Mapping the origin of HER2 plasticity in breast cancer

Emory University, Atlanta GA

Investigators

Abstract

PROJECT SUMMARY While HER2+ breast cancers exhibit a favorable outcome due to the use of HER2-targeted agents, response depends on HER2 status; tumors with residual HER2 expression (HER2-low) do not respond. HER2-low status have been described in triple negative (TNBC) and ER+ breast cancers, and includes primary tumors, metastases, and circulating tumor cells (CTCs). Recently, patient benefit has expanded to HER2-low tumors with the development of HER2-targeted antibody-drug conjugates (ADCs), which suggest that the presence of a small reservoir of HER2-low cells is therapeutically actionable. CTCs isolated and cultured from HER2-, metastatic ER+ and TNBC patients can divide to produce HER2+ cells with as few as four population doublings, without the acquisition of genomic alterations that activate HER2. Similar results were obtained from HER2+ CTCs, which can dynamically yield HER2- daughter cells with similar division kinetics. While these results suggest that HER2-low breast cancers respond to HER2-targeted ADCs at least in part because of the maintenance of a HER2+, heterogeneous state, current studies do not provide mechanistic insight to explain how HER2 expression is dynamically regulated in breast cancer, nor whether dynamic HER2 expression can be augmented in order to improve patient outcome. Because prior studies demonstrate the (1) rapid and plastic conversion of HER2- cells to HER2+ cells and vice versa, and that (2) this process occurs in the absence of known genetic events or changes that support HER2 expression or activity, we hypothesize that epigenetic, or epigenomic, features drive the dynamic expression of HER2+ cells in otherwise HER2- tumors. To this test hypothesis, we will employ characterized cell culture models of heterogeneous HER2+ breast cancer and HER2-low TNBC, and characterize epigenomic features of HER2 lineage evolution. First we will define exogenous factors that influence HER2 heterogeneity and plasticity, and extend these studies by examining whether intrinsic features of HER2 (e.g., protein stability or DNA methylation) contribute to HER2 dynamics. We will then employ lineage trajectory analyses with single cell multi-omics (scRNAseq and ATACseq) to establish the transcriptional features that enable HER2+ daughter cells to arise from HER2- parent cells, and vice versa. Inclusion of single cell ATAC-seq will inform how chromatin accessibility contributes to the mechanisms that enable HER2 plasticity at single cell resolution. Lastly, because HER2-targed ADCs such as T-DXd improve patient outcomes for HER2-low breast cancers, we will examine how the use of T-DXd modulates the HER2-low reservoir and observed plasticity between HER2- and HER2+ cell states. Successful completion of this project will characterize the non-genetic features that contribute to dynamic and heterogeneous HER2 expression, and begin to address larger question of whether epigenetic therapies could be employed to augment the production of HER2+ cells in otherwise HER2- tumors, which is therapeutically actionable.