Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy

TLDR

Chemo‑resistance is a leading cause of cancer‑related mortality. The study aimed to uncover divergent modes of chemo‑resistance in tumor cells. Single‑cell transcriptomics was used to analyze tumor cells for these resistance mechanisms. Higher intra‑tumor heterogeneity favors selection of pre‑existing drug‑resistant cells, whereas phenotypically homogeneous cells employ epigenetic plasticity—driven by H3K27ac gain on resistance‑associated chromatin, loss of SOX2, and gain of SOX9—to trans‑differentiate under drug pressure, and this adaptation can be reversed by BRD4 inhibition with JQ1, underscoring stem‑cell‑switch‑mediated epigenetic plasticity as a therapeutic target.

Abstract

Chemo-resistance is one of the major causes of cancer-related deaths. Here we used single-cell transcriptomics to investigate divergent modes of chemo-resistance in tumor cells. We observed that higher degree of phenotypic intra-tumor heterogeneity (ITH) favors selection of pre-existing drug-resistant cells, whereas phenotypically homogeneous cells engage covert epigenetic mechanisms to trans-differentiate under drug-selection. This adaptation was driven by selection-induced gain of H3K27ac marks on bivalently poised resistance-associated chromatin, and therefore not expressed in the treatment-naïve setting. Mechanistic interrogation of this phenomenon revealed that drug-induced adaptation was acquired upon the loss of stem factor SOX2, and a concomitant gain of SOX9. Strikingly we observed an enrichment of SOX9 at drug-induced H3K27ac sites, suggesting that tumor evolution could be driven by stem cell-switch-mediated epigenetic plasticity. Importantly, JQ1 mediated inhibition of BRD4 could reverse drug-induced adaptation. These results provide mechanistic insights into the modes of therapy-induced cellular plasticity and underscore the use of epigenetic inhibitors in targeting tumor evolution.