Why was a Protein Facility started in the first place?

The idea, which we pioneered together with Oncode Investigator Titia Sixma, was to offer our colleagues at the NKI that like to work with genes, the chance to work with proteins. Looking at mutations in the DNA, or the levels of RNA that correlate with the abundance of proteins, or even at proteomics that tell you a lot more about the actual proteins, is of course amazingly important. But, at the end of the day, it’s the proteins that do the job. To understand biological mechanisms, you need to understand how proteins work. Also, most drugs target proteins: understanding protein function, having assays that measure protein activity, understanding protein structure, are also key for drug discovery.

At the same time, the technical expertise that one needs to work with proteins is very different than working with DNA and RNA, each protein is different and there are no “kits” or universal protocols. So, we decided to put together all the experience that has been accumulated in our groups on how to make proteins for biochemical and biophysical experiments, including structure analysis. So, the Protein Facility was started, hiring Patrick Celie to run it, and building a small team of experts that focused on helping people at the NKI to work with proteins.

How did it go on after that?

The facility started with the main goal of making proteins, but soon after we realised that a key was also building assays for finding out how proteins interact with other proteins - with DNA and RNA, lipids, polysaccharides, but also with small molecules. There were even more technical issues around it, you need a lot of different Biophysical methods to study macromolecular interactions properly, and you need to commission and maintain the machines that you use. We also realised, that most academic labs tended to have their favourite machine to look at proteins and protein interactions. Because something worked at some point for the lab for one project using a certain, people would stick using that approach. That was suboptimal in our opinion, and we felt we needed the different technologies consolidated in a single site.

What happened next?

This has led to an NWO Groot grant that we applied for and received. That allowed us to purchase quite a few machines for measuring macromolecular interactions and make them available to other labs in the Netherlands. Having the national experience, allowed us to then join European programs for offering the Protein Facility first to Instruct-ERIC and then to iNEXT, a horizon 2020 program. Together with generous support from the NKI, we also hired Alex Fish to help user plan and execute their macromolecular biophysics experiments, which was crucial. By now the protein facility has the expertise, on one hand to make proteins, and on the other hand, to measure protein interactions.

Another very important function of the facility, has always been the crystallization of macromolecules, which is something that in the last few years (with cryo-EM taking the center stage) became less popular. But we think its popularity is going to increase again with initiatives like Oncode-PACT – that we will be looking towards making small molecules, lead compounds and drugs within academia.

How can the facility be used?

If you want to screen a big chemical library, like the one available within Oncode, by a biochemical essay - you will need the target protein. And we can make that protein for you. You might also need monoclonal antibody, for which you have the hybridoma, but you might need grams for it. We can make such an antibody for a fraction of the cost most commercial services will ask. If people want to set up an assay or miniaturize an assay to get ready for screening campaigns for libraries, we can also help to set up the assay for that screen, optimize it, miniaturize it, and that on top of making the protein. If you want to have the structure of a protein, these days not to look at the structure, but to look at how a drug binds, we can help you make the protein, crystalize it and even determine the structure.

Besides these, if you have two proteins and you know that they interact, for example from some cell-based assay, and you want to see if this interaction is direct, and you want to quantify this interaction - again we can help make the proteins and measure the characteristics of that interaction.

How did Oncode help the facility?

Oncode helped to keep the momentum. The facility is core funded by the NKI, and Oncode allowed us to have additional personnel for the facility, and that was very timely to keep the facility going, especially during the COVID-19 period. Because of this, we could work on projects that otherwise we could not have done, we had the equipment but not enough “hands”. Funding for extra personnel for two years allowed to us to engage in twelve new projects.

Can you mention some of these projects?

Mario van der Stelt asked for our support to make and crystalize a protein - for a class of compounds that he had and was developing towards lead compounds. Two researchers from Geert Kops’ lab (Hubrecht Institute) applied to make proteins for more basic research – starting a new, curiosity driven project. Jacques Neefjes (LUMC) asked our support to make a large quantity of a protein in a system that was not available in Leiden, and that would have taken months to set up. And Madelon Maurice (UMCU) initially asked support with a couple of proteins, and then started a collaboration with the facility, for a new NWO grant for which many proteins would be needed.

Why do you think it’s important for Oncode to have such a facility available for the community?

I think it fits Oncode’s mission to begin with – looking towards translational research for new drugs. There are groups that, working in that direction, will need assays, and for that they will need proteins, and we are in a good position to really accelerate that. And also, do it in the best way possible, faster, better, cheaper and more efficient.

This also needs a bit of a cultural change. There are now a couple of groups that have the expertise, and more than five groups that make use of this expertise. We discovered over the years that we can get more and more unlikely clients, people that would not have thought of making proteins for their project. But they came to us, they did it, and this was helpful – from getting high profile publications, to making breakthroughs in translation, and starting collaborations with medicinal chemists. An example for this is Reuven Agami (NKI). He had never really done work with proteins, and now, after working with us, he published his results in a high-profile publication and started work with a medicinal chemist and they made compounds towards a target. We need to convince more people to get out of their comfort zone and engage more actively in protein research.