Our research projects are usually anchored on a quantitative proteomics based investigation of a cardiac phenotype. 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 cardiac 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. 

Experimental and analytical strategies are developed as per project requirements. Common  strategies applied by our group encompass Mass spectrometry based proteomics approaches:

• Global quantitative proteomics experiments.
• Global quantitative phosphoproteomics experiments.
• Laser capture microdissection from FFPE heart sections combined with mass spectrometry investigation
• Protein interaction analysis.

As well as complementary experimental approaches such as:

• Nuclei isolations from cardiac tissue for single nucleus RNA sequences
• Spatial transcriptomics profiling

Analytical approaches include:

• Analysis of all types of quantitative proteomics data
• Analysis and integration with matched snRNAseq data
• Analysis and integration with matched spatial transcriptomics data

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 8,000 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. The protein abundances measured translates into an explanation for the electrophysiological phenotype.

Single cell RNA-seq

We strive to use the latest technologies in our projects and to pursue multi-modal investigations. By combining global proteomics data with information from single cell RNA sequencing, we can address the cardiac cell populations involved in the responses investigated. The figure 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. Recently we also discovered how different wiring in the phosphorylation signaling networks are involved in the impact of exercise on the cardiac disorder ARVC

Optical voltage mapping in zebrafish

We use multiple experimental strategies to functionally follow up on the findings we make. One strategy we apply is optogenetics. We use zebrafish as a model organism to study human cardiac diseases and generate 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.