Harnessing multi-omics to define cytokine-modulated antigen processing and presentation

Antigen presentation is the fundamental and complex process in which a cell breaks down proteins into small fragments (peptides) and presents these on its surface to activate or modulate immune cells. While this is employed by both “professional” and “non-professional” antigen presenting cells, the pathways that they use differ dramatically. Both processes are affected by the activity of cytokines, molecules secreted by various immune cells that initiate intracellular signalling cascades upon binding to target cells. However, our understanding of exactly how these cytokines affect antigen processing and presentation is extremely limited. This project will use a highly innovative, multi-omics pipeline to delineate how cytokines remodel antigen processing pathways at distinct functional levels, including gene expression (transcriptomics), protein-protein interactions (subcellular fractionation and size exclusion chromatography coupled with mass spectrometry) and antigen presentation (immunopeptidomics). This exciting project will expose you to a wide range of ‘wet-lab’ and bioinformatics techniques, and has the potential to redefine our understanding of a key aspect of immunology relevant to many aspects of human health, including infection, cancer and autoimmunity. A keen interest in both experimental and computational biology is therefore essential.