Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance).

Abstract

<b>Purpose:</b> We profiled circulating tumor cells (CTCs) to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC).<b>Methods:</b> CTCs were isolated from 105 patients with MBC using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACS), 28 of whom had serial CTC analysis (74 samples, 2-5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (<i>n</i> = 151) and genome-wide copy-number analysis by array comparative genomic hybridization (aCGH; <i>n</i> = 49).<b>Results:</b> Combined transcriptional and genomic profiling showed that CTCs were 26% <i>ESR1</i>^-<i>ERBB2</i>^-, 48% <i>ESR1⁺ERBB2</i>^-, and 27% <i>ERBB2⁺</i> Serial testing showed that <i>ERBB2</i> status was more stable over time compared with <i>ESR1</i> and proliferation (<i>MKI67</i>) status. While cell-to-cell heterogeneity was observed at the single-cell level, with increasingly stable expression in larger pools, patient-specific CTC expression "fingerprints" were also observed. CTC copy-number profiles clustered into three groups based on the extent of genomic aberrations and the presence of large chromosomal imbalances. Comparative analysis showed discordance in <i>ESR1</i>/ER (27%) and <i>ERBB2</i>/HER2 (23%) status between CTCs and matched primary tumors. CTCs in 65% of the patients were considered to have low proliferation potential. Patients who harbored CTCs with high proliferation (<i>MKI67</i>) status had significantly reduced progression-free survival (<i>P</i> = 0.0011) and overall survival (<i>P</i> = 0.0095) compared with patients with low proliferative CTCs.<b>Conclusions:</b> We demonstrate an approach for complete isolation of EPCAM-positive CTCs and downstream comprehensive transcriptional/genomic characterization to examine the biology and assess breast cancer biomarkers in these cells over time. <i>Clin Cancer Res; 24(6); 1486-99. ©2018 AACR</i>.