Sven Eyckerman Lab

Research focus

​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 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 (see 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.

Publications

SFINX: Straightforward Filtering Index for Affinity Purification-Mass Spectrometry Data AnalysisTiteca K, Meysman P, Gevaert K, Tavernier J, Laukens K, Martens L, Eyckerman SJOURNAL OF PROTEOME RESEARCH, 15, 332-8, 2016
Toward clinical proteomics on a next-generation sequencing platformTurner D, Tuytten R, Janssen K, Lammertyn J, Wuyts J, Pollet J, Eyckerman S, Brown C, Kas KANALYTICAL CHEMISTRY, 83, 666-70, 2011
Large-scale protein interactome mapping: strategies and opportunitiesLievens S, Eyckerman S, Lemmens I, Tavernier JExpert Review of Proteomics, 7, 679-90, 2010
Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cellsEyckerman S, Lemmens I, Catteeuw D, Verhee A, Vandekerckhove J, Lievens S, Tavernier JNATURE METHODS, 2, 427-433, 2005
Design and application of a cytokine- receptor-based interaction trapEyckerman S, Verhee A, Van Der Heyden J, Lemmens I, Van Ostade X, Vandekerckhove J, Tavernier JNATURE CELL BIOLOGY, 3, 1114-1119, 2001

News

Talking protein tags, novel ideas and tech innovation

05/11/2016 - As one of our Expert Scientists, Sven Eyckerman knows all about the ‘tech’ in ‘biotechnology’. Together with his VIB-Ghent University research team, he has been working on several innovative biotechnologies.

Interesting news from VIB Medical Biotechnology Center UGent

29/07/2016 - The labs of Jan Tavernier, Kris Gevaert and Sven Eyckerman from the VIB Medical Biotechnology Center, UGent tackle some of the most fundamental life sciences questions in their research into the detection and analysis of protein-protein interaction.

Genome engineering of quantifiable protein tags: Western blot on the way down?

06/06/2016 - Professor Sven Eyckerman (VIB/UGent) and colleagues developed a set of universal protein tags that warrant protein quantification via targeted proteomics techniques.

VIB/UGent researchers use viral particles to trap intact mammalian protein complexes

28/04/2016 - VIB/UGent developed Virotrap, a viral particle sorting approach for purifying protein complexes under native conditions. This catches a bait protein together with its associated protein partners in virus-like particles that are budded from human cells.

Sven Eyckerman

Sven Eyckerman

Research area(s)

Bio

PhD: Ghent Univ., Ghent, Belgium, 2002
Postdoc: Swiss Inst. for Experimental Cancer Res. (ISREC), Lausanne, Switzerland, 2004-06
Sr Scientist: Pronota NV, Ghent, Belgium, 2006-09
Postdoc: VIB, Jan Tavernier and Kris Gevaert Lab, Ghent, 2008-14
VIB Expert Technologist since January 2015

Contact Info

VIB-UGent Center for Medical BiotechnologyUGentAlbert Baertsoenkaai 3 9000 GENTRoute description