High-dimensional characterization of phagosome composition, control and phagocytic receptor redundancy

Project Summary
The phagosome is a dynamically formed organelle that is generated upon phagocyte encounter with
cargo. Phagocytic receptors and other extracellular receptors engage with cargo-derived ligands prior to the
formation of the phagocytic cup at the cell membrane and subsequent phagocytosis. Following phagosome
formation, a dynamic series of steps proceed involving organelle trafficking and fusion. Ultimately, these
collective molecular events influence and shape phagosome function which is often characterized through the
lens of phagosome biochemistry (pH, metal ion abundance, oxidative radicals, and enzyme activity).
While many of the stereotyped features of phagosome maturation and biochemistry have been studied,
there has been relatively fewer studies that take an integrated systems-level view from signaling to phagosome
biochemistry. Furthermore, while the field has defined several features of general phagocytosis, phagosome
biology is incredibly complex. Several distinct cell types can perform phagocytosis ranging from professional
phagocytes (ex: macrophages, neutrophils, dendritic cells) to non-professional phagocytes (ex: fibroblasts).
Adding another layer of complexity, phagocytes engulf a diverse array of cargo ranging from pathogens to
apoptotic bodies. Combined with the temporal maturation of the phagosome, these three axes construct a
complex landscape for phagosome biology. In depth study of this landscape has not been performed limiting our
fundamental understanding of molecular control of this organelle.
Here, we propose a research program centered around the question: “how is control of phagosome
biology achieved?” To address these questions, my research program integrates approaches in genetics, protein
engineering, systems biology, immunology, and microbiology. We seek to address three knowledge gaps in our
program initially. (1) Is there crosstalk in signaling among receptors (phagocytic and soluble ligand) during
phagocytosis? (2) How do cargo and phagocyte identity instruct phagosome composition? (3) What are the
molecular circuits that control phagosome biochemistry? Over the next five years, we will develop a strategy to
examine higher-order interactions in phagocytosis signaling. Furthermore, we will engineer specific cargo
capable of performing proximity labeling in the phagosome. Lastly, we will define the molecular circuits that
control phagosome biochemistry. These questions are inextricably coupled, and our program operates in a highly
collaborative manner. Supporting our experimental systems is a strong quantitative modeling and analytical
framework equipped to derive novel insights from high-throughput experiments and propose new experimental
directions. Together, these strengths position us in a unique manner to address longstanding questions in
phagosome biology.

Grant Number: 5R35GM142900-05
NIH Institute/Center: NIH
Principal Investigator: Bryan Bryson