Abstract GS4-02: Investigating genomic and phenotypic evolution of triple negative breast cancer chemoresistance and metastasis in patient-derived xenografts
Authors: Echeverria Gloria V , Xu Mingchu , Shao Jiansu , Zhang Xiaomei , Jeter-Jones Sabrina , Zhou Xinhui , Moulder Stacy L , Marszalek Joseph R , Heffernan Timothy P , Symmans Fraser W , Chang Jeffrey T , Piwnica-Worms Helen 
Published: March 2020

Abstract
Approximately 50% of patients with newly diagnosed triple negative breast cancer (TNBC) will have substantial residual cancer burden following neoadjuvant chemotherapy (NACT), resulting in distant metastasis and death for most patients. While intra-tumor heterogeneity (ITH) is pervasive in TNBC, the functional contributions of heterogeneous tumor cell populations to resistance and metastasis remain unclear.
To investigate tumor evolution, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC. A subset of PDX models exhibited partial tumor regression following standard front-line NACT, but repopulated tumors with chemo-sensitive cells after a drug holiday, suggesting that resistance may be mediated by a plastic state. Cellular barcoding and genomic sequencing revealed that residual tumors entered a transient chemotherapy-tolerant phenotypic state not mediated by clonal selection. Altered tumor cell metabolism was a functional vulnerability of residual tumor cells. Residual tumors exhibited heightened mitochondrial load and oxidative capacity compared to pre-treatment tumors. Furthermore, treatment with IACS-010759, a small molecule inhibitor of electron transport chain Complex I currently in phase I clinical development, significantly delayed the regrowth of residual tumors. Features of the residual tumor state were also observed in serial biopsies obtained pre- and post-AC from TNBC patients (NCT02276443). While the mechanisms contributing to altered mitochondrial metabolism in chemoresistant TNBCs remain unclear, preliminary findings suggest that altered mitochondrial dynamics may contribute to the enhanced dependence on oxidative phosphorylation in residual tumors. Collectively, these studies reveal that a reversible phenotypic state characterized by altered tumor cell metabolism can confer chemoresistance and that the residual tumor state may be a novel therapeutic window for chemoresistant TNBC.
NACT resistance leads to distant metastasis, often to multiple organs, in most TNBC patients. However, the relatedness of metastases across diverse secondary sites is not well understood. To model the metastatic cascade, sub-lines of orthotopic PDX models harboring a bioluminescent label were generated. Cellular barcoding and genomic sequencing analyses were conducted on primary mammary tumors and lung, liver, and brain metastases from PDX models. Only a minority of primary tumor clones were detected in metastases, indicating that a selective bottleneck had occurred. While each metastatic lesion harbored numerous low-abundance barcoded lineages, only a select few (&lt;10) outgrew and were predominant. Interestingly, the exact same barcoded lineages predominated in lung, liver, and brain metastases. To delineate the transcriptomic profiles of metastatic subclones, single-cell RNA sequencing analyses are being conducted on primary tumors and multi-organ metastases from PDX models. These studies have revealed transcriptomic ITH in primary and metastatic tumors, with stable patterns of transcriptomic ITH in spatially distinct metastases. Furthermore, metastases exhibited reproducible enrichment of a low-abundance primary tumor transcriptomic subpopulation. Together, these studies will elucidate transcriptomic programs associated multi-organ metastasis in TNBC and are expected to enable rational therapeutic targeting strategies.
Citation Format: Gloria V Echeverria, Mingchu Xu, Jiansu Shao, Xiaomei Zhang, Sabrina Jeter-Jones, Xinhui Zhou, Stacy L Moulder, Joseph R Marszalek, Timothy P Heffernan, Fraser W Symmans, Jeffrey T Chang, Helen Piwnica-Worms. Investigating genomic and phenotypic evolution of triple negative breast cancer chemoresistance and metastasis in patient-derived xenografts [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr GS4-02.