Journal Article

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

Tyson, Darren R., Harris, Leonard A., Hayford, Corey E., Robbins, C. Jack, Quaranta, Vito, Frick, Peter L.

2021

Overview

Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among and within multiple versions and clonal sublines of PC9, a commonly used EGFR mutant nonsmall cell lung cancer (NSCLC) cell line. We resolve genetic, epigenetic, and stochastic components of this variability using a theoretical framework in which distinct genetic states give rise to multiple epigenetic “basins of attraction,” across which cells can transition driven by stochastic noise. Using mutational impact analysis, single-cell differential gene expression, and correlations among Gene Ontology (GO) terms to connect genomics to transcriptomics, we establish a baseline for genetic differences driving drug response variability among PC9 cell line versions. Applying the same approach to clonal sublines, we conclude that drug response variability in all but one of the sublines is due to epigenetic differences; in the other, it is due to genetic alterations. Finally, using a clonal drug response assay together with stochastic simulations, we attribute subclonal drug response variability within sublines to stochastic cell fate decisions and confirm that one subline likely contains genetic resistance mutations that emerged in the absence of drug treatment.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Antineoplastic Agents - pharmacology / Biology and Life Sciences / Cancer therapies / Cell Death - drug effects / Cell division / Cell fate / Cell Line, Tumor / Computer Simulation / Epidermal growth factor / Epidermal growth factor receptors / Epigenesis, Genetic - drug effects / Epigenetics / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Neoplastic - drug effects / Genetic aspects / Genetic Heterogeneity - drug effects / Genome, Human / Genomics / Growth factors / Heterogeneity / Humans / Impact analysis / Lung cancer / Medicine and Health Sciences / Models, Biological / Mutation / Neoplasms - genetics / Neoplasms - pathology / Non-small cell lung carcinoma / Phenotype / Physiological aspects / Research and analysis methods / Stochastic Processes / Stochasticity / Transcriptome - drug effects / Transcriptome - genetics / Tumor cells / Tumors / Variability