Our research projects are frequently centered on quantitative proteomics investigations of cardiac phenotypes. In that sense projects often start with a mass spectrometry based proteomics investigation that is subsequently followed up by orthogonal experimental approached. We are a technology centered group and work on development of high-throughput quantitative approaches applied to basic and translational projects in cardiovascular research. The figure to the right illustrates our efforts in integrating information from proteomics based investigations of protein complexes in heart tissue with genomics data of a cardiac phenotype to pinpoint novel regulators of cardiac physiology. 

Quantitative proteomics

One of our main efforts lie in development of high-throughput quantitative approaches for dynamic analysis of deep cardiac proteomes, which we apply to basic and translational projects in cardiac research. We use our technologies to quantify protein changes in cardiac disease states by analyzing human heart biopsies. To the left is an illustration from a study where we used quantitative proteomics to quantify all proteins in the cardiac pacemaker region, the sinus node. With the technology we can quantify abundances of more than 7,000 cardiac proteins. The figure illustrates the quantitative information of a small subset of these, specifically of the ion channels involved in the cardiac action potential generation.

Single cell RNA-seq

We strive to always use the latest technologies in our projects. We are accordingly combining our proteomics efforts with single-cell transcriptomics analyses, which allows us to identify exactly which cellular components in complex cardiac tissue samples give rise to the protein regulation we identify. Below is an example of single cell transcriptomics data we generated from the cardiac sinus node.

Phospho-proteomics and Post-Translational Modifications

Phosphorylation mediated signaling is a primary mechanism for dynamical signaling responses in the heart. We are developing and applying quantitative phosphoproteomics approaches to quantify phosphorylation mediated signaling directly in cardiac tissue samples. We have previously reported the beta-adrenergic signaling response in heart tissue, as illustrated in the figure on the left. We are currently extending our efforts to also study less described post translational modifications in the heart. 

Optical voltage mapping in zebrafish

We use multiple experimental strategies to functionally follow up on the findings we make. One of the main methods we apply is optogenetics. We use the zebrafish as a model organism to study human cardiac diseases by generating knockdowns using CRISPR/Cas9 technology. Hearts of genetically modified animals are phenotyped and we measure the cardiac electrical activity and calcium transients using voltage sensitive dyes. These approaches facilitate interpretation of the molecular mechanism behind cardiac diseases at the organ level.

As many cardiac diseases are primarily associated with dysfunction of one of the four cardiac chambers we are also performing detailed investigations of the protein-specific differences among the four chambers. We believe this will be key information to identify novel pharmaceutical targets with chamber-specific impact.

Please refer to publications (PMID:24952909) and (PMID:23737553) for specific examples of the experimental approaches we apply to better our understanding of cardiac molecular regulatory mechanisms.

To the right is an example of specific protein phosphorylation sites we have identified to be regulated upon beta-adrenergic stimulation of the heart. That study was our first proof-of-principle investigation of a quantitative investigation of phosphorylation mediated signaling directly in cardiac tissue, laying the foundation for our cardiac proteomics efforts.