Biology subjects

Myers, P. J.

Publications and source records attributed to Myers, P. J..

3 recordsLinked to original sources

bioRxiv2025

Systems-level Consequences of Low RAF Abundance for EGFR-ERK Signaling

The RAF kinases are central links between RAS, once activated by receptor tyrosine kinases (RTKs), and the extracellular signal-regulated kinases (ERK). In many cancer cells, RAFs are the least abundantly expressed RTK-ERK pathway proteins and can be present at just hundreds of copies per cell at the plasma membrane, but the consequences of limited RAF expression are unclear. By developing continuum and stochastic computational models of the epidermal growth factor receptor (EGFR)-ERK pathway, we showed that low RAF abundance creates stoichiometric bottlenecks between RTKs and ERK with concomitant stochastic RAF dynamics that propagate to weakly expressed downstream pathway proteins. Advanced sensitivity and Sloppiness analyses identified RAS activation and RAS-RAF interactions as strong determinants of signaling in low-RAF settings and revealed an efficient model fitting approach. RAF bottlenecks were predicted to impede ERK activation by oncogenic RAS mutants and explained a tendency for RAF1 membrane localization to be noisy. This work provides quantitative insight into a common, yet unexplored, regime for EGFR-ERK signaling and a systematic approach to develop and characterize dynamic models of receptor-mediated signaling. STATEMENT OF SIGNIFICANCERAF kinases connect receptors to the mitogenic ERK signaling pathway by translocating to the plasma membrane, but in a substantial fraction of cancer cell contexts RAFs are greatly outnumbered by other pathway proteins, potentially creating an unrecognized and consequential signaling bottleneck. We trained a novel computational model of EGFR-ERK signaling and characterized it comprehensively using integrated multivariate sensitivity analyses and Sloppiness analysis. The results revealed that low RAF abundance suppresses EGFR-mediated ERK activation, limits the effects of upstream oncogenic RAS mutants, and creates stochastic RAF dynamics that can propagate downstream. Thus, the canonical EGFR-ERK pathway exhibits divergent behaviors in a parameter space representative of a substantial fraction of cancer cell settings.

systems biology↗

bioRxiv2022

A histone methylation-MAPK signaling axis drives durable epithelial-mesenchymal transition in hypoxic pancreas cancer

Here, we show that hypoxia drives especially long-lasting epithelial-mesenchymal transition (EMT) in pancreatic ductal adenocarcinoma (PDAC) primarily through a positive-feedback histone methylation-MAPK signaling axis. We find that transformed cells preferentially undergo EMT in hypoxic tumor regions in multiple model systems and that hypoxia drives a cell-autonomous EMT in PDAC cells which, unlike EMT in response to growth factors, can last for weeks. We further demonstrate that hypoxia reduces histone demethylase KDM2A activity, suppresses PP2 family phosphatase expression, and activates MAPKs to post-translationally stabilize histone methyltransferase NSD2, leading to an H3K36me2-dependent EMT in which hypoxia-inducible factors play only a supporting role. This mechanism can be antagonized in vivo by combinations of MAPK inhibitors that may be effective in multi-drug therapies designed to target EMT.

cancer biology↗

bioRxiv2021

A reaction-diffusion model predicts the intracellular length scale over which EGFR-initiated GAB1-SHP2 complexes persist

Activation of receptor tyrosine kinases (RTKs) promotes the intracellular assembly of protein complexes formed through phosphotyrosine-SH2 domain linkages. These interactions are weak and reversible, and the dephosphorylation of uncomplexed phosphorylated proteins can be rapid enough to reduce the time and length scales of protein complex persistence distal from the receptor. This limitation may be overcome by cytosolic kinases that rephosphorylate constituent complex proteins as they diffuse. To develop quantitative understanding of the spatiotemporal regulation of these processes, we generated a reaction-diffusion model describing how membrane-bound epidermal growth factor receptor (EGFR) activates the SH2 domain-containing protein tyrosine phosphatase SHP2 by assembling SHP2 complexes with the adaptor GRB2-associated binder 1 (GAB1). Src family kinases (SFKs) were included as a diffusible EGFR-activated intermediary kinase for GAB1. Contrary to the textbook picture of EGFR-mediated SHP2 activation, the model predicts that GAB1-SHP2 complexes can remain intact distal from membrane-retained EGFR at [~]80% of their plasma membrane concentration over the entire intracellular length scale. Parameter sensitivity analysis identified SFK inactivation as one of the most important kinetic processes controlling GAB1-SHP2 spatial persistence, revealing the key role of repeated adaptor phosphorylation in maintaining SHP2 activity. A simple order of magnitude analysis of the controlling rate processes supports the predictions of the coupled differential equation model. Furthermore, proximity ligation assays and immunofluorescence microscopy in carcinoma cells demonstrate that GAB1-SHP2 complexes are increasingly cytoplasmic and distal from EGFR as time proceeds after acute EGFR activation, consistent with model predictions. These results provide quantitative insight into a mechanism that may be alternately tuned for different receptors and downstream effector complexes to enable receptor control of signaling at a distance. STATEMENT OF SIGNIFICANCEThe textbook understanding of receptor-mediated signaling involves the assembly of protein complexes at the receptor cytosolic tail and complex movement within the cell by protein trafficking. However, reaction-diffusion processes can also play an important role in distributing signaling proteins throughout the cell, potentially quite distal from signal-initiating receptors. Indeed, receptors can activate cytosolic kinases that may maintain the phosphorylation-dependent complexation of downstream effector complexes through many rounds of complex dissociation and protein dephosphorylation. Here, we develop quantitative understanding of this mode of signal regulation through development of a mechanistic computational model and demonstrate, with experimental validation, that membrane-bound receptors can regulate signaling through downstream effector complexes over the entire intracellular length scale.

systems biology↗