Phenotypic deconvolution in heterogeneous cancer cell populations using drug screening data

Abstract

Tumor heterogeneity is an important driver of treatment failure in cancer since therapies often select for drug-tolerant or drug-resistant cellular subpopulations that drive tumor growth and recurrence. Profiling the drug-response heterogeneity of tumor samples using traditional genomic deconvolution methods has yielded limited results, due in part to the imperfect mapping between genomic variation and functional characteristics. Here, we leverage mechanistic population modeling to develop a statistical framework for profiling phenotypic heterogeneity from standard drug screen data on bulk tumor samples. This method, called PhenoPop, reliably identifies tumor subpopulations exhibiting differential drug responses, and estimates their drug-sensitivities and frequencies within the bulk. We apply PhenoPop to synthetically-generated cell populations, mixed cell-line experiments, and multiple myeloma patient samples, and demonstrate how it can provide individualized predictions of tumor growth under candidate therapies. This methodology can also be applied to deconvolution problems in a variety of biological settings beyond cancer drug response. MotivationTumors are typically comprised of heterogeneous cell populations exhibiting diverse phenotypes. This heterogeneity, which is correlated with tumor aggressiveness and treatment failure, confounds current drug screening efforts aimed at informing therapy selection. In order to optimally select treatments, understanding the frequency and drug-response profile of individual subpopulations within a tumor is critical. Furthermore, quantitative profiles of tumor drug-response heterogeneity, in combination with predictive mathematical modeling of tumor dynamics, can be used to design effective temporal drug-sequencing strategies for tumor reduction. Here, we present a method that enables the deconvolution of tumor samples into individual sub-components exhibiting differential drug-response. This method relies on standard bulk drug-screen measurements and outputs the frequencies and drug-sensitivities of tumor subpopulations. This framework can also be applied more broadly to deconvolve cellular populations with heterogeneous responses to a variety of external stimuli and environmental factors.