Research @ the Eyckerman Group

“We are working on innovative technologies to create and improve organism wide protein-protein interaction maps. These maps reveal rich and functionally relevant data for every protein in the network.”

Several strategies currently exist to address all possible associations between proteins, also called the interactome, not only on the single protein but also on a proteome-wide level. These strategies can be divided in the divided in the binary approaches which rely on the expression of both bait and prey to perform a test for the interaction, and the co-complex methods, wherein the protein complex is purified from a lysate. The result of this work is a physical interaction map of all possible associations between proteins for a certain organism. Popular methods include the yeast two-hybrid system and the MAPPIT platform (Jan Tavernier lab) for the binary approaches, and Affinity Purification coupled to Mass Spectrometry (AP-MS) as an example of the co-complex methods. Although these contributions are clearly essential to grasp the inherent complexity of protein complex biology, the underlying technologies are not perfect, and are typically deployed in generic cell systems. Moreover, the functional implications of these associations remain hidden in the complex networks which are typically generated in high throughput studies.

We aim to improve the co-complex methods on different levels with the ultimate goal to provide a high resolution context-dependent association profile for the protein of interest. Virtually all available methods rely on lysis or homogenization as a first step in the protocol. With the Virotrap platform (developed on the interface of the Tavernier and Gevaert labs), we prevent the need for lysis by trapping the protein complex under native conditions in virus-like particles that bud from human cells. Classical proteomic approaches can then reveal the content of these particles. The unique data generated by Virotrap required new analysis tools resulting in ‘Sfinx’, a straightforward filtering strategy which outperforms available tools, also on AP-MS datasets.
The recent revolution in genome engineering technology, mainly driven now by CRISPR/Cas9, provides unique opportunities in the fields of proteomics and interactomics. We are pursuing the implementation of these genome engineering approaches to push co-complex analysis at the endogenous protein level to complement antibody-based approaches. Currently we are exploring the use of both very small epitope tags and of larger multifunctional tags not only for classical AP-MS pulldown analysis, but also to characterize the targeted proteins in unrivaled detail. Combination of different in house strategies and recently developed technologies (e.g. BioID) should provide a unique interaction profile, which is dependent on the origin and activation state of the cell. This data will be complemented with functional data coming from profiling approaches. Both protein and transcriptome profiling, in combination with different perturbance efforts, will allow the functional reconstruction of signal pathways.