Single-Cell Identification of Melanoma Biomarkers in Circulating Tumor Cells

SIMPLE SUMMARY: Identification and investigation of cancer biomarkers is a pivotal area of modern cancer research. One such biomarker that has garnered considerable attention in the field is a class of free-floating tumor cells found in the blood known as circulating tumor cells (CTCs). Existing methods for CTC isolation tend to isolate cells based on a single marker enrichment that fails to capture the full heterogeneity that is commonplace in tumor cell populations. By incorporating a broader antibody cocktail, we designed a new approach to isolate CTCs for single-cell RNA analysis. Using common melanoma markers, a consistent and cost-effective approach was developed that we demonstrate to be successful with both patient and cultured cells. This methodology provides a framework to capture a more heterogeneous population of CTCs with wide applications in both research and clinical fields. ABSTRACT: The current standard for investigating tumors is surgical biopsy, which is costly, invasive, and difficult to perform serially. As an adjunct, circulating tumor cells (CTCs)—cells that have broken away from the primary tumor or metastatic sites—can be obtained from a blood draw and offer the potential for obtaining serial genetic information and serving as biomarkers. Here, we detail the potential for melanoma CTCs to serve as biomarkers and discuss a clinically viable methodology for single-cell CTC isolation and analysis that overcomes previous limitations. We explore the use of melanoma CTC biomarkers by isolating and performing single-cell RNA sequencing on CTCs from melanoma patients. We then compared transcriptional profiles of single melanoma CTCs against A375 cells and peripheral blood mononuclear cells to identify unique genes differentially regulated in circulating melanoma tumor cells. The information that can be obtained via analysis of these CTCs has significant potential in disease tracking.