SRA

Circulating Tumor Cells (CTCs) encompass multiple analytes, interrogated by sampling blood from patients with cancer. However, the clinical utility of tumor cell-based liquid biopsy has proven to be limited since CTCs are rare, and current technologies cannot process larger blood volumes required to isolate a sufficient number of tumor cells. We have described a high-throughput microfluidic prototype utilizing high-flow channels and amplification of cell sorting forces through magnetic lenses. Here, we apply this technology to analyze patient-derived leukapheresis products, interrogating a mean blood volume of 5.83 liters from patients with metastatic cancer and achieving a median of 2,799 CTCs per patient. Isolation of many CTCs from individual patients enables characterization of their morphological and molecular heterogeneity, including cell and nuclear size and RNA expression. It also allows robust detection of gene copy number variation (CNV), a definitive cancer marker with potential diagnostic applications. High-volume microfluidic enrichment of CTCs constitutes a new dimension in liquid biopsies. Overall design: We performed single-cell RNA-seq for cells displaying CNV isolated from leukapheresis product [PMID: 32641515] from two metastatic castration resistant prostate cancer patients, GU-1 and GU-2. Of the 30 cells from GU-1, 27 were EpCAM+ and/or PSMA+ using a SONY sorter SH800, and three were EpCAM- and PSMA-. For GU-2 63 were EpCAM+ and/or PSMA+ using the SONY sorter and 11 were EpCAM- and PSMA-. We also performed single-cell RNA-seq for three cells isolated from the BRx68 cultured circulating tumor cells [PMID: 25013076] and for three white blood cells from a healthy donor.