Longitudinal genetic characterization of circulating tumor cells in metastatic breast cancer patients

Background: Little is known about the evolution of genetic aberrations during metastatic cancer progression and in response to systemic treatment. Obtaining repeated tissue biopsies is often impractical. On the other hand, it has been shown that circulating tumor cells (CTCs) can be easily followed during disease course and genetic characterization at the single cell level is possible with high reliability Methods: Individual CTCs of a ER+ and HER2- de novo metastatic breast cancer patient treated with weekly paclitaxel/gemcitabine as first line therapy, were collected at three different time points (before start, after one and two cycles of treatment). Whole peripheral blood was enriched using the CellSearch® system and CTCs were sorted by DEPArrayTM device. The whole genome of single CTCs was amplified with Ampli1TM WGA kit and WGA quality was assessed by Ampli1TM QC Kit. Genome wide single cell copy number variation (CNV) profile was evaluated with Agilent SurePrint 180k array comparative genomic hybridization (aCGH). Results: CTCs count at CellSearch was 22, 75 and 15 at three time points respectively. A total of 25 single CTCs were collected and 23 (92%) showed high Genome Integrity Index (GII) as measured by Ampli1TM QC kit (GII = 3 or 4). For each time point multiple CTCs (3, 6 and 3 respectively) were selected for single cell aCGH analysis. The genomic profile was strikingly similar (1q gain, 12p, 13p, 16q and 17p losses) across individual cells of the same blood sample and throughout different time points evaluated. After 3 cycles of therapy a disease progression was documented by CAT-scan. Discussion: The observed high GII, low genetic heterogeneity and stable genome across different time points suggests the presence of an aggressive clone resistant to the treatment and cancer-associated genes analysis for sequence variants by NGS targeted sequencing is ongoing. Further patients with longitudinal follow-up will be enrolled in order to evaluate if the heterogeneity between aCGH profile at a given time point and longitudinal evolution of aCGH profiles can be associated with early treatment response. Results will be presented at the conference.