Abstract 1609: Comprehensive multi-omic analysis of circulating tumor cells isolated from a metastatic triple-negative breast cancer patient to identify pathogenic genomic aberrations
Authors: Howard Kellie , Austin Sharon , Ramirez Arturo , Ritter Leila , Boles Debbie , Cox James , Lo Fang Yin , Deutsch Kerry , Subia Christopher , Saloranta Tuuli , Heying Nicole , Collins Heather , Leonti Amanda , Maassel Lindsey , Stilwell Jackie , Kaldjian Eric , Dorschner Michael , Blau Anthony , Eisenberg Marcia , Anderson Steven , Madan Anup 
Published: August 2015

Abstract
Increasing evidence confirms the prognostic relevance of Circulating Tumor Cells (CTCs) in a variety of cancers including advanced breast cancer. Recent data also suggests that CTCs are a useful tool for monitoring treatment and identifying potential targets for therapeutic intervention. The objective of this study was to investigate technologies that can be used for defining the genomic landscape of CTCs in order to compare the derived genomic information (1) among CTCs to assess genetic heterogeneity and (2) with that derived from bone-marrow metastasis tissue biopsy (BMM) samples to assess how reflective the molecular profile from CTCs is to the metastasis. To evaluate these potential applications, positive CTCs were identified using the AccuCyte -CyteFinder (AC/CF) system (RareCyte, Seattle WA) from the blood of a patient with triple negative breast cancer (TNBC). Twenty CTCs and twenty white blood cells (WBCs) were picked from slides using the AC/CF system. To determine whether tumor specific genomic characteristics are reflected in the isolated cells, we used whole genome amplification (WGA) followed by next-generation sequencing to perform a comprehensive analysis using WBCs as genome controls. Whole genome, exome and targeted sequencing of known cancer-associated genes using Illumina and Life Tech panels identified mutations in TP53, PTEN, ERBB2, STK11, ABL1, HRAS, MLL2 and INPPL1 which were present in the CTCs alone and not in the WBCs. Further analysis comparing the results between CTCs revealed that the majority of the identified mutations were specific to individual CTCs revealing a high degree of genetic heterogeneity. Only 5% of mutations were shared between at least 40% of the CTCs examined and included mutations in ATM, ALK, BRAF, NOTCH1, ATR, JAK3, COL1A1 and XPC. Additionally, all of the profiled CTCs contained two novel mutations in LPP and HLA-A which were not present in the WBCs. Mutations in these genes have recently been associated with aggressive solid tumors. Genetic heterogeneity was also observed in the WBC population enabling the calculation and subsequent subtraction of background noise associated with WGA of single cells. Molecular information derived from the CTCs is being compared to multiple BMM samples from the same patient. Additional analyses of copy number and structural variations and transcriptomic analysis are being performed in order to gain further insights into the genetic heterogeneity of CTCs and identify genomic markers to establish the utility of CTCs as a non-invasive real-time liquid biopsy for breast cancer.
Citation Format: Kellie Howard, Sharon Austin, Arturo Ramirez, Leila Ritter, Debbie Boles, James Cox, Fang Yin Lo, Kerry Deutsch, Christopher Subia, Tuuli Saloranta, Nicole Heying, Heather Collins, Amanda Leonti, Lindsey Maassel, Jackie Stilwell, Eric Kaldjian, Michael Dorschner, Anthony Blau, Marcia Eisenberg, Steven Anderson, Anup Madan. Comprehensive multi-omic analysis of circulating tumor cells isolated from a metastatic triple-negative breast cancer patient to identify pathogenic genomic aberrations. [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 1609. doi:10.1158/1538-7445.AM2015-1609