Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing.

摘要

The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the cell population. Stress tolerance is attributed to heterogeneity of gene expression within the cell population to ensure the survival of a minority cell population. I performed whole-transcriptome sequencing analyses of metastatic human breast cancer cells, MDA-MB-231, subjected to the chemotherapeutic agent Paclitaxel at the single-cell and cell-population levels. Here, I show that specific transcriptional programs are enacted within untreated, stressed, and drug-tolerant cell groups, while generating high heterogeneity between single-cells within and between groups. I further demonstrate that drug-tolerant cells contain specific expressed single nucleotide variants (RNA variants) residing in genes involved in microtubule organization and stabilization as well as cell adhesion and cell surface signaling. Unexpectedly, drug-tolerant cells rapidly reacquire Paclitaxel sensitivity, high cell-to-cell transcript variability, and a gene expression profile similar to that of the untreated cells within a few rounds of cell division. Thus, single-cell analyses reveal the dynamics of the stress response in terms of cell-specific RNA variants driving heterogeneity, the survival of a minority cell population through generation of specific RNA variants, and the efficient reconversion of stress-tolerant cells back to normalcy.