Abstract P2-03-07: Deep clonal profiling identifies distinct mechanisms of heterogeneity and evolution in breast cancer

Background: Breast tumors exhibit intratumor heterogeneity resulting in targeted therapy resistance and other challenges in disease management. To address the sources of heterogeneity, we performed a unique, in-depth analysis of clonal architecture in primary chemoradiation-naive breast cancers. We combined DNA content-based flow cytometry and ploidy analysis with aCGH and next-generation sequencing (NGS) in multiple biopsies from the tumors and involved lymph nodes (LNs). Material and methods: We used DNA content-based flow sorting to isolate nuclei from distinct populations of diploid and aneuploid tumor cells in surgical tumor samples from two chemoradiation-naive patients. Each sorted tumor cell population was interrogated with aCGH and exome NGS. In Patient #1, we used 12 fresh frozen sections morphologically mapped from within a HER2+, ER+, PR- primary invasive ductal carcinoma (IDC) of histological grade 3 with LN involvement and 2-3 sections from 2 out of 5 LNs. In Patient #2, 11 morphologically mapped fresh frozen sections were analyzed from a grade 2, ER+, PR+, HER2+, BRCA2 mutant LN- IDC. In parallel, matching samples were processed for IHC assays. Results: We identified multiple co-existing aneuploid populations within the biopsies. The 17 primary and LN biopsies from Patient #1 fell into 6 distinct ploidy groups albeit with aberrant but homogenous aCGH profiles, characterized by SARC amplification and homozygous deletions in ROBO1 and ROBO2. In contrast a dominant ploidy was identified throughout Patient #2 but with heterogeneous aCGH profiles. Mutation profiles obtained through exome sequencing further confirmed that ploidy was the main driver in Patient #1 whereas copy number aberrations played the key role in Patient #2 with the BRCA2 mutation (R3129X). A dendrogram based on exome variant calls of the aneuploid populations in Patient #1 strongly correlated with ploidy group and further revealed the specific clonal population characterized by a 5N ploidy and homozygous mutations in TP53 and PIK3CA as the progenitor to the ploidies present in the distant LNs. Strikngly, both patients had no HER2 amplification or mutation across their clonal populations, contradicting the initial IHC staining in a single core biopsy. Conclusions Rather than inferring the presence of distinct tumor cell populations, our novel flow-sorting based approach of first identifying the clonal populations and then interrogating their genomes, provides an objective method of exploring the sources and clinical significance of tumor heterogeneity. Our approach of clonal analysis has broad implications in the study of tumor heterogeneity and the identification of drivers in breast and other solid tumors that can advance more effective treatment and clinical management of patients with this disease. Citation Format: Princy Francis, Lucretia M Alvarez, Elizabeth Lenkiewicz, Mia Champion, Lisa Evers, Karen L Anderson, Ann E McCullough, Michael T Barrett, Barbara Pockaj. Deep clonal profiling identifies distinct mechanisms of heterogeneity and evolution in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-07.