Abstract S6-06: High-depth massively parallel sequencing reveals heterogeneity between primary tumor and metastatic deposits in de novo metastatic breast cancer patients prior to exposure to systemic therapy
Authors: Bidard F-C , Ng CK , Piscuoglio S , Pierga J-Y , Cottu P , Norton L , Weigelt B , Sigal B , Reis-Filho JS 
Published: August 2014

Background: Breast cancers are often composed of mosaics of tumor cells that in addition to the founder genetic events harbor private genetic aberrations. Previous studies comparing the repertoire of mutations in primary breast cancers and their metachronous metastatic deposits that developed after systemic therapy revealed differences in their clonal composition and mutational repertoire. It is unclear, however, whether the differences documented could be attributed to the metastatic process itself or because of selective pressure from systemic therapies. Hence we sought to investigate whether the metastatic process would constitute a biological ‘bottleneck’ resulting in the selection of clones fittest to metastasize. We subjected primary breast cancers and their synchronous metastatic deposits from patients who presented with de novo metastatic disease and who had not received any systemic therapy to gene copy number analysis and high-depth massively parallel sequencing.

Materials and Methods: Frozen primary tumor and distant metastases biopsies were obtained from 7 patients with de novo metastatic disease (i.e. stage IV breast cancer at presentation) enrolled in the ESOPE study (Institut Curie, Paris). DNA samples extracted from microdissected tumors and from peripheral blood were subjected to high-depth (250x) whole exome sequencing and SNP6 copy number profiling. The impact of spatial heterogeneity was further assessed by targeted sequencing of paraffin-embedded samples from additional, independent pre-treatment biopsies of the primary tumor and matched metastasis from the same patients. Driver mutations were defined by bioinformatic methods; for single nucleotide variants (SNVs), CHASM and FATHMM were employed and for insertions/ deletions (indels), only frameshift or truncating mutations in genes normally expressed in breast tissue were included.

Results: In de novo metastatic breast cancers, without any pretreatment, significant genomic differences were observed between primary and metastatic deposits in all cases. A median number of 105 (32-224) and 54 (10-57) SNVs and indels were found, respectively, of which 36 (9-139) and 11 (1-19) were shared between the primary tumors and the de novo metastases, respectively. Although a substantial proportion of driver SNVs and indels were found in common between primary tumors and their respective metastatic deposits (median: 29% (17%-38%)), 50% (25%-78%) of driver SNVs and 79% (60%-90%) of the potentially pathogenic indels were restricted either to the primary or the metastatic deposit, including driver mutations affecting epithelial-to-mesenchymal transition (EMT)-related genes in 3 patients, namely TGFB1, SMAD4 and TCF7L2.

Conclusions: This is, to the best of our knowledge, the first study reporting on the differences in the mutational repertoire between primary tumors and metastatic deposits in de novo metastatic breast cancer patients who have not received systemic therapy. Our findings suggest that the breast cancer metastatic process likely constitutes a biological bottleneck with selection of subclones harboring specific driver genetic aberrations, often affecting EMT-related genes.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S6-06.