Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer
Abstract Background Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases. Methods We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix microfluidics system to isolate cells based on size and deformability, independent of a priori knowledge of cell surface marker expression. Results Gene expression separated CTCs, metastatic biopsies, and PB into distinct groups despite heterogeneity between patients and sample types. CTCs showed higher expression of immune oncology targets compared with corresponding metastases and PB. Predictive biomarker (n = 64) expression was highly concordant for CTCs and metastases. Repeat observation data post-treatment demonstrated changes in the activation of different biological pathways. Somatic single nucleotide variant analysis showed increasing mutational complexity over time. Conclusion We demonstrate that RNA-Seq of CTCs could serve as a surrogate biomarker for breast cancer macrometastasis and yield clinically relevant insights into disease biology and clinically actionable targets. Visual Abstract Primary tumor cells (left side) disseminate via the blood stream to seed distant metastases (right side). Peripheral blood can be used for enrichment of CTCs (potentially representative of the full heterogeneity of a patient’s cancer) as a liquid biopsy. RNA-Seq can identify predictive biomarker expression in enriched CTCs as a surrogate for macrometastatic tissue biopsies. Different colored circles represent different cancer cell clones, representing heterogeneity in the primary tumor, and increased heterogeneity in metastatic tumors.