Resistance to targeted cancer therapy arises from pre-existing rare-cell expression variability followed by drug-induced epigenetic reprogramming
Sydney Shaffer1, Margaret Dunagin1, Stefan Torborg1, Eduardo Torre1, Benjamin Emert1, Clemens Krepler2, Marilda Beqiri2, Katrin Sproesser2, Patricia Brafford2, Elliott Eggan1, Meenhard Herlyn2, Arjun Raj1
1Department of Bioengineering, University of Pennsylvania; 2The Wistar Institute, Molecular and Cellular Oncogenesis Program, Melanoma Research Center, Philadelphia, PA
Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures. Often, resistance results from a secondary mutation in rare cells, but other times, there is no clear genetic cause, leaving the possibility of non-genetic rare cell variability. In this work, we adapt the experimental framework Luria and Delbruck to discover that resistance to targeted therapy in melanoma is not heritable. We next show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug. This variability involves infrequent, semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The addition of drug then induces an epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming is a progressive process consisting of a loss of SOX10-mediated differentiation followed by activation of new signaling pathways, partially mediated by activity of Jun-AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics. We find that other cell types also exhibit sporadic expression of many of these same marker genes, suggesting the existence of a general rare-cell expression program.