Nowadays data are starting to play a central role in biological sciences, enabling researchers to make great strides in combating serious illnesses. Interview with Professor Ernest Fraenkel, a researcher at MIT, who is pursuing an innovative approach to studying interactions between cells and the proteins and other molecules they contain, based on data.

[Portrait d'innovateur] Ernest Fraenkel place les données au cœur de ses recherches sur les maladies graves

Doesn’t he have an atypical profile for a biologist?

Well, US professor Ernest Fraenkel is no ordinary research biologist. After his high school principal persuaded him to join an experimental science teaching programme, he took a liking as a young man to working on science projects in laboratories. He even dropped out of school at one stage to devote himself to lab work. ‟Physics, chemistry, and biology were taught together in this experimental programme. My early experience was that they were all deeply connected,” he tells us.  His talent and passion for biology led him to Harvard where he decided first of all to improve his grounding in chemistry and physics. He was looking for a data-rich field, as this was what fascinated him most. However, ‟at the time there was still very little data in the domain of biology”. This is how he developed a great interest in structural biology, which uses tools such as X-ray crystallography to analyse biological molecules, subjects he went on to study in more depth at Harvard and then the Massachusetts Institute of Technology (MIT). He remembers this period as the ‟great beginning of data-use in biology.” Under a programme at the Whitehead Institute for Biomedical Research, Fraenkel even succeeded in getting his own work space and funding to freely pursue his own interests. This period was one of real transition. ‟It was then that I became a systems biologist, moving from the study of individual proteins or small groups of proteins to studying the existence of thousands of proteins.” In the end he joined MIT’s newly-established Department of Biological Engineering.


His innovation ?

Biology is a field where work tends to be based on hypotheses. The approach is always the same. You start off with a hypothesis and then test whether or not it is correct. However, systems biology opens the doors to a completely different way of thinking: ‟The initial hypothesis is perhaps not based on an observation which researchers can make straightaway, and it may be that we have to take a step backwards to observe the system by not looking just at the behaviour of a gene or a protein, but by measuring, as far as we can, all the proteins, all the genes, and all the small molecules. The hypothesis may emerge from our observation of the system and the data we have harvested,” Professor Fraenkel explains. This is where his innovative side comes into play: ‟My greatest innovation has been to offer a holistic interpretation of the data.” Working hand in hand with a team of ten researchers around him on a daily basis, Fraenkel is trying to build a single model incorporating all types of data – and in so doing to radically change the entire approach to biology. The scientific community is still rather doubtful about this innovative method of learning biology, although the Professor’s work has won recognition on many occasions. Fraenkel has received a number of awards and works with research teams in Europe, notably in Italy, who specialise in serious illnesses and machine learning, which is a sub-field of Artificial Intelligence.

La biologie des systèmes, étude des réseaux

              Systems biologist Professor Fraenkel is looking to boost progress in medical research

What impact is his work having?

At the present time Fraenkel and his colleagues are not yet able to present any concrete results from their work. However, they have high ambitions: to find far more effective, more targeted treatments for illnesses, and fast.

Their technique enables them to identify key interactions between cells, which means they do not have to take a view skewed by hypotheses based on inadequate observations. ‟We try to identify which genes or proteins we really have to worry about,” he stresses. They hope in the near future to be able to respond quickly to viruses such as Ebola, providing treatments that really work. At the moment the team is busy focusing on degenerative illnesses such as Huntington’s disease and Glioblastoma, a type of brain tumour.

So what does the future hold for data-driven biology ?

Data is a central component for the future of biology.” Ernest Fraenkel believes that in the coming years researchers will be able to incorporate directly into patient data the sort of molecular data on which they focus in their work, i.e. data collected on patients in hospitals. ‟Being able to collect all the data and analyse it together simultaneously could prove a real catalyst in the fight against serious illness,” he argues. However, drawing on databases built up by pharmaceutical companies and getting hold of tests results that are not yet available for research purposes is likely to prove a considerable challenge. Another hurdle to surmount will be social policy issues relating to the use of personal data. ‟How can we protect patients? How can we reassure patients that their data is being used properly?” These types of questions need answering and must be resolved if medical science is to make further progress.

By Pauline Canteneur