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

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