Dying cells are a significant source of inflammation. Macrophages avoid cell death induced-inflammation by recognising and phagocytosing dying cells with exposed phosphatidylserine. This process is termed efferocytosis and leads to the reprogramming of macrophages towards a wound-healing, anti-inflammatory state. Efferocytosis induces substantial morphological changes and the engagement of many receptors and trafficking components. We apply a systems-level proteomic analysis of efferocytosing macrophages to dissect this diverse process and to identify regulators that serve as potential therapeutic targets.
We employed high-sensitivity phosphoproteome and ubiquitinome analyses of bone marrow-derived macrophages engulfing apoptotic T-cells and identified dynamic modifications on receptors and other signalling components, both established and novel, implicating pathways not previously linked to efferocytosis. The analysis of proteins released by efferocytosing cells revealed extensive shedding of inflammatory receptors and an increased release of proteins degrading and building the extracellular matrix. Further functional analysis will help us interpret the regulation of all these factors on efferocytosis and macrophage programming.