Variability within rare cell states enables multiple paths toward drug resistance

Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA fluorescence in situ hybridization to directly capture rare cells that give rise to cellular behaviors of interest. Applying Rewind to BRAF(V600E) melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of similar to 1:1,000-1:10,000 cells) and relative persistence of MAP kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences among several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones after drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.

Automated summary

Differences in molecular features among individual cells can lead to dramatic differences in cell fate, such as the survival or death of cancer cells upon drug treatment. The Rewind methodology combines genetic barcoding with RNA fluorescence in situ hybridization to capture rare cells that give rise to cellular behaviors of interest. By applying Rewind to BRAF(V600E) melanoma, researchers traced drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors, revealing hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.