Integration of multiple imaging platforms to uncover cardiovascular defects in adult zebrafish

Application of an automated analysis framework for pulsed-wave Doppler cardiac ultrasound measurements to generate reference data in adult zebrafish

High-frequency cardiac ultrasound is the only well-established method to characterize in vivo cardiovascular function in adult zebrafish noninvasively. Pulsed-wave Doppler imaging allows measurements of blood flow velocities at well-defined anatomical positions, but the measurements and results obtained using this technique need to be analyzed carefully, taking into account the substantial baseline variability within one recording and the possibility for operator bias. To address these issues and to increase throughput by limiting hands-on analysis time, we have developed a fully automated processing pipeline. This framework enables the fast, unbiased analysis of all cardiac cycles in a zebrafish pulsed-wave Doppler recording of both atrioventricular valve flow as well as aortic valve flow without operator-dependent inputs. Applying this automated pipeline to a large number of recordings from wild-type zebrafish shows a strong agreement between the automated results and manual annotations performed by an experienced operator. The reference data obtained from this analysis showed that the early wave peak during ventricular inflow is lower for female compared with male zebrafish. We also found that the peaks of the ventricular inflow and outflow waves as well as the peaks of the regurgitation waves are all correlated positively with body surface area. In general, the presented reference data, as well as the automated Doppler measurement processing tools developed and validated in this study will facilitate future (high-throughput) cardiovascular phenotyping studies in adult zebrafish ultimately leading to a more comprehensive understanding of human (genetic) cardiovascular diseases.

Outlining cardiac ion channel protein interactors and their signature in the human electrocardiogram

Protein-protein interactions are essential for normal cellular processes and signaling events. Defining these interaction networks is therefore crucial for understanding complex cellular functions and interpretation of disease-associated gene variants. We need to build a comprehensive picture of the interactions, their affinities and interdependencies in the specific organ to decipher hitherto poorly understood signaling mechanisms through ion channels. Here we report the experimental identification of the ensemble of protein interactors for 13 types of ion channels in murine cardiac tissue. Of these, we validated the functional importance of ten interactors on cardiac electrophysiology through genetic knockouts in zebrafish, gene silencing in mice, super-resolution microscopy and patch clamp experiments. Furthermore, we establish a computational framework to reconstruct human cardiomyocyte ion channel networks from deep proteome mapping of human heart tissue and human heart single-cell gene expression data. Finally, we integrate the ion channel interactome with human population genetics data to identify proteins that influence the electrocardiogram (ECG). We demonstrate that the combined channel network is enriched for proteins influencing the ECG, with 44% of the network proteins significantly associated with an ECG phenotype. Altogether, we define interactomes of 13 major cardiac ion channels, contextualize their relevance to human electrophysiology and validate functional roles of ten interactors, including two regulators of the sodium current (epsin-2 and gelsolin). Overall, our data provide a roadmap for our understanding of the molecular machinery that regulates cardiac electrophysiology.

Development of a digital zebrafish phantom and its application to dedicated small-fish PET

Objective. We are developing a small-fish positron emission tomography (PET) scanner dedicated to small aquatic animals relevant for biomedical and biological research, e.g. zebrafish. We plan to use Monte Carlo simulations to optimize its configuration and the required water-filled imaging chambers. Our objectives were: (1) to create a digital 3D zebrafish phantom using conventional micro-CT, (2) include the phantom into a simulated PET environment based on the framework GATE, and (3) investigate the effects of the water environment on the reconstructed images. Approach. To create the phantom, we performed ex vivo measurements of zebrafish specimen using a tabletop micro-CT and compared three methods to fixate the specimen. From segmented micro-CT images we created digital emission and transmission phantoms which were incorporated in GATE via tessellated volumes. Two chamber sizes were considered. For reference, a simulation with the zebrafish in air was implemented. The simulated data were reconstructed using CASToR. For attenuation correction, we used the exact attenuation information or a uniform distribution (only water). Several realizations of each scenario were performed; the reconstructed images were quantitatively evaluated. Main results. Fixation in formalin led to the best soft-tissue contrast at the cost of some specimen deformation. After attenuation correction, no significant differences were found between the reconstructed images. The PET images reflected well the higher uptake simulated in the brain and heart, despite their small size and surrounding background activity; the swim bladder (no activity) was clearly identified. The simplified attenuation map, consisting only of water, slightly worsened the images. Significance. A conventional micro-CT can provide sufficient image quality to generate numerical phantoms of small fish without contrast media. Such phantoms are useful to evaluate in-silico small aquatic animal imaging concepts and develop imaging protocols. Our results support the feasibility of zebrafish PET with an aqueous environment.

Modeling Human Cardiac Arrhythmias: Insights from Zebrafish

Cardiac arrhythmia, or irregular heart rhythm, is associated with morbidity and mortality and is described as one of the most important future public health challenges. Therefore, developing new models of cardiac arrhythmia is critical for understanding disease mechanisms, determining genetic underpinnings, and developing new therapeutic strategies. In the last few decades, the zebrafish has emerged as an attractive model to reproduce in vivo human cardiac pathologies, including arrhythmias. Here, we highlight the contribution of zebrafish to the field and discuss the available cardiac arrhythmia models. Further, we outline techniques to assess potential heart rhythm defects in larval and adult zebrafish. As genetic tools in zebrafish continue to bloom, this model will be crucial for functional genomics studies and to develop personalized anti-arrhythmic therapies.