Abstract A34: Single cell genomic profiling of circulating tumor cells (CTCs) in metastatic disease to characterize disease heterogeneity
Authors: Greene Stephanie , Rodriguez Angel , Lee Jerry , Leitz Laura , Landers Mark , Jendrisak Adam , Graf Ryon , Werner Shannon , Wang Yipeng , Dittamore Ryan , Marrinucci Dena 
Published: May 2016

Background: Inter- and intra-patient tumor heterogeneity can have a drastic impact on the efficacy of targeted therapy without accurate patient stratification. Emerging literature suggests wide-spread prevalence of intra-tumor heterogeneity (ITH) across most major solid tumor types driven by separate subclonal genomic alterations, thus highlighting the need to understand the proportion of heterogeneous tumor subclonal populations with clinically relevant genomic alterations. Circulating tumor cells (CTCs) have been shown to reflect the active metastatic populations, and Epic Sciences' non-enrichment CTC analysis platform allows for single cell resolution and a more accurate estimate genomic heterogeneity within the population. Here, we demonstrate Epic Sciences CTC Platform capabilities to characterize individual CTCs from a simple blood draw for known markers of therapeutic sensitivity related to genome wide instability (PARP inhibitors, immune check-point inhibitor sensitivity), amplification or deletion of clinically relevant tumor suppressors or oncogenes (PI3K inhibitors or AR targeted therapy), and/or single nucleotide and INDEL variants (Tyrosine Kinase Inhibitor sensitivity).

Methods: Healthy donor blood was spiked with well-characterized cancer cell lines to create mock test samples for downstream single-cell genomic analysis. CTCs were enumerated and characterized using the Epic Sciences Platform. Identified single CTCs were recovered, and their whole genome amplified and characterized for the presence of genome wide instability, specific tumor suppressor loss, and oncogene amplification or point mutations by whole genome sequencing and/or mutation specific PCR. Large-scale state transitions (LSTs) and percent genome alterations (PGAs) were measured as surrogates of genomic instability. Z-scores were calculated in specific genomic loci containing tumor suppressor or oncogenes to characterize their amplification or deletion.

Results: In healthy donor blood spiked with prostate cancer cell lines (PC3, VCaP or LnCaP), overall genomic instability was observed across a wide dynamic range. Loss of the PTEN tumor suppressor, associated with sensitivity to PI3K inhibitors, was confirmed in PC3 cells. Amplification of the androgen receptor (AR), associated with resistance to AR targeted therapies, was confirmed in VCaP cells. In blood spiked with lung adenocarcinoma the T790M EGFR point mutation, associated with resistance to TKIs, was also detected reproducibly. Genomic profiling of CTCs from prostate cancer patients have shown significant intra-patient heterogeneity in copy number alterations, genomic instabilities and number of mutations.

Conclusions: The data shown here demonstrate the feasibility of detecting actionable genomic alterations at the single cell level using the Epic CTC platform. Understanding CTC heterogeneity has great potential for more accurate patient stratification prior to treatment with targeted therapies.

Citation Format: Stephanie Greene, Angel Rodriguez, Jerry Lee, Laura Leitz, Mark Landers, Adam Jendrisak, Ryon Graf, Shannon Werner, Yipeng Wang, Ryan Dittamore, Dena Marrinucci. Single cell genomic profiling of circulating tumor cells (CTCs) in metastatic disease to characterize disease heterogeneity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A34.