Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model

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 silicoprediction 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

The histone methyltransferase SETD2 negatively regulates cell size

Cell size varies between cell types but is tightly regulated by cell intrinsic and extrinsic mechanisms. Cell size control is important for cell function, and changes in cell size are frequently observed in cancer. Here, we uncover a role for SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Using multiple independent perturbation strategies, we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also increase cell size. In addition, ectopic overexpression of a decoy SRI domain increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development

Virtual histology of the human heart using optical coherence tomography

Optical coherence tomography (OCT) allows for the visualization of micron-scale structures within nontransparent biological tissues. For the first time, we demonstrate the use of OCT in identifying components of the cardiac conduction system and other structures in the explanted human heart. Reconstructions of cardiac structures up to 2 mm below the tissue surface were achieved and validated with Masson Trichrome histology in atrial, ventricular, sinoatrial nodal, and atrioventricular nodal preparations. The high spatial resolution of OCT provides visualization of cardiac fibers within the myocardium, as well as elements of the cardiac conduction system; however, a limiting factor remains its depth penetration, demonstrated to be ∼2 mm in cardiac tissues. Despite its currently limited imaging depth, the use of OCT to identify the structural determinants of both normal and abnormal function in the intact human heart is critical in its development as a potential aid to intracardiac arrhythmia diagnosis and therapy

Gender Differences in Electrophysiological Gene Expression in Failing and Non-Failing Human Hearts

<div><p>The increasing availability of human cardiac tissues for study are critically important in increasing our understanding of the impact of gender, age, and other parameters, such as medications and cardiac disease, on arrhythmia susceptibility. In this study, we aimed to compare the mRNA expression of 89 ion channel subunits, calcium handling proteins, and transcription factors important in cardiac conduction and arrhythmogenesis in the left atria (LA) and ventricles (LV) of failing and nonfailing human hearts of both genders. Total RNA samples, prepared from failing male (n = 9) and female (n = 7), and from nonfailing male (n = 9) and female (n = 9) hearts, were probed using custom-designed Taqman gene arrays. Analyses were performed to explore the relationships between gender, failure state, and chamber expression. Hierarchical cluster analysis revealed chamber specific expression patterns, but failed to identify disease- or gender-dependent clustering. Gender-specific analysis showed lower expression levels in transcripts encoding for K_v4.3, KChIP2, K_v1.5, and K_ir3.1 in the failing female as compared with the male LA. Analysis of LV transcripts, however, did not reveal significant differences based on gender. Overall, our data highlight the differential expression and transcriptional remodeling of ion channel subunits in the human heart as a function of gender and cardiac disease. Furthermore, the availability of such data sets will allow for the development of disease-, gender-, and, most importantly, patient-specific cardiac models, with the ability to utilize such information as mRNA expression to predict cardiac phenotype.</p> </div

Ventricular remodeling in heart failure.

<p>(A) Ventricular remodeling of major ion channel subunits and accessory proteins in heart failure. (B) Regional specificity of targets in failing and nonfailing hearts of both genders.</p

Gender dependent remodeling in the LA.

<p>(A) Gender dependent atrial remodeling of major ion channel subunits and accessory proteins in failing and nonfailing hearts of both genders. (B) Relative expression levels of failing LA samples of both genders. The white data points indicate the patient with a documented history of AF.</p

Clinical characteristics of failing hearts.

*<p>left ventricular end diastolic volume</p>**<p>ventricular tachycardia.</p>†<p>ejection fraction</p>a<p>permanent pacemaker.</p>‡<p>ischemic cardiomyopathy</p>b<p>biventricular device.</p>§<p>implantable cardioverter defibrillator</p>c<p>left ventricular assist device.</p>||<p>nonsustained ventricular tachycardia</p>d<p>atrial fibrillation.</p>#<p>ventricular fibrillation</p>e<p>nonischemic cardiomyopathy.</p

Gender dependent ventricular remodeling of major repolarizing ion channel subunits and accessory proteins in failing and nonfailing hearts of both genders.

<p>Gender dependent ventricular remodeling of major repolarizing ion channel subunits and accessory proteins in failing and nonfailing hearts of both genders.</p