Estimates of emitted fluorescence based on these attenuation values in 8-mm-thick tissue suggest that 90% of the transillumination signal originates from a 4-mm-thick layer near the illuminated surface. A 69% fraction of the recorded signal originates from > or =1 mm below the surface. Transillumination recordings may be combined with endocardial and epicardial surface recordings to obtain information about three-dimensional propagation in the thickness of the myocardial wall. We show an example in which transillumination reveals an intramural reentry, undetectable in surface recordings.
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paper_title: 3D multifunctional integumentary membranes for spatiotemporal cardiac measurements and stimulation across the entire epicardium

paper_content:

Tools for cardiac physiological mapping are important for basic and clinical cardiac research. Here the authors use 3D printing to create a thin, elastic silicone sheath that fits tightly around the entire epicardium and contains sensors to measure a variety of physiological parameters of the beating heart ex vivo.
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paper_title: Quantifying spatial localization of optical mapping using Monte Carlo simulations

paper_content:

Optical mapping techniques used to study spatial distributions of cardiac activity can be divided into two categories; (1) broad-field excitation method, in which hearts stained with voltage or calcium sensitive dyes are illuminated with broad-field excitation light and fluorescence is collected by image or photodiode arrays; (2) laser scanning method, in which illumination uses a scanning laser and fluorescence is collected with a photomultiplier tube. The spatial localization of the fluorescence signal for these two methods is unknown and may depend upon light absorption and scattering at both excitation and emission wavelengths. We measured the absorption coefficients (/spl mu//sub a/), scattering coefficients (/spl mu//sub s/), and scattering anisotropy coefficients (g) at representative excitation and emission wavelengths in rabbit heart tissue stained with di-4-ANEPPS or co-stained with both Rh237 and Oregon Green 488 BAPTA 1. Monte Carlo models were then used to simulate absorption and scattering of excitation light and fluorescence emission light for both broad-field and laser methods in three-dimensional tissue. Contributions of local emissions throughout the tissue to fluorescence collected from the tissue surface were determined for both methods. Our results show that spatial localization depends on the light absorption and scattering in tissue and on the optical mapping method that is used. A tissue region larger than the laser beam or collecting area of the array element contributes to the optical recordings.
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paper_title: Simulating photon scattering effects in structurally detailed ventricular models using a Monte Carlo approach

paper_content:

Light scattering during optical imaging of electrical activation within the heart is known to significantly distort the optically-recorded action potential (AP) upstroke, as well as affecting the magnitude of the measured response of ventricular tissue to strong electric shocks. Modelling approaches based on the photon diffusion equation have recently been instrumental in quantifying and helping to understand the origin of the resulting distortion. However, they are unable to faithfully represent regions of non-scattering media, such as small cavities within the myocardium which are filled with perfusate during experiments. Stochastic Monte Carlo (MC) approaches allow simulation and tracking of individual photon `packets' as they propagate through tissue with differing scattering properties. Here, we present a novel application of the MC method of photon scattering simulation, applied for the first time to the simulation of cardiac optical mapping signals within unstructured, tetrahedral, finite element computational ventricular models. The method faithfully allows simulation of optical signals over highly-detailed, anatomically-complex MR-based models, including representations of fine-scale anatomy and intramural cavities. We show that optical action potential upstroke is prolonged close to large subepicardial vessels than further away from vessels, at times having a distinct `humped' morphology. Furthermore, we uncover a novel mechanism by which photon scattering effects around vessels cavities interact with `virtual-electrode' regions of strong de-/hyper-polarised tissue surrounding cavities during shocks, significantly reducing the apparent optically-measured epicardial polarisation. We therefore demonstrate the importance of this novel optical mapping simulation approach along with highly anatomically-detailed models to fully investigate electrophysiological phenomena driven by fine-scale structural heterogeneity.
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paper_title: Synthesis of voltage-sensitive optical signals: application to panoramic optical mapping.

paper_content:

Fluorescent photon scattering is known to distort optical recordings of cardiac transmembrane potentials; however, this process is not well quantified, hampering interpretation of experimental data. This study presents a novel model, which accurately synthesizes fluorescent recordings over the irregular geometry of the rabbit ventricles. Using the model, the study aims to provide quantification of fluorescent signal distortion for different optical characteristics of the preparation and of the surrounding medium. A bi-domain representation of electrical activity is combined with finite element solutions to the photon diffusion equation simulating both the excitation and emission processes, along with physically realistic boundary conditions at the epicardium, which allow simulation of different experimental setups. We demonstrate that distortion in the optical signal as a result of fluorescent photon scattering is truly a three-dimensional phenomenon and depends critically upon the geometry of the preparation, the scattering properties of the tissue, the direction of wavefront propagation, and the specifics of the experimental setup. Importantly, we show that in an anatomically accurate model of ventricular geometry and fiber orientation, the morphology of the optical signal does not provide reliable information regarding the intramural direction of wavefront propagation. These findings underscore the potential of the new model in interpreting experimental data.
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paper_title: Whole-Heart Modeling: Applications to Cardiac Electrophysiology and Electromechanics

paper_content:

Recent developments in cardiac simulation have rendered the heart the most highly integrated example of a virtual organ. We are on the brink of a revolution in cardiac research, one in which computational modeling of proteins, cells, tissues, and the organ permit linking genomic and proteomic information to the integrated organ behavior, in the quest for a quantitative understanding of the functioning of the heart in health and disease. The goal of this review is to assess the existing state-of-the-art in whole-heart modeling and the plethora of its applications in cardiac research. General whole-heart modeling approaches are presented, and the applications of whole-heart models in cardiac electrophysiology and electromechanics research are reviewed. The article showcases the contributions that whole-heart modeling and simulation have made to our understanding of the functioning of the heart. A summary of the future developments envisioned for the field of cardiac simulation and modeling is also presented. Biophysically based computational modeling of the heart, applied to human heart physiology and the diagnosis and treatment of cardiac disease, has the potential to dramatically change 21st century cardiac research and the field of cardiology.
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paper_title: Shedding light onto live molecular targets

paper_content:

Optical sensing of specific molecular targets and pathways deep inside living mice has become possible as a result of a number of advances. These include design of biocompatible near-infrared fluorochromes, development of targeted and activatable 'smart' imaging probes, engineered photoproteins and advances in photon migration theory and reconstruction. Together, these advances will provide new tools making it possible to understand more fully the functioning of protein networks, diagnose disease earlier and speed along drug discovery.
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paper_title: ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation

paper_content:

Channelrhodopsins (ChRs) are used to optogenetically depolarize neurons. We engineered a variant of ChR, denoted red-activatable ChR (ReaChR), that is optimally excited with orange to red light (λ ∼590-630 nm) and offers improved membrane trafficking, higher photocurrents and faster kinetics compared to existing red-shifted ChRs. Red light is less scattered by tissue and is absorbed less by blood than the blue to green wavelengths that are required by other ChR variants. We used ReaChR expressed in the vibrissa motor cortex to drive spiking and vibrissa motion in awake mice when excited with red light through intact skull. Precise vibrissa movements were evoked by expressing ReaChR in the facial motor nucleus in the brainstem and illumination with red light through the external auditory canal. Thus, ReaChR enables transcranial optical activation of neurons in deep brain structures without the need to surgically thin the skull, form a transcranial window or implant optical fibers.
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paper_title: Optogenetic versus Electrical Stimulation of Human Cardiomyocytes: Modeling Insights.

paper_content:

Optogenetics provides an alternative to electrical stimulation to manipulate membrane voltage, and trigger or modify action potentials (APs) in excitable cells. We compare biophysically and energetically the cellular responses to direct electrical current injection versus optical stimulation mediated by genetically expressed light-sensitive ion channels, e.g., Channelrhodopsin-2 (ChR2). Using a computational model of ChR2(H134R mutant), we show that both stimulation modalities produce similar-in-morphology APs in human cardiomyocytes, and that electrical and optical excitability vary with cell type in a similar fashion. However, whereas the strength-duration curves for electrical excitation in ventricular and atrial cardiomyocytes closely follow the theoretical exponential relationship for an equivalent RC circuit, the respective optical strength-duration curves significantly deviate, exhibiting higher nonlinearity. We trace the origin of this deviation to the waveform of the excitatory current—a nonrectangular self-terminating inward current produced in optical stimulation due to ChR2 kinetics and voltage-dependent rectification. Using a unifying charge measure to compare energy needed for electrical and optical stimulation, we reveal that direct electrical current injection (rectangular pulse) is more efficient at short pulses, whereas voltage-mediated negative feedback leads to self-termination of ChR2 current and renders optical stimulation more efficient for long low-intensity pulses. This applies to cardiomyocytes but not to neuronal cells (with much shorter APs). Furthermore, we demonstrate the cell-specific use of ChR2 current as a unique modulator of intrinsic activity, allowing for optical control of AP duration in atrial and, to a lesser degree, in ventricular myocytes. For self-oscillatory cells, such as Purkinje, constant light at extremely low irradiance can be used for fine control of oscillatory frequency, whereas constant electrical stimulation is not feasible due to electrochemical limitations. Our analysis offers insights for designing future new energy-efficient stimulation strategies in heart or brain.
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paper_title: Independent optical excitation of distinct neural populations

paper_content:

Sequencing the transcriptomes of more than 100 species of alga yields new channelrhodopsins with promising properties for optogenetics. A far red–shifted channelrhodopsin, Chrimson, opens up new behavioral capabilities in Drosophila, and alongside a fast yet light-sensitive blue channelrhodopsin, Chronos, enables independent excitation of two neuronal populations in brain slices.
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paper_title: Quantifying spatial localization of optical mapping using Monte Carlo simulations

paper_content:

Optical mapping techniques used to study spatial distributions of cardiac activity can be divided into two categories; (1) broad-field excitation method, in which hearts stained with voltage or calcium sensitive dyes are illuminated with broad-field excitation light and fluorescence is collected by image or photodiode arrays; (2) laser scanning method, in which illumination uses a scanning laser and fluorescence is collected with a photomultiplier tube. The spatial localization of the fluorescence signal for these two methods is unknown and may depend upon light absorption and scattering at both excitation and emission wavelengths. We measured the absorption coefficients (/spl mu//sub a/), scattering coefficients (/spl mu//sub s/), and scattering anisotropy coefficients (g) at representative excitation and emission wavelengths in rabbit heart tissue stained with di-4-ANEPPS or co-stained with both Rh237 and Oregon Green 488 BAPTA 1. Monte Carlo models were then used to simulate absorption and scattering of excitation light and fluorescence emission light for both broad-field and laser methods in three-dimensional tissue. Contributions of local emissions throughout the tissue to fluorescence collected from the tissue surface were determined for both methods. Our results show that spatial localization depends on the light absorption and scattering in tissue and on the optical mapping method that is used. A tissue region larger than the laser beam or collecting area of the array element contributes to the optical recordings.
---
paper_title: Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

paper_content:

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
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paper_title: Alternans and spiral breakup in human ventricular tissue model

paper_content:

Ventricular fibrillation (VF) is one of the main causes of death in the Western world. According to one hypothesis, the chaotic excitation dynamics during VF are the result of dynamical instabilities in action potential duration (APD) the occurrence of which requires that the slope of the APD restitution curve exceeds 1. Other factors such as electrotonic coupling and cardiac memory also determine whether these instabilities can develop. In this paper we study the conditions for alternans and spiral breakup in human cardiac tissue. Therefore, we develop a new version of our human ventricular cell model, which is based on recent experimental measurements of human APD restitution and includes a more extensive description of intracellular calcium dynamics. We apply this model to study the conditions for electrical instability in single cells, for reentrant waves in a ring of cells, and for reentry in two-dimensional sheets of ventricular tissue. We show that an important determinant for the onset of instability is the recovery dynamics of the fast sodium current. Slower sodium current recovery leads to longer periods of spiral wave rotation and more gradual conduction velocity restitution, both of which suppress restitution-mediated instability. As a result, maximum restitution slopes considerably exceeding 1 (up to 1.5) may be necessary for electrical instability to occur. Although slopes necessary for the onset of instabilities found in our study exceed 1, they are within the range of experimentally measured slopes. Therefore, we conclude that steep APD restitution-mediated instability is a potential mechanism for VF in the human heart.
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paper_title: Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model

paper_content:

The mechanisms underlying many important properties of the human atrial action potential (AP) are poorly understood. Using specific formulations of the K + , Na + , and Ca 2+ currents based on data recorded from human atrial myocytes, along with representations of pump, exchange, and background currents, we developed a mathematical model of the AP. The model AP resembles APs recorded from human atrial samples and responds to rate changes, L-type Ca 2+ current blockade, Na + /Ca 2+ exchanger inhibition, and variations in transient outward current amplitude in a fashion similar to experimental recordings. Rate-dependent adaptation of AP duration, an important determinant of susceptibility to atrial fibrillation, was attributable to incomplete L-type Ca 2+ current recovery from inactivation and incomplete delayed rectifier current deactivation at rapid rates. Experimental observations of variable AP morphology could be accounted for by changes in transient outward current density, as suggested experimentally. We conclude that this mathematical model of the human atrial AP reproduces a variety of observed AP behaviors and provides insights into the mechanisms of clinically important AP properties.
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paper_title: A comprehensive multiscale framework for simulating optogenetics in the heart

paper_content:

Optogenetics has emerged as an alternative method for electrical control of the heart, where illumination is used to elicit a bioelectric response in tissue modified to express photosensitive proteins (opsins). This technology promises to enable evocation of spatiotemporally precise responses in targeted cells or tissues, thus creating new possibilities for safe and effective therapeutic approaches to ameliorate cardiac function. Here we present a comprehensive framework for multiscale modelling of cardiac optogenetics, allowing both mechanistic examination of optical control and exploration of potential therapeutic applications. The framework incorporates accurate representations of opsin channel kinetics and delivery modes, spatial distribution of photosensitive cells, and tissue illumination constraints, making possible the prediction of emergent behaviour resulting from interactions at sub-organ scales. We apply this framework to explore how optogenetic delivery characteristics determine energy requirements for optical stimulation and to identify cardiac structures that are potential pacemaking targets with low optical excitation thresholds.
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paper_title: Computational Optogenetics: A Novel Continuum Framework for the Photoelectrochemistry of Living Systems

paper_content:

Electrical stimulation is currently the gold standard treatment for heart rhythm disorders. However, electrical pacing is associated with technical limitations and unavoidable potential complications. Recent developments now enable the stimulation of mammalian cells with light using a novel technology known as optogenetics. The optical stimulation of genetically engineered cells has significantly changed our understanding of electrically excitable tissues, paving the way towards controlling heart rhythm disorders by means of photostimulation. Controlling these disorders, in turn, restores coordinated force generation to avoid sudden cardiac death. Here, we report a novel continuum framework for the photoelectrochemistry of living systems that allows us to decipher the mechanisms by which this technology regulates the electrical and mechanical function of the heart. Using a modular multiscale approach, we introduce a non-selective cation channel, channelrhodopsin-2, into a conventional cardiac muscle cell model via an additional photocurrent governed by a light-sensitive gating variable. Upon optical stimulation, this channel opens and allows sodium ions to enter the cell, inducing electrical activation. In side-by-side comparisons with conventional heart muscle cells, we show that photostimulation directly increases the sodium concentration, which indirectly decreases the potassium concentration in the cell, while all other characteristics of the cell remain virtually unchanged. We integrate our model cells into a continuum model for excitable tissue using a nonlinear parabolic second order partial differential equation, which we discretize in time using finite differences and in space using finite elements. To illustrate the potential of this computational model, we virtually inject our photosensitive cells into different locations of a human heart, and explore its activation sequences upon photostimulation. Our computational optogenetics tool box allows us to virtually probe landscapes of process parameters, and to identify optimal photostimulation sequences with the goal to pace human hearts with light and, ultimately, to restore mechanical function.
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paper_title: Mapping of cardiac electrical activation with electromechanical wave imaging: an in silico-in vivo reciprocity study.

paper_content:

BACKGROUND ::: Electromechanical wave imaging (EWI) is an entirely noninvasive, ultrasound-based imaging method capable of mapping the electromechanical activation sequence of the ventricles in vivo. Given the broad accessibility of ultrasound scanners in the clinic, the application of EWI could constitute a flexible surrogate for the 3-dimensional electrical activation. ::: ::: ::: OBJECTIVE ::: The purpose of this report is to reproduce the electromechanical wave (EW) using an anatomically realistic electromechanical model, and establish the capability of EWI to map the electrical activation sequence in vivo when pacing from different locations. ::: ::: ::: METHODS ::: EWI was performed in 1 canine during pacing from 3 different sites. A high-resolution dynamic model of coupled cardiac electromechanics of the canine heart was used to predict the experimentally recorded electromechanical wave. The simulated 3-dimensional electrical activation sequence was then compared with the experimental EW. ::: ::: ::: RESULTS ::: The electrical activation sequence and the EW were highly correlated for all pacing sites. The relationship between the electrical activation and the EW onset was found to be linear, with a slope of 1.01 to 1.17 for different pacing schemes and imaging angles. ::: ::: ::: CONCLUSION ::: The accurate reproduction of the EW in simulations indicates that the model framework is capable of accurately representing the cardiac electromechanics and thus testing new hypotheses. The one-to-one correspondence between the electrical activation and the EW sequences indicates that EWI could be used to map the cardiac electrical activity. This opens the door for further exploration of the technique in assisting in the early detection, diagnosis, and treatment monitoring of rhythm dysfunction.
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paper_title: Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

paper_content:

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
---
paper_title: Purkinje-mediated Effects in the Response of Quiescent Ventricles to Defibrillation Shocks

paper_content:

In normal cardiac function, orderly activation of the heart is facilitated by the Purkinje system (PS), a specialized network of fast-conducting fibers that lines the ventricles. Its role during ventricular defibrillation remains unelucidated. Physical characteristics of the PS make it a poor candidate for direct electrical observation using contemporary experimental techniques. This study uses a computer modeling approach to assess contributions by the PS to the response to electrical stimulation. Normal sinus rhythm was simulated and epicardial breakthrough sites were distributed in a manner consistent with experimental results. Defibrillation shocks of several strengths and orientations were applied to quiescent ventricles, with and without PS, and electrical activation was analyzed. All shocks induced local polarizations in PS branches parallel to the field, which led to the rapid spread of excitation through the network. This produced early activations at myocardial sites where tissue was unexcited by the shock and coupled to the PS. Shocks along the apico-basal axis of the heart resulted in a significant abbreviation of activation time when the PS was present; these shocks are of particular interest because the fields generated by internal cardioverter defibrillators tend to have a strong component in the same direction. The extent of PS-induced changes, both temporal and spatial, was constrained by the amount of shock-activated myocardium. Increasing field strength decreased the transmission delay between PS and ventricular tissue at Purkinje-myocardial junctions (PMJs), but this did not have a major effect on the organ-level response. Weaker shocks directly affect a smaller volume of myocardial tissue but easily excite the PS, which makes the PS contribution to far field excitation more substantial than for stronger shocks.
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paper_title: Multiscale Computational Models for Optogenetic Control of Cardiac Function

paper_content:

The ability to stimulate mammalian cells with light has significantly changed our understanding of electrically excitable tissues in health and disease, paving the way toward various novel therapeutic applications. Here, we demonstrate the potential of optogenetic control in cardiac cells using a hybrid experimental/computational technique. Experimentally, we introduced channelrhodopsin-2 into undifferentiated human embryonic stem cells via a lentiviral vector, and sorted and expanded the genetically engineered cells. Via directed differentiation, we created channelrhodopsin-expressing cardiomyocytes, which we subjected to optical stimulation. To quantify the impact of photostimulation, we assessed electrical, biochemical, and mechanical signals using patch-clamping, multielectrode array recordings, and video microscopy. Computationally, we introduced channelrhodopsin-2 into a classic autorhythmic cardiac cell model via an additional photocurrent governed by a light-sensitive gating variable. Upon optical stimulation, the channel opens and allows sodium ions to enter the cell, inducing a fast upstroke of the transmembrane potential. We calibrated the channelrhodopsin-expressing cell model using single action potential readings for different photostimulation amplitudes, pulse widths, and frequencies. To illustrate the potential of the proposed approach, we virtually injected channelrhodopsin-expressing cells into different locations of a human heart, and explored its activation sequences upon optical stimulation. Our experimentally calibrated computational toolbox allows us to virtually probe landscapes of process parameters, and identify optimal photostimulation sequences toward pacing hearts with light.
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paper_title: Methodology for patient-specific modeling of atrial fibrosis as a substrate for atrial fibrillation.

paper_content:

Personalized computational cardiac models are emerging as an important tool for studying cardiac arrhythmia mechanisms, and have the potential to become powerful instruments for guiding clinical anti-arrhythmia therapy. In this article, we present the methodology for constructing a patient-specific model of atrial fibrosis as a substrate for atrial fibrillation. The model is constructed from high-resolution late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) images acquired in vivo from a patient suffering from persistent atrial fibrillation, accurately capturing both the patient's atrial geometry and the distribution of the fibrotic regions in the atria. Atrial fiber orientation is estimated using a novel image-based method, and fibrosis is represented in the patient-specific fibrotic regions as incorporating collagenous septa, gap junction remodeling, and myofibroblast proliferation. A proof-of-concept simulation result of reentrant circuits underlying atrial fibrillation in the model of the patient's fibrotic atrium is presented to demonstrate the completion of methodology development.
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paper_title: Mechanistic inquiry into the role of tissue remodeling in fibrotic lesions in human atrial fibrillation.

paper_content:

Atrial fibrillation (AF), the most common arrhythmia in humans, is initiated when triggered activity from the pulmonary veins propagates into atrial tissue and degrades into reentrant activity. Although experimental and clinical findings show a correlation between atrial fibrosis and AF, the causal relationship between the two remains elusive. This study used an array of 3D computational models with different representations of fibrosis based on a patient-specific atrial geometry with accurate fibrotic distribution to determine the mechanisms by which fibrosis underlies the degradation of a pulmonary vein ectopic beat into AF. Fibrotic lesions in models were represented with combinations of: gap junction remodeling; collagen deposition; and myofibroblast proliferation with electrotonic or paracrine effects on neighboring myocytes. The study found that the occurrence of gap junction remodeling and the subsequent conduction slowing in the fibrotic lesions was a necessary but not sufficient condition for AF development, whereas myofibroblast proliferation and the subsequent electrophysiological effect on neighboring myocytes within the fibrotic lesions was the sufficient condition necessary for reentry formation. Collagen did not alter the arrhythmogenic outcome resulting from the other fibrosis components. Reentrant circuits formed throughout the noncontiguous fibrotic lesions, without anchoring to a specific fibrotic lesion.
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paper_title: ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation

paper_content:

Channelrhodopsins (ChRs) are used to optogenetically depolarize neurons. We engineered a variant of ChR, denoted red-activatable ChR (ReaChR), that is optimally excited with orange to red light (λ ∼590-630 nm) and offers improved membrane trafficking, higher photocurrents and faster kinetics compared to existing red-shifted ChRs. Red light is less scattered by tissue and is absorbed less by blood than the blue to green wavelengths that are required by other ChR variants. We used ReaChR expressed in the vibrissa motor cortex to drive spiking and vibrissa motion in awake mice when excited with red light through intact skull. Precise vibrissa movements were evoked by expressing ReaChR in the facial motor nucleus in the brainstem and illumination with red light through the external auditory canal. Thus, ReaChR enables transcranial optical activation of neurons in deep brain structures without the need to surgically thin the skull, form a transcranial window or implant optical fibers.
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paper_title: Optical mapping of optogenetically shaped cardiac action potentials

paper_content:

Light-mediated silencing and stimulation of cardiac excitability, an important complement to electrical stimulation, promises important discoveries and therapies. To date, cardiac optogenetics has been studied with patch-clamp, multielectrode arrays, video microscopy, and an all-optical system measuring calcium transients. The future lies in achieving simultaneous optical acquisition of excitability signals and optogenetic control, both with high spatio-temporal resolution. Here, we make progress by combining optical mapping of action potentials with concurrent activation of channelrhodopsin-2 (ChR2) or halorhodopsin (eNpHR3.0), via an all-optical system applied to monolayers of neonatal rat ventricular myocytes (NRVM). Additionally, we explore the capability of ChR2 and eNpHR3.0 to shape action-potential waveforms, potentially aiding the study of short/long QT syndromes that result from abnormal changes in action potential duration (APD). These results show the promise of an all-optical system to acquire action potentials with precise temporal optogenetics control, achieving a long-sought flexibility beyond the means of conventional electrical stimulation.
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paper_title: Independent optical excitation of distinct neural populations

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Sequencing the transcriptomes of more than 100 species of alga yields new channelrhodopsins with promising properties for optogenetics. A far red–shifted channelrhodopsin, Chrimson, opens up new behavioral capabilities in Drosophila, and alongside a fast yet light-sensitive blue channelrhodopsin, Chronos, enables independent excitation of two neuronal populations in brain slices.
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paper_title: Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation

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Channelrhodopsin2 Current During the Action Potential: “Optical AP Clamp” and Approximation
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paper_title: Cardiac optogenetics

paper_content:

Optogenetics is an emerging technology for optical interrogation and control of biological function with high specificity and high spatiotemporal resolution. Mammalian cells and tissues can be sensitized to respond to light by a relatively simple and well-tolerated genetic modification using microbial opsins (light-gated ion channels and pumps). These can achieve fast and specific excitatory or inhibitory response, offering distinct advantages over traditional pharmacological or electrical means of perturbation. Since the first demonstrations of utility in mammalian cells (neurons) in 2005, optogenetics has spurred immense research activity and has inspired numerous applications for dissection of neural circuitry and understanding of brain function in health and disease, applications ranging from in vitro to work in behaving animals. Only recently (since 2010), the field has extended to cardiac applications with less than a dozen publications to date. In consideration of the early phase of work on cardiac optogenetics and the impact of the technique in understanding another excitable tissue, the brain, this review is largely a perspective of possibilities in the heart. It covers the basic principles of operation of light-sensitive ion channels and pumps, the available tools and ongoing efforts in optimizing them, overview of neuroscience use, as well as cardiac-specific questions of implementation and ideas for best use of this emerging technology in the heart.
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paper_title: Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

paper_content:

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silico prediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. Using optical action potential clamp, we experimentally validated model-predicted ChR2 behavior in guinea pig ventricular myocytes. The model was then incorporated in a variety of cardiac myocytes, including human ventricular, atrial and Purkinje cell models. We demonstrate the ability of ChR2 to trigger action potentials in human cardiomyocytes at relatively low light levels, as well as the differential response of these cells to light, with the Purkinje cells being most easily excitable and ventricular cells requiring the highest irradiance at all pulse durations. This new experimentally-validated ChR2 model will facilitate virtual experimentation in neural and cardiac optogenetics at the cell and organ level and provide guidance for the development of in vivo tools.
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paper_title: KCNJ2 mutation in short QT syndrome 3 results in atrial fibrillation and ventricular proarrhythmia.

paper_content:

We describe a mutation (E299V) in KCNJ2, the gene that encodes the strong inward rectifier K(+) channel protein (Kir2.1), in an 11-y-old boy. The unique short QT syndrome type-3 phenotype is associated with an extremely abbreviated QT interval (200 ms) on ECG and paroxysmal atrial fibrillation. Genetic screening identified an A896T substitution in a highly conserved region of KCNJ2 that resulted in a de novo mutation E299V. Whole-cell patch-clamp experiments showed that E299V presents an abnormally large outward IK1 at potentials above -55 mV (P < 0.001 versus wild type) due to a lack of inward rectification. Coexpression of wild-type and mutant channels to mimic the heterozygous condition still resulted in a large outward current. Coimmunoprecipitation and kinetic analysis showed that E299V and wild-type isoforms may heteromerize and that their interaction impairs function. The homomeric assembly of E299V mutant proteins actually results in gain of function. Computer simulations of ventricular excitation and propagation using both the homozygous and heterozygous conditions at three different levels of integration (single cell, 2D, and 3D) accurately reproduced the electrocardiographic phenotype of the proband, including an exceedingly short QT interval with merging of the QRS and the T wave, absence of ST segment, and peaked T waves. Numerical experiments predict that, in addition to the short QT interval, absence of inward rectification in the E299V mutation should result in atrial fibrillation. In addition, as predicted by simulations using a geometrically accurate three-dimensional ventricular model that included the His-Purkinje network, a slight reduction in ventricular excitability via 20% reduction of the sodium current should increase vulnerability to life-threatening ventricular tachyarrhythmia.
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paper_title: Optogenetics-enabled dynamic modulation of action potential duration in atrial tissue: feasibility of a novel therapeutic approach.

paper_content:

AIMS ::: Diseases that abbreviate the cardiac action potential (AP) by increasing the strength of repolarizing transmembrane currents are highly arrhythmogenic. It has been proposed that optogenetic tools could be used to restore normal AP duration (APD) in the heart under such disease conditions. This study aims to evaluate the efficacy of an optogenetic treatment modality for prolonging pathologically shortened APs in a detailed computational model of short QT syndrome (SQTS) in the human atria, and compare it to drug treatment. ::: ::: ::: METHODS AND RESULTS ::: We used a human atrial myocyte model with faster repolarization caused by SQTS; light sensitivity was inscribed via the presence of channelrhodopsin-2 (ChR2). We conducted simulations in single cells and in a magnetic resonance imaging-based model of the human left atrium (LA). Application of an appropriate optical stimulus to a diseased cell dynamically increased APD, producing an excellent match to control AP (<1.5 mV deviation); treatment of a diseased cell with an AP-prolonging drug (chloroquine) also increased APD, but the match to control AP was worse (>5 mV deviation). Under idealized conditions in the LA (uniform ChR2-expressing cell distribution, no light attenuation), optogenetics-based therapy outperformed chloroquine treatment (APD increased to 87% and 81% of control). However, when non-uniform ChR2-expressing cell distribution and light attenuation were incorporated, optogenetics-based treatment was less effective (APD only increased to 55%). ::: ::: ::: CONCLUSION ::: This study demonstrates proof of concept for optogenetics-based treatment of diseases that alter atrial AP shape. We identified key practical obstacles intrinsic to the optogenetic approach that must be overcome before such treatments can be realized.
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Title: Computational modeling of cardiac optogenetics: Methodology overview & review of findings from simulations

Section 1: Introduction
Description 1: Introduce the field of cardiac optogenetics, discuss the potential of low-energy light for electrophysiological control, and outline the aim of the review.

Section 2: Modeling cardiac optogenetics at the protein scale
Description 2: Discuss the steps towards multiscale simulation at the protein level, focusing on the electrophysiological behavior of opsins, especially channelrhodopsin-2 (ChR2).

Section 3: Modeling cardiac optogenetics at the myocyte scale
Description 3: Describe modeling efforts at the myocyte level, including direct expression of opsins in cardiac myocytes and electrical coupling of opsin-rich donor cells to myocytes.

Section 4: Modeling cardiac optogenetics at the tissue scale
Description 4: Explain the incorporation of realistic spatial patterns of opsin-expressing cells at the tissue level, highlighting the significance of heterogeneous patterns.

Section 5: Modeling cardiac optogenetics at the organ scale
Description 5: Outline the steps needed to simulate the dynamics of excitation and contraction in biophysically-detailed models of the heart, including representation of optical stimuli and light-tissue interactions.

Section 6: Effects of cardiac cell type on energy required for optogenetics-based stimulation
Description 6: Discuss how different cardiac cell types impact the energy required for optical stimulation, considering variations in action potential properties and membrane currents.

Section 7: Optogenetics-based cardiac pacing
Description 7: Investigate factors influencing optogenetics-based cardiac pacing, including multicellular and coupling effects, optical irradiance thresholds, and spatial distribution of light-sensitive cells.

Section 8: Dynamic modulation of atrial action potential duration (APD)
Description 8: Explore the potential of optogenetics to modulate action potential duration, highlighting potential therapeutic applications and limitations observed in simulations.

Section 9: Conclusions
Description 9: Summarize the main findings of cardiac optogenetics modeling, stressing its potential to advance light-based therapies and guide the development of new optogenetic tools for cardiac applications.

Section 10: Conflicts of interest statements
Description 10: Declare any potential conflicts of interest the authors may have regarding the work presented in the review.