Profiling signaling polarity in chemotactic cells

Abstract

Cell movement requires morphological polarization characterized by formation of a leading pseudopodium (PD) at the front and a trailing rear at the back. However, little is known about how protein networks are spatially integrated to regulate this process at the system level. Here, we apply global proteome profiling in combination with newly developed quantitative phosphoproteomics approaches for comparative analysis of the cell body (CB) and PD proteome of chemotactic cells. The spatial relationship of 3,509 proteins and 228 distinct sites of phosphorylation were mapped revealing networks of signaling proteins that partition to the PD and/or the CB compartments. The major network represented in the PD includes integrin signaling, actin regulatory, and axon guidance proteins, whereas the CB consists of DNA/RNA metabolism, cell cycle regulation, and structural maintenance. Our findings provide insight into the spatial organization of signaling networks that control cell movement and provide a comprehensive system-wide profile of proteins and phosphorylation sites that control cell polarization.bioinformatics ͉ chemotaxis ͉ phosphoproteomics ͉ proteomics ͉ cell migration D irected cell migration or chemotaxis in response to a chemokine gradient is involved in development, immune function, angiogenesis, as well as pathological processes associated with inflammation and cancer cell metastasis (1). Cell locomotion is a highly polarized process characterized by protrusion of a leading pseudopodium (PD) (lamellipodium) at the front and establishment of a trailing rear compartment or tail region at the back (1, 2). This process is regulated through organization of the actin-myosin cytoskeleton in response to signal transduction processes that operate downstream of chemokine and integrin adhesion receptors. These receptors serve as antennae to sense changes in chemokine and extracellular matrix gradients, which provide navigational cues to direct cell movement. However, the molecular signaling mechanisms that control cell polarity and chemotaxis are not fully understood.Emerging evidence indicates that cell behavior is regulated by the complex organization of multiple signaling networks in time and space. The specific propagation of biological information in a complex biological system is achieved through the spatiotemporal assembly of multiprotein scaffolds, protein activation cascades, protein turnover, and specific posttranslational modifications of proteins, including the phosphorylation and dephosphorylation of specific amino acid residues. Although significant progress has been made in identification of specific signaling proteins and regulatory pathways that mediate cell migration, little is known about how these signals are integrated into spatial networks to achieve morphological polarity and directional movement at a system level.To understand the complexity of signal organization in migrating cells, our laboratory developed a system that facilitates the differential purification of the PD and cell body (CB) co...

Pseudopodium-enriched atypical kinase 1 regulates the cytoskeleton and cancer progression

“…S1A) (9). To identify kinases and their substrates that spatially regulate these processes, we used a strategy that allows for the large-scale purification of pseudopodia actively extending toward an LPA gradient (9)(10)(11). The relative differences in pY proteins from pseudopodia were compared with pY proteins isolated from purified cell bodies by using pY immunoaffinity purification followed by MudPIT (14).…”

“…Therefore, understanding how this structure is regulated is crucial to understanding how cells migrate and invade tissues during cancer progression. To this end, we described a novel method for purifying the pseudopodia from cells for signal transduction and proteomic studies (9)(10)(11). Using this fractionation method and quantitative mass spectrometry (MS), we have profiled the relative differences in the pseudopodium and cell body proteomes (10).…”

“…To this end, we described a novel method for purifying the pseudopodia from cells for signal transduction and proteomic studies (9)(10)(11). Using this fractionation method and quantitative mass spectrometry (MS), we have profiled the relative differences in the pseudopodium and cell body proteomes (10). Although this approach has identified important new pseudopodial proteins, it did not provide a robust method for detailed analysis of phosphotyrosine (pY) proteins or kinases present in this subcellular structure (10).…”

“…Using this fractionation method and quantitative mass spectrometry (MS), we have profiled the relative differences in the pseudopodium and cell body proteomes (10). Although this approach has identified important new pseudopodial proteins, it did not provide a robust method for detailed analysis of phosphotyrosine (pY) proteins or kinases present in this subcellular structure (10). pY proteins are difficult to detect because of their low abundance and typically require an enrichment step before MS analysis (12,13).…”

Protrusion-localized STAT3 mRNA promotes metastasis of highly metastatic hepatocellular carcinoma cells in vitro

“…The tight actin bundle in a filopodium forms a projection to allow the cell to infiltrate into small gaps [6] . Proteomic analyses of filopodia and lamellipodia have revealed the extent of the proteome of these cellular protrusions [7] . However, it is still unclear how proteins are specifically targeted to or maintained in these subcellular domains.…”