Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer

TLDR

Tyrosine kinase inhibitors are effective for cancers with RTK mutations, yet responses are short‑lived because patients develop drug resistance. This study maps single‑cell transcriptional heterogeneity underlying drug tolerance and tests combination agents that target tolerant subpopulations. The authors performed scRNA‑seq on cell lines, xenografts, and patient tumors, identified tolerant‑cell markers, and used the LINCS database to predict and validate small molecules that selectively inhibit these cells. They found distinct tolerant subpopulations enriched for EMT, vesicle transport, drug metabolism, and cholesterol homeostasis, and showed that crizotinib combined with EGFR inhibitors prevents the emergence of EGFR‑tolerant clones.

Abstract

Tyrosine kinase inhibitors were found to be clinically effective for treatment of patients with certain subsets of cancers carrying somatic mutations in receptor tyrosine kinases. However, the duration of clinical response is often limited, and patients ultimately develop drug resistance. Here, we use single-cell RNA sequencing to demonstrate the existence of multiple cancer cell subpopulations within cell lines, xenograft tumors and patient tumors. These subpopulations exhibit epigenetic changes and differential therapeutic sensitivity. Recurrently overrepresented ontologies in genes that are differentially expressed between drug tolerant cell populations and drug sensitive cells include epithelial-to-mesenchymal transition, epithelium development, vesicle mediated transport, drug metabolism and cholesterol homeostasis. We show analysis of identified markers using the LINCS database to predict and functionally validate small molecules that target selected drug tolerant cell populations. In combination with EGFR inhibitors, crizotinib inhibits the emergence of a defined subset of EGFR inhibitor-tolerant clones. In this study, we describe the spectrum of changes associated with drug tolerance and inhibition of specific tolerant cell subpopulations with combination agents.