Abstract 1497: Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized trial (ARTEMIS; NCT02276443)
Authors: Seth Sahil , Huo Lei , Rauch Gaiane M. , Adrada Beatriz , Piwnica-Worms Helen , Lim Bora , Thompson Alastair M. , Mittendorf Elizabeth A. , Heffernan Timothy , Litton Jennifer K. , Symmans William F. , Draetta Giulio F. , Futreal Andrew P. , Chang Jeffrey T. , Moulder Stacy L. 
Published: September 2020

Abstract
Background: The heterogeneity of TNBC results in a spectrum of responses to NAST: 30-40% of patients (pts) have a pathologic complete response (pCR) with an excellent prognosis. Several methods have been used to measure and evaluate residual disease, including ultrasound, MRI scans, histo-pathology. In addition to these, we hypothesize that comprehensive molecular profiling of longitudinal biopsies, with an integrative evaluation of sub-clonal selection and changes in molecular pathways, will serve as a critical biomarker for chemotherapy, and subsequent targeted therapy trials.
Methods: Pts with stage I-III TNBC began a planned 4 cycles of Adriamycin-based chemo (AC). Biopsies were performed pre (mandatory) and post (optional) AC. Volumetric change by ultrasound (VUS) at completion of AC (or progression) was calculated. Pts with sensitive disease received subsequent taxane-based (T) therapy. Pts with insensitive disease were offered phase II trials. Pathologic response was assessed at surgical resection in 85 pts (Training N=55, Validation N=30). Matched samples, pre and post AC (N = 85 pts) underwent transcriptomic and genomic profiling. Samples were classified into six previously identified ARTEMIS subtypes of TNBC (ART-Type) and immune deconvolution and estimation were performed using RNA-Seq profiles. Multiplex IHC using the Vectra platform is being used to validate results from bulk RNASeq experiments. Somatic mutations and copy-number changes were evaluated using, Mutect2, Sequenza (and FACETs), and PhyloWGS (and PyClone).
Results: Predominately, tumors reacted to AC in 4 different patterns with variation in immune and EMT related pathways. Enrichment of EMT (Group 4) was associated with poor prognosis and higher RCB (10.3% vs 42% pCR rates, p&lt;0.05). The global changes in transcription led to ART-Type switching in all subtypes (44% of pts), except LAR subtype. This subtype was enriched in Group 3 (low overall change), and associated with PIK3CA mutations. MYC amplification was more prevalent (40%) in Group 4, associated with higher EMT and poor prognosis than other groups (28%). Multiple time points were leveraged to constrain sub-clonal clustering and enhance the accuracy of phylogenetic tree construction. Significant sub-clonal selection was detected in 22% of evaluable cases with pre and post biopsies (N=55), with analysis of the validation cohort underway. Molecular subtypes were marginally associated with overall and progression-free survival.
Conclusions: Molecular profiling of longitudinal TNBC samples reveals distinct response patterns in tumors and their micro-environments upon treatment with AC. Integrative analysis of genomic and transcriptomic changes can lead to better stratification of response to NAST. These patterns were indicative of pathologic response in the initial cohort (N=55). Analysis of the second cohort (N=30) will be presented as a validation cohort.
Citation Format: Sahil Seth, Lei Huo, Gaiane M. Rauch, Beatriz Adrada, Helen Piwnica-Worms, Bora Lim, Alastair M. Thompson, Elizabeth A. Mittendorf, Timothy Heffernan, Jennifer K. Litton, William F. Symmans, Giulio F. Draetta, Andrew P. Futreal, Jeffrey T. Chang, Stacy L. Moulder. Longitudinal response and selection under neoadjuvant systemic therapy (NAST) in triple-negative breast cancer (TNBC): Profiling results from a randomized trial (ARTEMIS; NCT02276443) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1497.