Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics

Simple Summary In addition to millions of normal red and white blood cells, the blood of cancer patients contains a variety of very rare cell types associated with the tumor. A simple blood draw or 'liquid biopsy' can, thus, provide important information about the state of the disease no matter where it exists in the body. In this paper, we describe a method for imaging all rare cells in a blood draw and the means to define each cell type using a combination of genomic, proteomic, and morphological measurements to distinguish tumor cells from mesenchymal and endothelial cells that are present in the tumor microenvironment. We compare the results of this assay among multiple prostate and breast cancer patients and show that this cellular profiling method is valid across patients and cancer types and may provide important biomarkers for assessing disease in real time. Bi-directional crosstalk between the tumor and the tumor microenvironment (TME) has been shown to increase the rate of tumor evolution and to play a key role in neoplastic progression, therapeutic resistance, and a patient's overall survival. Here, we set out to use a comprehensive liquid-biopsy analysis to study cancer and specific TME cells in circulation and their association with disease status. Cytokeratin+, CD45- circulating rare cells (CRCs) from nine breast and four prostate cancer patients were characterized through morphometrics, single-cell copy number analysis, and targeted multiplexed proteomics to delineate cancer cell lineage from other rare cells originating in the TME. We show that we can detect epithelial circulating tumor cells (EPI.CTC), CTCs undergoing epithelial-to-mesenchymal transition (EMT.CTC) and circulating endothelial cells (CECs) using a universal rare event detection platform (HDSCA). Longitudinal analysis of an index patient finds that CTCs are present at the time of disease progression, while CECs are predominately present at the time of stable disease. In a small cohort of prostate and breast cancer patients, we find high inter-patient and temporal intra-patient variability in the expression of tissue specific markers such as ER, HER2, AR, PSA and PSMA and EpCAM. Our study stresses the importance of the multi-omic characterization of circulating rare cells in patients with breast and prostate carcinomas, specifically highlighting overlapping and cell type defining proteo-genomic characteristics of CTCs and CECs.