Unraveling the regulation of phosphorylation in insulin singaling from temporal large-scale phosphoproteomics

Abstract

Homeostasis is essential for normal function of the mammalian body. On a cellular scale biological processes are tightly controlled by dynamic intracellular signalling mechanisms. Cells use intricate signalling networks to respond to environmental cues and appropriately regulate functions such as differentiation, metabolism and proliferation. Deregulated signalling can result in complex diseases such as cancer, neurodegenerative diseases and cancer. Signals inside cells are transmitted via protein phosphorylation. Protein phosphorylation is a reversible chemical modification where a phosphate group is attached to a protein by enzymes (kinases). Phosphatases are responsible for the reverse reaction. Protein phosphorylation occurs on rapid time-scales (milliseconds to seconds), making it an ideal carrier of these signals. Advances in mass spectrometry-based proteomics have led to the identification of many tens of thousands of phosphorylation sites. The improvement of the technique has also recently allowed us to measure phosphorylation over time on a large scale. The analysis on these temporal datasets did not differ from the analysis applied to static datasets. However, temporal data offers more possibilities for knowledge discovery and more intricate analysis methods can be applied to interrogate the time course data. This work focuses on the development and application of analysis techniques for large-scale temporal phosphoproteomics data. Using these techniques it is possible to identify kinases that are involved in a signalling process, it is possible to predict which phosphorylation sites are important and it is possible to find gaps in the knowledge of a signalling network. The results from this work will direct further experimental studies. Taken together, the analysis techniques applied in this work can help our understanding of intracellular signalling and this in turn can facilitate drug discovery