Molecular leukaemia puzzle

Chemist Matt Fuchter and his collaborators Hugh Brady, a biologist and Peter DiMaggio, a proteomics expert are studying the enzyme DOT1L, a histone methyltransferase implicated in leukaemia. The aim of their project is to figure out how DOT1L dysregulation causes leukaemia and whether switching off DOT1L using an inhibitory drug kills leukaemic cells. Further, they are exploring whether DOT1L has a role in other cancers.

This biological problem can also be framed as a molecular puzzle; who is DOT1L methylating?

Like its fellow methyltransferases, DOT1L works by taking a methyl group from a co-factor called S-adenosyl methionine (SAM) and transfers it to a protein. To keep tabs on where the methyl group is going, one can attach a trackable tag to it, but the problem is one of specificity. SAM is a co-factor for a large number of enzymes, so simply tagging the methyl group on SAM is not enough, it would be like tagging all the £5 notes in circulation and trying to work out how just one person was spending their money.

Consequently, if a cofactor is used by any number of enzymes, how can you modify it so that only one of its enzymes can see it? The solution is a chemical one. SAM works rather like a master key, versatile enough to fit many locks; however, one can make it specific for DOT1L alone. Inspection of the SAM docking bay inside DOT1 showed that it is possible to design an artificial SAM with a ‘bump’ protruding from the surface that allows it to fit perfectly into DOT1L’s internal architecture, but nowhere else.

This is now a juicy proteomics problem…to find proteins carrying the tagged methyl group is an absorbing technical challenge

If the artificial SAM is introduced into cells with a suitable tag labelling its methyl group, it should be possible to look for the proteins that DOT1L is methylating. This is now a juicy proteomics problem; developing the mass spectrometry and data analysis tools necessary to find the proteins carrying the tagged methyl group is an absorbing technical challenge.

This project demonstrates multidisciplinary collaboration in practice and a major challenge in this type of work is to keep each partner intellectually engaged given that the motivation for that engagement will differ between disciplines. Matt Fuchter colleagues says that he, “may get the biggest kick out of a new synthesis, rather than focusing on the application of their chemical probes to gain biological knowledge. But others are more biologically orientated; problems in biology can be reframed in a chemical way.”

The DOT1L project covers a broad spectrum of research, from a chemical engineering and detection challenge to the potential for drug development—it is tackling a big-picture problem

with the best tools for the job, which is a good example of how multidisciplinary collaborations should work. And there are other advantages to working with other disciplines. “It’ is nice to collaborate outside your field as nobody needs to be top dog”, says biologist Hugh Brady. “You know your strengths and weaknesses and respect your collaborators. But you need to find people who will listen carefully to your problem and discuss it with you, rather than tell you what to do without properly engaging.”

Peter DiMaggio is amused by some of the differences in approach that he has noticed; “Chemists normally work in closed systems with fairly well-defined variables, as such, they do not always appreciate the need for controls and engineers are a bit the same.” He continued, “in a multidisciplinary lab, engineers and chemists design biology experiments with very few controls and only the biologists understand just how many controls are required!”

There are biological problems out there that chemists, physicists and engineers may already have a way to answer and if we all start talking to each other

All three agree that what marks out a really good biologist is an almost intuitive ability to look at a biological experiment and spot the anomalies that hint at new knowledge, rather than get sidetracked by artefacts. That is why, says Matt, “it is important to have a biologist’s view in a collaboration, particularly in complex models of disease.”

Hugh has found some advantages in having chemists around too, they are very goal-driven. “Matt and Pete want endpoints and output, they do not tolerate wishy-washy endless biology experiments; however, they are also somewhat flummoxed by the length of time our experiments take!”

To finish, Matt sums up why multidisciplinary collaboration is so essential; “there are biological problems out there that chemists, physicists and engineers may already have a way to answer and if we all start talking to each other, we will get where we want to go a whole lot faster.”