Abstract 3889: Genetic heterogeneity and distinct driver mutations in synchronous primary and metastatic breast cancers from therapy-naïve patients

Abstract

Abstract Background: The metastatic process may constitute a biological bottleneck and may select for clones with genetic alterations that are distinct from those found in the dominant clone of the primary tumor. Here we sought to define whether the repertoires of somatic mutations found in biopsies of primary tumors would differ from those of their respective metastatic lesions in patients who did not receive any form of systemic therapy. Methods: Flash frozen diagnostic biopsies from primary tumors and their distant metastases were obtained from 9 prospectively accrued treatment-naïve patients with stage IV breast cancer at presentation (3 estrogen receptor (ER)+/HER2+, 2 ER+/HER2-, 2 ER-/HER2+ and 2 ER-/HER2-). Metastatic lesions from the liver (5), bone (2), skin (1) or contra-lateral axillary lymph node (1) were biopsied. An additional formalin-fixed paraffin embedded (FFPE) biopsy of each primary tumor and metastasis, as well as plasma from 5 patients, were obtained. DNA from microdissected frozen samples and peripheral blood, as well as plasma from one patient, was subjected to high-depth whole exome sequencing and gene copy number profiling. DNA from all biopsies (frozen/FFPE) and plasma was subjected to targeted capture massively parallel sequencing for all single nucleotide variants (SNVs) and insertions and deletions (indels) found by exome sequencing and all exons of the 100 most frequently mutated genes in breast cancer. Driver mutations were defined by state-of-the-art bioinformatic methods and literature curation. Results: In all cases, we detected founder genetic events in the modal population of primary tumors and their respective metastatic lesions (12-146 non-synonymous SNVs and 1-16 indels). Substantial genetic differences were observed between primary and their metastasis from these therapy-naïve patients, with a median of 9 non-synonymous mutations (range 0-42, median 9.6% of mutations) restricted to the primary tumor and not found in either biopsies of the metastases, and a median of 19 (range 1-73, median 20.2%) non-synonymous mutations restricted to the metastasis and not found in either biopsies of the primary tumors. The repertoire of mutations restricted to the metastatic lesions was unique to each case; however, we observed an enrichment of genes involved in the epithelial-to-mesenchymal transition (e.g. TCF7L2, SMAD4, KRIT1 and L1CAM). Plasma DNA analysis revealed that only 3.2%-38.3% of the mutations found in the primary tumor or its metastatic deposit could be detected in plasma. Conclusions: Therapy-naïve primary breast cancers and their metastatic deposits differ in their repertoire of genetic alterations, even when two biopsies of each primary tumor and metastatic lesions are analyzed. The assessment of targetable genetic alterations in single biopsies from primary tumors may not be sufficient for the optimal selection of precision medicine-based therapies. Citation Format: Charlotte K. Y. Ng, Francois-Clement Bidard, Salvatore Piscuoglio, Raymond S. Lim, Jean-Yves Pierga, Paul Cottu, Anne Vincent-Salomon, Agnes Viale, Larry Norton, Brigitte Sigal, Britta Weigelt, Jorge S. Reis-Filho. Genetic heterogeneity and distinct driver mutations in synchronous primary and metastatic breast cancers from therapy-naïve patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3889. doi:10.1158/1538-7445.AM2015-3889