Analyzing the biomolecular composition of the plasma membrane

15 December 2011
There are very powerful technologies available for detecting changes in gene expression on a genome-wide scale.
Unfortunately, these technologies only provide indirect indications about the biomolecular composition of the entire cell, while spatial information about the location of the changes in the cell is usually also missing. This is a huge challenge for researchers. However, Wim Annaert, VIB Department of Developmental and Molecular Genetics, K.U. Leuven, tackled this challenge together with Imec researchers and two VIB research groups at UGent. Instead of
targeting the entire cell/tissue, they developed a new strategy for the comprehensive analysis of the biomolecular composition of only the plasma membrane. 
This study is the result of interdepartmental collaboration. Could you provide more details?
Wim: First of all, the idea came out of interaction with Imec, where Staf Borghs and his team are using nano particles to generate nano switches. Based on this, we developed a new generation of
superparamagnetic nano particles that, when introduced into cells, only associated with the cell
surface. This allowed us to isolate plasma membranes magnetically in the quantities and with
the purity needed to analyze not only the proteome but also the lipidome and even post-translational changes. This drew the interest of Kris Gevaert and Nico Callewaert in the UGent VIB groups. And with the input of Johan Swinnen (K.U.Leuven) for the lipidome analysis, the project became not just interdepartmental but also interinstitutional.

You applied this novel technology in your Alzheimer research? Could you explain this?
We did. The new technology allowed us to unravel the alternative function of presenilins. Besides its catalyst role in the ß-secretase complex, presenilin 1 also plays a role in endosomal membrane transport and protein turnover. Preliminary research in our lab had shown that cells incapable of producing presenilin (so-called presenilin knockout cells) had a very different morphology. They are strikingly round in contrast to the more elongated shape of normal fibroblasts. This could, in our opinion, only be explained by a significant difference in the biomolecular composition (i.e. proteins and lipids) at the cell surface.

With the aid of the new technology, we compared the biomolecular composition of the plasma
membrane of knockout cells with that of wild type cells and found that a set of proteins and lipids were indeed selectively less represented at the cell surface in knockout cells.

What is the impact of your findings?
The study confirms the non-catalytic function of presenilins in protein transport. One surprise was
that both the protein and lipid changes could be traced back to the same selective endosomal
transport route – a new part of the story that we are currently finalizing. By analyzing the lipid and protein composition simultaneously, we more quickly tracked down a possible mechanism behind this function of presenilin.
Thus we delivered proof of principle for this new isolation technology. The real added value is that
this method has a very strong generic character – it is now potentially possible to generate integral
‘fingerprints’ of the plasma membrane of any cell, which opens up new possibilities in experimental
medicine. Many diseases are accompanied by changes in the biomolecular composition of the
plasma membrane, while two thirds of the current drugs target plasma membrane components.
Identifying changes at the level of protein or lipid composition may, in the future, generate new
biomarkers or target molecules for the development of new drugs.

Thimiri Govinda Raj et al.
A novel strategy for the comprehensive analysis of thebiomolecular composition of isolated plasma membranes
Molecular Systems Biology 2011