A multi-level formalism to capture the characteristics of hybrid phenotypes in Epithelial-Mesenchymal Plasticity

Abstract

Epithelial-mesenchymal plasticity (EMP) is a cell-fate switching program that enables cells to adopt a spectrum of phenotypes ranging from epithelial (E) to mesenchymal (M) and hybrid E/M states. Hybrid E/M phenotypes are considered optimal for cancer metastasis due to their association with metastatic initiation and traits such as stemness, drug resistance, and collective migration. Boolean models of gene regulatory networks (GRNs) underlying EMP have provided valuable insights into the dynamics of E and M phenotypes. However, these models fail to capture hybrid phenotypes effectively, as Boolean frameworks allow only binary gene expression, while hybrid E/M cells exhibit partial expression of both E and M genes. To address this limitation, we modified a threshold-based Boolean formalism to incorporate intermediate gene expression levels. The resulting multilevel model reveals new hybrid steady states with partial expression of both E and M genes, expanding the phenotypic landscape beyond that captured by traditional Boolean models. These hybrid states exhibit lower frustration and higher abundance, indicating enhanced stability. By resolving degeneracy in the dynamics, we further demonstrate that hybrid states identified by the multilevel model are more stable. These findings suggest that adding minimal complexity to Boolean models can uncover previously hidden qualitative features of phenotypic landscapes governed by GRNs.