Phenotypic Pliancy and the Breakdown of Epigenetic Polycomb Mechanisms

Abstract Epigenetic regulatory mechanisms allow multicellular organisms to develop distinct specialized cell identities despite having the same total genome. Cell-fate choices are based on gene expression programs and environmental cues that cells experience during embryonic development, and are usually maintained throughout the life of the organism despite new environmental cues. The evolutionarily conserved Polycomb group (PcG) proteins form Polycomb Repressive Complexes that help orchestrate these developmental choices. Post-development, these complexes actively maintain the resulting cell fate, even in the face of environmental perturbations. Given the crucial role of these polycomb mechanisms in providing phenotypic fidelity (i.e. maintenance of cell fate), we hypothesize that their dysregulation after development will lead to decreased phenotypic fidelity allowing dysregulated cells to sustainably switch their phenotype in response to environmental changes. We call this abnormal phenotypic switching phenotypic pliancy . We introduce a general computational evolutionary model that allows us to test our systems-level phenotypic pliancy hypothesis in-silico and in a context-independent manner. We find that 1) phenotypic fidelity is an emergent systems-level property of PcG-like mechanism evolution, and 2) phenotypic pliancy is an emergent systems-level property resulting from this mechanism’s dysregulation. Since there is evidence that metastatic cells behave in a phenotypically pliant manner, we hypothesize that progression to metastasis is driven by the emergence of phenotypic pliancy in cancer cells as a result of PcG mechanism dysregulation. We corroborate our hypothesis using single-cell RNA-sequencing data from metastatic cancers. We find that metastatic cancer cells are phenotypically pliant in the same manner as predicted by our model. Significance Statement We introduce the concept of cellular phenotypic pliancy– sustained abnormal phenotypic switching in response to environmental changes– and demonstrate that such behavior can be caused by dysregulation of Polycomb mechanisms. To overcome the incomplete knowledge about these mechanisms in higher organisms, we develop an abstract computational model to study the emergence of phenotypic pliancy from a general systems-level view by confirming our hypothesis over a wide range of simulated gene-regulatory networks and Polycomb mechanism patterns. We corroborate our hypothesis and model predictions using single-cell RNA-seq metastatic cancer datasets. Our hypothesis has the potential to shed light on a general phenomenon for complex diseases where abnormal phenotypic switching is relevant.