Proteomics, proteases, systems biology, inflammation, immunity
The goal of my lab is to understand how proteolytic post-translational modifications lead to the activation or inactivation of immune responses in inflammatory diseases. By the irreversible processing of bioactive proteins and signaling molecules, proteases modulate all aspects of biology. We focus on proteases and their substrates on a cell, tissue, biopsy or organism-wide scale. Projects: 1- Unraveling how calcium signaling regulates calpain proteolytic networks Selected proteins have evolved to bind Ca2+ to buffer its levels, and alterations in Ca2+ homeostasis initiate or terminate multiple cellular signaling pathways that govern cell shape, adhesion, migration, and viability. Activation of G protein-coupled receptors (GPCRs) can trigger intracellular Ca2+ release through the downstream generation of 1,4,5-inositol trisphosphate (IP3). When IP3 binds to its cognatereceptor (IP3R) in the endoplasmic reticulum, Ca2+ concentrations rise from ~100 nM to more than 1 mM (>10-fold increase) dictating profound changes on cellular functions. Among the key downstream effectors of Ca2+ signaling are a family of 15 cysteine proteases called calpains, which are directly activated at their catalytic sites by changes in intracellular Ca2+ levels. These proteases regulate diverse cellular processes through targeted proteolysis and precise processing of multiple protein substrates. We are using systems biology approaches to identify novel calpain substrates and understand their effect on cellular functions and immune signaling. 2- Multi-omics analysis of macrophage polarization Tissues are an interactive, multi-cell and dynamic environment linked to the surrounding stroma by signaling networks that regulate gene and protein expression as well as post-translational modifications. Within inflamed joints, wounds or tumors, immune cells collaborate to this highly dynamic environment by modulating the genetic landscape and web of proteins as they are reacting to the threat. Among the multitude of infiltrating immune cells, mononuclear phagocytes are necessary for the clearance of pathogens and the resolution of inflammation during innate and adaptive immunity. The mononuclear phagocyte system is a highly dynamic and complex system that can be unified based upon progenitor cells but disjointed based upon the stimuli they are responding to. They are responsive and activated by various cell products and cytokines thus giving rise to a panoply of populations with distinct functions. The classically activated macrophages are induced by IFNg and/or LPS (TH1) whereas alternatively activated macrophages (TH2) have several activators including IL4, IL13, IL10, glucocorticoids (GC), immune complexes (IC) and/or transforming growth factor β (TGFβ). To understand the global changes of macrophage reactivity and their substrates within whole tissues or fluids, wide-scale systems biology approaches offer the opportunity to integrate and capture such complexity. Extensive transcriptomics information has been published in the last decade but still little is known about the partitioned macrophage populations’ proteome and their protease substrates.