How ‘contextualizing’ proteins is driving medical breakthroughs

A few decades ago, biology was dominated by the dogma that one gene codes for one protein. But more recent research shows that the biological fate of cells is determined at least as important by the environment in which they are located. This ‘context’ determines the final appearance of the gene products for each cell type (the so-called proteoforms), which are responsible for proper cell function.

Cells ‘read’ their environment, as it were, and send out messages. What’s more, these signals – also called biomarkers – are often the first to contain molecular signs of disease, which means that their detection can be significantly advanced. Therefore, from a medical point of view, such extracellular signaling substances are at least as valuable as the countless biomolecules that make up the contents of a cell type.

It is therefore no coincidence that the leading trade journal Nature at the beginning of this year the so-called spatial multi-omics included in the list of the seven technologies to watch in 2022. It is important to mention that this methodology can be applied generically and is therefore not only aimed at studying a particular disease. In other words, there are many potential developments in which spatial multi-omics can be used.

A company that has been focusing on this method for some time is the Belgian start-up ProteoFormiX. “In fact, it is striking that no one else is working on it yet, because I proclaimed the basic idea behind our method 30 years ago,” says CEO Peter Verhaert. “We scan tissue sections pixel by pixel with a mass spectrometer and make molecular photos of them. This makes the peptides, the small proteins with a signaling function, visible,” explains Verhaert. The tissues do not need to be stored in a specific way for this type of research. This also makes the approach extremely suitable for gaining insights into as yet unexplained syndromes.

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Our technology has really been proven right this year.

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However, this method collects such a large amount of data that, in fact, it cannot be used with the classical analysis methods. “That was a challenge. Moreover, the pathologically relevant information is often buried under an excess of noise. That is why we are developing algorithms that are able to extract the right data from this big data,” explains Verhaert. This is comparable to astrophotography, where in order to make beautiful images of galaxies, the relevant data must also be filtered from a mass noise.

Thanks in part to European support from the European Institute for Innovation and Technology, investments from imec.istart and the BlueHealth Innovation Center, and a subsidy from VLAIO, ProteoFormiX can incubate at JLABS@BE, the Johnson & Johnson Innovation Center on the Janssen Pharmaceutica campus. Verhaert also saw a clear change in perception there in the past year. “I have invested a lot of time in convincing the potential of our approach. That phase is now clearly over. Our technology has really been proven right this year,” says Verhaert.

ProteoFormiX hopes to be able to grow further in the coming years through structural collaborations with a number of large hospitals and international biobanks. “Actually, it has yet to start for all of us. From that perspective, I hope that we will also receive support from major pharmaceutical players and thus be able to convert the potential of our technology into concrete results in pathology control,” concludes Verhaert.

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