Opening up the interactome

The completion of the human genome sequence just over a decade ago was a triumph for biomedical research. We have since expanded our knowledge through projects such as the Encyclopedia of DNA elements (ENCODE), which aimed to identify all the functional elements within the genome.

The ultimate goal is knowledge of how the genes work in different pathways and how these pathways function in disease and development is the ultimate goal. To accomplish this we will need to systematically map all the protein-protein interactions in a cell.
Researchers in multiple labs across North America and Europe have now moved closer to connecting genotype with phenotype with the publication of a new human interactome map1. This map, which took nine years to generate, is based on a systematic screen of 13,000 human proteins and uncovered a whopping 14,000 interactions.
Yet the authors estimate that a mere 5 to 10 percent of the total interactome is covered by the protein-protein interactions they have identified. Nonetheless the results of this study offer at least a five-fold improvement over previous interactome maps.
A high-throughput yeast two hybrid approach was used to identify the multiple interactions, in which 82 million protein pairs were each tested four times in two different configurations for their ability to activate a reporter gene in yeast. These interactions were then validated using three independent methods: testing whether the protein pair could reconstitute a membrane-bound receptor complex, using the well-based nucleic acid programmable protein array and reconstituting a fluorescent protein.
Results from the new interactome map support the long-held suspicion that proteins implicated in cancer participate in disproportionate numbers of protein interactions. The ongoing sequencing studies of tumour genomes may be enhanced by the additional insights into these protein-protein interactions, helping to distinguish ‘driver’ mutations that cause cancer from ‘passenger’ mutations that are just along for the ride.
Though this latest map provides a valuable resource it presents a static view of the proteome. Beyond this level of analysis scientists aim to examine the dynamic changes that take place within cells and the adaptive responses of the proteome to environmental stresses. Future efforts may focus on tissue-specific proteins, post-translational modification that affect protein-protein interactions and proteins produced from alternatively spliced transcripts.
It has been estimated that at any one time there are approximately 130,000 interactions in any cell2. Considering this the interactome will undoubtedly shape up to be far more complicated than the genome sequence has proven to be, but this study has allowed the beginnings of this map to be documented. 
The authors of this interactome study are already at work expanding the current interactome map to a more comprehensive study of 17,000 proteins.
1. Rolland et al., Cell, 159:1212-26 (2014).
2. Venkatesan et al., Nature Methods, 6:83-90 (2009).