GSE113890
The whole transcriptional landscape of circulating tumor cells compared to metastases in stage IV breast cancer
Metastasis is responsible for the vast majority of breast cancer related deaths. Metastatic breast cancer (MBC) is inherently different than primary breast cancer (BC), evolving under selection pressure at different organ sites or during systemic therapy.   The current ASCO guidelines call for biopsy of a metastatic site to guide decision making for systemic therapy. Yet, biopsies of macro metastasis are  oftentimes not feasible in the clinical setting. Circulating tumor cells (CTCs) have been shown to be prognostic in MBC, but their use as clinical biomarker beyond CTC enumeration has been limited. A better understanding of CTC-biology compared to  metastasis may shed light on treatment opportunities and help advance the application of CTCs as liquid biopsies in clinical practice. The ANGLE Parsortix system is a microfluidics device that separates CTCs based on size and deformability, without the need for  cell-surface marker selection. Our lab has previously demonstrated the feasibility of gene expression profiling of rare CTCs. Here, we evaluated whether whole transcriptome sequencing (RNA Seq) gene expression profiling of ANGLE Parsortix isolated CTCs may serve as a surrogate for biopsies of macro metastases. CTCs from 21 MBC patients were enumerated and captured from 10mL peripheral blood (PB) via the ANGLE Parsortix system.  RNA Seq was  performed on fresh metastatic tumor biopsies (mets), CTCs and peripheral blood from all patients.  Biopsy sites included: skin (n=1), lung (n=1), pleural effusion (n=5), pericardial effusion (n=1), breast (n=3), lymph node (n=2), brain (n=4), liver (n=1), ascites (n=3), cerebrospinal fluid (n=2) and bone (n=1).  19/21 patients were included in subsequent data analysis. We present the whole transcriptomic landscape of CTCs with comparison to metastases and peripheral blood all acquired prior to treatment of  Stage IV breast cancer.  Multiple genes, including oncogenes, breast epithelial, mesenchymal genes and cancer stem cell genes were found with higher expression in CTCs versus metastases.  When focusing on 66 known potentially clinically actionable genes in breast cancer, represented by 7 molecular signaling pathways, CTCs did not show significantly different patterns of expression versus mets compared to PB.  RNA Seq of CTCs  may be utilized to identify alterations in MBC patients that are potentially clinically actionable. Overall design: For n=19 patients, fresh metastatic tissue biopsies were compared to circulating tumor cells (CTCs).  Both metastatic tissue biopsies and CTCs were compared to peripheral blood (PB) to control for the normal leukocyte population of each patient. Please note that there are 21 MBC patients, but only 19 were included in subsequent data analysis. The other 2 patiens had very low coverage for either CTC, PB, or Met sample. In such cases, the patient was excluded in the intrapatient analysis but the samples with good coverage were included in the global analysis.  The other 5 patients (78534, 111951, 111956, 111958, 111961) are controls (with only blood samples). This series includes 3 samples of PBS buffer for negative controls.