Abstract B029: Epigenetic adaptability as a targetable trait underlying therapy resistance
Authors: Xieraili Aobuli , Froid Matthew , Marusyk Andriy 
Published: May 2022

Despite the development of effective targeted agents for the treatment of cancer, targeted therapies eventually fail in advanced, metastatic non-small cell lung cancer (NSCLC) as tumors acquire resistance. Historically, acquired therapy resistance has been attributed to genetic mutational mechanisms. Recent growing body of evidence indicates the importance of non-genetic (epigenetic) mechanisms as essential contributors to both initial ability of cells to survive therapy as well as bona fide resistance. Most commonly, resistance through epigenetic mechanisms is viewed from a perspective of well-defined specific phenotypic states, such as “epithelial mesenchymal transition” (EMT) and “stemness”. However, our resent study showed that the same parental sub-populations under selection with distinct Tyrosine kinase inhibitors (TKIs) give rise to predictably distinct TKIs-specific resistance, indicating that adaptability/phenotypic plasticity in general, rather than specific phenotypic states, might be key for ability of cells to evolve resistance to therapies. Therefore, we hypothesized that gradual, multifactorial development of resistance is fueled by cancer cell plasticity that could be exploited to discover vulnerabilities of therapy resistant cell state. Consequently, targeting of key molecular machinery responsible for this plasticity/adaptability is expected to delay acquisition of resistance. To this end, we took advantage of observations in a cell line model of ALK+ NSCLC, H3122, that develops strong, predictable resistance, when subjected to different clinically approved ALK-TKIs, primarily through non-mutational mechanisms. We found that individual single cell derived subclones display reproducible differences in the ability to develop resistance to ALK-TKIs and unrelated stressors, including distinct pharmacological inhibitors, physical stressors, growth factor deprivation. In parallel as an unbiased approach, we asked whether distinct stressors select for cells with shared clonal origin, we performed in vitro selection with different TKIs as well as other stressor and in vivo metastatic assays using H3122 cells labelled with unique barcodes by complex Clone-Tracer library followed by next generation sequencing (NGS). Next, we attempted to identify targetable molecular mechanisms, responsible for the ability of cells to adapt, performed bulk RNA sequencing with single-cell derived clones which showed different adaptability to TKIs and other stressors. In addition, we are utilizing agent-based mathematical modeling to further explore the dynamic changes of clonal heterogeneity in acquired resistance. We believe our ongoing experiments including the Clone-Tracer experiment, bulk RNA-seq data analysis and their validation, and mathematical modeling will provide a paradigm-wide shift in the understanding of acquired resistance from the current prevalent mutation-centric mechanism paradigm which may lead us to design evolutionary-informed therapy approaches to the resistance before it arises.

Citation Format: Aobuli Xieraili, Matthew Froid, Andriy Marusyk. Epigenetic adaptability as a targetable trait underlying therapy resistance [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B029.