Phosphoproteomics Uncovers Up To 100 Potential Cancer Drug Targets

A number of proteins that could play a critical role in propagating signals within cells that can lead to uncontrolled cell growth have been uncovered by University of Copenhagen researchers. Uncontrolled cell growth is one of the hallmarks of cancer.

The protein researchers, from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, used mass spectrometry-based proteomics and mouse fibroblast cells. The results may prove important to the development of new so-called tyrosine phosphatase-inhibiting drugs for patients suffering from different types cancer, as well as other types of diseases such as Noonan syndrome.

Globally, cancer is one of the leading causes of death, according to the World Health Organization. In Denmark, one in every three Danes develops cancer at some point in their lives, according to statistics from the Danish Cancer Society.

Shp-2 Protein

The researchers focused on the protein communication and signalling that takes place inside the cells.

Misregulation of protein signalling often leads to an increase in the production of tumours. By understanding the mechanisms and regulation of these signals, the researchers can specifically target the proteins responsible with drugs.

Using mass spectrometry phosphoproteomics to analyse the proteins of cells treated with various growth hormones in combination with advanced data analysis, the researchers discovered proteins that manipulate the communication processes inside the cells initiated by cell receptors and thus inhibit the development of cancer. When inhibited, the prominent protein Shp-2 caught the researchers’ attention.

“This, in fact, leads to the deactivation of a very prominent cell growth pathway, which is the main pathway that people often try to target in cancer cells,”

explained Professor Jesper Velgaard Olsen from the research group.

At the beginning of the study, the researchers knew of a handful of proteins regulated by Shp-2. However, using the mass spectrometry analyses, the researchers discovered around 100 potential new targets, revealing a far more complexity than previously considered.

Now, the researchers need to do further studies to determine the role and mechanisms of these proteins.

“Now, we are doing follow-up projects, looking specifically at leukaemia, where the cancer cells have mutations in these different receptors that can be regulated by Shp-2,”

said Postdoc Tanveer Singh Batth.

Tyrosine Kinase Inhibitors

Cancer patients are often treated with tyrosine kinase inhibitors, which block pathways inside the cells to inhibit tumour growth. However, many develop resistance to current clinical inhibitors; thus, there is a substantial need to find new proteins that can be used as drug targets.

The researchers’ new discoveries can be used in the development of personalised medicine, in which preventive treatments can be targeted at the patients’ personal DNA or protein expression profiles.

“It will be a drug that can be used only in a world with personalised medicine, where it will not be given to for example all leukaemia patients, but only to those with mutations in one of the receptor tyrosine kinases where we now know this Shp-2 protein operates,”

said Professor Jesper Velgaard Olsen.

Phosphoproteomics

Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a post-translational modification.

Phosphorylation is a key reversible modification that regulates protein function, subcellular localization, complex formation, degradation of proteins and therefore cell signalling networks. With all of these modification results, it is estimated that between 30% – 65% of all proteins may be phosphorylated, some multiple times. Based on statistical estimates from many datasets, 230,000 156,000 and 40,000 phosphorylation sites should exist in human, mouse, and yeast, respectively.

Compared to expression analysis, phosphoproteomics provides two additional layers of information. First, it provides clues on what protein or pathway might be activated because a change in phosphorylation status almost always reflects a change in protein activity. Second, it indicates what proteins might be potential drug targets as exemplified by the kinase inhibitor Gleevec.

While phosphoproteomics will greatly expand knowledge about the numbers and types of phosphoproteins, its greatest promise is the rapid analysis of entire phosphorylation based signalling networks.

Batth, Tanveer S. et al.
Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling
Cell Reports , Volume 22 , Issue 10 , 2784 – 2796

Image: University of Copenhagen