Interactomics: taking apart the cellular machinery

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Among the booming omics disciplines, such as genomics, proteomics, or metabolomics, the field of interactomics is perhaps less known. VIB – UGent expert scientist Sven Eyckerman feels passionate about this topic, as he has devoted his career to studying the interactions between proteins and their impact on functionality. His team is developing techniques to unravel which protein complexes are formed in the cells more accurately, resulting in a greater understanding of cell biology. Identifying the complexes involved in disease could lead to new therapeutic targets and strategies. Furthermore, the group’s analytical techniques are already being applied for drug profiling.

A complex matter of protein complexes

“Proteins are molecules that exert activity in cells,” Eyckerman explains. “Most often, they will not do this on their own, but in the form of protein complexes resembling machines,” he continues. “To understand the functionality of a cell, you must figure out which machines are present, what their components are, and what they do.”

The interest in protein interactions is not new. Similar to other omics fields, research on them has started decades ago, initially to understand signaling pathways. However, studying these interactions is very challenging. Based on the environment involved, they can be very different, so no universal analytical technology for them is available. “Broadly speaking, two approaches can be identified,” Eyckerman says. “First, you have the genetic or binary systems, which tag two proteins of interest. The traditional method in this approach is the yeast two-hybrid method. At VIB, we have developed a similar method for human cell lines, called MAPPIT (at the Jan Tavernier lab). Second, affinity-based systems purify a single protein of interest and determine which proteins associate with it through traditional proteomic techniques, such as mass spectrometry.”

Better tools to explore the interactome map

In these affinity-based methods, the protein of interest is typically purified using monoclonal antibodies, which are expensive or sometimes unavailable. Furthermore, the purification is performed under harsh conditions that can disrupt protein complexes and compromise data. “These drawbacks are overcome in our Virotrap system,” Eyckerman states. “By coupling the protein of interest with a viral protein, it is automatically secreted in harmless virus-like particles. This process allows purification under physiological conditions without antibodies.”

With current techniques, researchers are building extensive lists of interactions that make up a map of the human interactome. However, this map still contains much background noise coming from false-positive interactions detected by current analytical techniques. These can be filtered out using bio-informatics tools. “One of our PhD students, Kevin Titeca, has created such a tool, called SFINX, dedicated to filtering Virotrap data,” Eyckerman says. “We were pleasantly surprised to find that it also outperformed existing tools for analyzing other interactomics data sets.”

Despite the impressive progress, the analytical tools in interactomics still need further refinement. “At the moment, we’re looking at a pool of cells, resulting in an average situation,” Eyckerman explains. “The ultimate goal is being able to count individual proteins in a single cell and pinpointing which molecules they interact with.”

Beyond theoretical insights

In parallel with the development of better analytical techniques, the first applications emerge. “In the past, attempts have been made to use drugs for disrupting specific protein complexes that are, for example, implicated in carcinogenic processes,” Eyckerman says, “but this has always proven to be very difficult. Based on recent insights, the pharmaceutical industry has achieved the first successes.” In addition to these therapeutic applications, VIB methods can also be used in drug profiling. “Determining which proteins interact with a molecule of interest is possible with MAPPIT and Virotrap,” he clarifies. “This allows you to see how specific a drug will bind to its target.”