Abstract GS5-05: Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state
Authors: Echeverria GV , Ge Z , Seth S , Jeter-Jones SL , Zhang X , Zhou X , Cai S , Tu Y , McCoy A , Peoples M , Lau R , Shao J , Sun Y , Bristow C , Carugo A , Ma X , Harris A , Wu Y , Moulder S , Symmans WF , Marszalek JR , Heffernan TP , Chang JT , Piwnica-Worms H 
Published: May 2019

Abstract
Approximately 50% of patients with localized triple negative breast cancer (TNBC) have substantial residual cancer burden following treatment with neoadjuvant chemotherapy (NACT), resulting in distant metastasis and death for most of these patients. While genomic and phenotypic intra-tumor heterogeneity are pervasive features of TNBCs at the time of diagnosis, the functional contributions of heterogeneous tumor cell populations to chemoresistance have not been elucidated.
To investigate tumor evolution accompanying NACT, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC, which retain intra-tumor heterogeneity characteristic of human TNBC. We discovered that some PDX models initially exhibited partial sensitivity to standard front-line NACT (Adriamycin plus Cytoxan, AC). Following AC, residual tumors were resistant to chemotherapy but repopulated tumors with chemo-sensitive cells if left untreated, indicating that tumor cells possessed inherent plasticity. To identify the tumor cell subpopulation(s) conferring chemoresistance, we conducted barcode-mediated clonal tracking in three independent PDX models by introducing a high-complexity pooled lentiviral barcode library into PDX tumor cells which were then orthotopically engrafted into recipient mice. Strikingly, residual tumors maintained the same heterogeneous clonal architecture as naïve tumors. Concordantly, whole-exome sequencing revealed conservation of genomic subclonal architecture throughout treatment. These results were corroborated by genomic sequencing of serial biopsies pre- and post-AC obtained directly from TNBC patients enrolled on an ongoing clinical trial at MD Anderson (ARTEMIS; NCT02276443). Together, these studies revealed that genomically distinct pre-treatment subclones were equally capable of surviving AC to reconstitute tumors after treatment.
To identify functional addictions of residual tumor cells, we conducted histologic and transcriptomic profiling. Residual tumors following AC-treatment exhibited extensive fibrotic desmoplasia and tumor cell pleomorphism in both PDX models and in serial biopsies obtained from TNBC patients enrolled on the ARTEMIS trial. Strikingly, these AC-induced features were reverted upon regrowth of residual tumors in PDXs and in patients' tumors. Similarly, residual tumors exhibited unique transcriptomic features, many of which are also de-regulated in cohorts of human TNBCs undergoing chemotherapy treatment. These features were nearly completely reverted after tumors regrew, suggesting that the residual tumor state may be a unique and transient therapeutic window. Gene set enrichment analyses revealed that residual tumors had increased activation of oxidative phosphorylation and decreased glycolytic signaling. Pharmacologic targeting of oxidative phosphorylation with a small-molecule inhibitor of mitochondrial electron transport chain complex I (IACS-010759) significantly delayed the regrowth of AC-treated residual tumors in three independent PDX models. Collectively, these studies reveal that a reversible phenotypic state can confer chemoresistance in the absence of genomic selection and that the residual tumor state is a novel therapeutic window for chemo-refractory TNBC.
Citation Format: Echeverria GV, Ge Z, Seth S, Jeter-Jones SL, Zhang X, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Lau R, Shao J, Sun Y, Bristow C, Carugo A, Ma X, Harris A, Wu Y, Moulder S, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS5-05.