Abstract 1693: Drug-tolerant persister cells contain heterogeneous subpopulations that utilize lung lineage pathways as drug resistance mechanism
Authors: Tian Yang , Jiang Feng , Jaffer Athina , Hopkins Benjamin , Jin Jian , Watanabe Hideo 
Published: June 2023

Abstract
Genomic discoveries of oncogenic driver alterations in lung cancer have led to development of effective target therapeutics; however, patients who initially respond to the therapy inevitably experience regrowth of the disease. Recent studies identified a reversible stage of cancer cells entering a quiescent state to ensure survival, called drug-tolerant persister (DTP) cells. The DTP stage is viewed as a major source of non-genetic drug resistance, while its epigenetic dynamic and regulatory mechanisms remain largely unknown. To determine the epigenetic activity reminiscent of a quiescent state during DTP development, we evaluated repressive epigenetic modifications during DTP progression and found that DTP cells had a markedly increased H3K27me3 level at the beginning of DTP stage. Treatment of EZH2 inhibitor together with target therapy synergistically inhibited cell growth, indicating the essential role of compressed chromatin structure for DTP survival. To further investigate the epigenomic heterogeneity of DTP cells, we performed single cell ATAC-seq on DTP cells. Unsupervised hierarchical clustering analysis revealed that the drug-induced DTP cells had two distinct populations compared with the untreated group with only one major population, suggesting an increased epigenomic heterogeneity. By analyzing the differentially accessible regions, motifs for TEADs and GATAs were specifically enriched in DTP cells, whose family members are well-established regulators of the lung development. This raised a possibility that the evolution of drug resistance shares similarities with organ regeneration, both require terminally differentiated cells regaining cell plasticity and serving as a progenitor cell to direct re-differentiation. Thus, we focused on alveolar lineage genes as a model to test our hypothesis that DTP cells hijack conserved developmental pathways for lung regeneration to ensure their survival and subsequent expansion. Our results showed that specific alveolar marker genes were transiently upregulated and exhibited translocation from cytoplasm to nuclei at early phase of DTP. Moreover, deletion of the alveolar lineage gene decreased cell re-growth under drug treatment. Our finding provides a new perspective of anti-relapse therapeutic strategies, that targeting lung lineage pathways to manipulate the activity of critical lineage factors during lung regeneration, for patients with minimal residual disease and relapse after target therapy.
Citation Format: Yang Tian, Feng Jiang, Athina Jaffer, Benjamin Hopkins, Jian Jin, Hideo Watanabe. Drug-tolerant persister cells contain heterogeneous subpopulations that utilize lung lineage pathways as drug resistance mechanism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1693.