Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles

Resistance to targeted therapies is a significant clinical problem, but eliminating resistant cancer cells has proven difficult. One potential reason for this difficulty is heterogeneity in the resistant population: even genetically homogeneous cancer cell populations can give rise to many resistant subtypes, each potentially with specific second-line drug vulnerabilities. Using high-throughput drug screening of clonally-derived resistant clones with varying transcriptomes and morphologies, we show that each clone had a distinct drug sensitivity profile. These results suggested that there are drugs that are effective against only subsets of resistant populations but in combination eliminate a large proportion of the resistant population. Using the individual clone sensitivity profiles, we prospectively identified combinations that were highly effective at eliminating most of the resistant population. Our results demonstrate the effectiveness of “subpopulation-directed synergy”, showing that considering population heterogeneity can reveal therapeutic opportunities otherwise masked by population averages, offering new strategies to combat therapy resistance. Overall design: RNA-seq profiling of clonal, drug-naïve melanoma cells (WM989 A6-G3) and resistant clones generated by isolating and expanding colonies generated by treating this parental cell line with vemurafenib or combination dabrafenib/trametinib