Abstract 4335: Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype
Authors: Xu Tong , Li Hongtao , Xu Rong , Wei Jenny , Li Meng , Liang Gangning , Goldkorn Amir 
Published: August 2019

Introduction: Subpopulations of highly tumorigenic, drug resistant cancer stem-like cells (CSCs) play a key role in cancer recurrence and progression. Surprisingly, these aggressive cells can arise repeatedly de novo from bulk tumor cells independently of mutational events. We investigated whether transition to and from a cancer stem-like state is associated with epigenetic alterations, such as DNA methylation and chromatin accessibility.

Materials and methods: Using FACS and Hoechst dye staining, side population (SP) cells marked by high tumorigenicity and drug resistance vs. non-side population (NSP) cells lacking these properties were isolated from bladder cancer cell lines. Global DNA methylation and chromatin accessibility were mapped for SP vs. NSP cells using AcceSssIble assay on the Infinium EPIC platform. Differential gene expression for SP vs. NSP cells was assayed by HuEx array. AcceSssIble and HuEx results were overlapped to generate a subset of genes with differential accessible promoter regions and expression. One such gene, E2F3, was validated by qRT-PCR and analyzed clinically using the Oncomine and Basespace online data mining engines, as well as functionally by lentiviral shRNA depletion in bladder cancer cells for cell migration, invasion and drug resistance. 5-AZA was used to modulate global DNA methylation in bladder cancer cells.

Results: SP and NSP subpopulations exhibited differential DNA methylation and chromatin accessibility at thousands of gene loci by AcceSssIble assay, and a majority of differential chromatin accessibility was independent of DNA methylation. When overlapped with HuEx data, 38 genes exhibited differential expression associated with differential promoter chromatin accessibility. One such gene validated by qRT-PCR was E2F3, a cell cycle regulator that was found to be associated with bladder cancer in the Oncomine and Basespace databases. In vitro E2F3 depletion by lentiviral shRNA resulted in smaller SP subpopulations and reduced cell migration, invasiveness, and drug resistance. Epigenetic interference with 5-AZA blocked the phenotypic transition, reduced SP subpopulations, and lowered E2F3 expression.

Conclusion: Rapid cyclical transition between the SP and NSP subpopulations was associated with dramatic shifts in chromatin accessibility with concomitant changes in gene expression of clinically relevant genes that drove the SP phenotype, cell migration, invasiveness, and drug resistance. These observations implicate epigenetic plasticity as a driver of the switch between cancer stem-like and non-cancer stem-like states, suggesting new potential therapeutic avenues to control cancer resistance and progression.

Citation Format: Tong Xu, Hongtao Li, Rong Xu, Jenny Wei, Meng Li, Gangning Liang, Amir Goldkorn. Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4335.