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Computational Analysis and Modeling of Cytoskeletal Organization During Phagocytosis

Year: 2024
Type: dissertation
Abstract: Phagocytosis, the biological process in which cells ingest large particles such as bacteria, is a key component of the innate immune response. After binding immunoglobulin G (IgG) coating a target, Fcg receptors (FcgR) are activated and phagocytosis is initiated. This receptor activation causes a signaling cascade that leads to formation of the phagocytic cup and culminates with ingestion of a target. In the experimental system termed “frustrated phagocytosis”, cells attempt to internalize fixed, micropatterned disks of IgG. Cells that engage in frustrated phagocytosis form “rosettes” of actin-enriched, adhesion-like structures called podosomes around the disks of IgG. Podosomes are important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy. Using persistent homology, a type of topological analysis, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed the “hourglass” shape of the podosome actin core, a protruding “knob” at the bottom of the core, and two actin networks extending from the core. Additionally, we present data that supports the involvement of Cdc42, a member of the Rho family of GTPases, in podosome rosette pattern formation. Cdc42 acts downstream of receptor activation, upstream of actin polymerization, and is known to play a role in polarity establishment. We demonstrate how the addition of negative feedback to existing reaction-diffusion models for GTPase spatiotemporal dynamics can generate the experimentally observed rosette pattern of podosomes. We show rosette pattern formation can occur through two general mechanisms. In the first mechanism, an intermediate species forms a ring of high activity around the IgG disk, which then promotes podosome formation. The second mechanism does not require initial ring formation but relies on spatial gradients of intermediate chemical species that are selectively activated over the IgG patch. Finally, we perform further simulations that suggest future experiments to test the validity of the models presented.
DOI: 10.17615/2rnv-st71
Language: English
Subfield: Cell Biology
Open Access status: green
OpenAlex ID: W6944127481
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