Phosphoproteomics in Research

By Shelley Farrar Stoakes, M.Sc., B.Sc.Reviewed by Sophie Mullany, BSc

Phosphoproteomics is an important tool in the life sciences, allowing for the study of regulatory changes with variation in conditions and time. The routine evaluation of protein phosphorylation in research has been aided by the development of protein mass spectrometry (MS). Phosphoproteomics enables the detection and quantification of important proteins containing a phosphate group as a post-translational modification. The consequent alterations to protein structure, function and interactions have been found to be responsible for the underlying mechanism of diseases, producing important targets for research.

Early Findings Through Phosphoproteomics

Traditional employment of phosphoproteomics was for the study of signaling systems and identification of substrates for kinases. Intracellular signal transduction is moderated through the phosphorylation of various signaling molecules by kinase enzymes. Kinases transport phosphate groups from ATP to target molecules. The resulting phosphorylated proteins often have altered activity levels. Quantitative phosphoproteomics have produced proteome-wide screens for identifying substrates of protein kinases.

Phosphoproteomics and Cancer Research

Phosphoproteomics is a promising new avenue for cancer research, with recent studies analyzing how the phosphoproteome changes during tumor development. Phosphoproteins also have the potential to be useful biomarkers for diagnostics and therapeutic targets. Dysregulation of kinase signaling pathways are associated with a variety of cancers. Phosphoproteomics has been used to identify aberrantly activated kinases and their downstream substrates. A recent study uncovered kinase signatures related to epithelial ovarian cancer. The phosphoproteomics analysis also found the phosphorylation of cyclin-dependent kinase CDK7, and its association with the activation of RNA polymerase II (POLR2A), characterized both patient-derived cancer samples and cancer cell lines. CDK7-dependent phosphorylation of POLR2A may therefore be responsible for cancer cell proliferation. The results indicate that CDK7 is an important therapeutic target for epithelial ovarian cancer. Further encouragement has been provided by research into covalent inhibitors of CDK7 and their ability to kill triple-negative breast cancer cells.

Phosphoproteomics and Diabetes Research

Phosphoproteomics has been employed in the hunt for novel biomarkers of type 2 diabetes and increased understanding of the fundamental biological pathways leading to the disease. Research into the mechanism underpinning the insulin-induced intracellular signaling pathway, which is important for a number of cellular processes related to aging and metabolic diseases, was developed through phosphoproteomics. . The pathway begins when insulin binds to its receptor, triggering tyrosine phosphorylation cascades that produce further cascade network activations. A greater understanding of connected signaling networks may be the key to unraveling the complex biological processes connecting obesity to type 2 diabetes. A study of the tyrosine phosphorylation cascade through MS and phosphotyrosine immunoprecipitation defined the tyrosine-phosphoproteome of the insulin signaling pathway. The temporal dynamics of protein phosphorylation was also investigated, with three differentially labeled cell populations being stimulated at different times. The study identified seven insulin effectors that had not previously been associated with insulin signaling. This method of phosphoproteomics is also capable of quantifying phosphopeptides in the insulin signaling pathway during condition variations.

Phosphoproteomics and Neurological Disease

The dysregulation of phosphorylation also appears to be associated with neurological disease. Parkinson's disease is a degenerative disorder connected to mutations of the gene encoding the enzyme LRRK2. Most current treatments of Parkinson's disease involve inhibiting LRRK2 to delay disease progression. There is still a limited understanding of the LRRK2 role in cells and why over-activation is harmful. A phosphoproteomic analysis has been utilized in finding other proteins regulated by LRRK2. The study found that LRRK2 directly phosphorylates key substrates in the Rab GTPase family and pathogenic LRRK2 increases phosphorylation, leading to alteration in substrate activity. The finding provides a potential target for the development of new therapies, though further studies are required to pinpoint the connection between altered Rab GTPases and the degeneration of the nervous system.

Further Reading

• All Proteomics Content
• What is Proteomics?
• Proteomics Uses
• Proteomics Methods
• Protein-Protein Interactions