Circulating tumor cells share RNA modules with early embryos and metastatic cancer

Circulating tumor cells (CTCs) represent a vector for cancer dissemination, and also a minimally invasive tool to monitor the evolution of cancer in patients, and evaluate the therapeutic response, resistance, and progression in patients. While DNA from CTCs is primarily used in this evaluation, RNA remains more informative, but more elusive to obtain. In this study, we uncover novel markers for the retrieval of all classes of CTCs, including new subclasses. We studied selected single-cell RNAseq profiles of CTCs from more than 3000 putative CTCs in the context of breast cancer and embryonic tissues. ScRNAseq data was analyzed from 550 bona fide CTCs, comparing their RNA programs with tumor and embryo cells. We identified three main different CTC subgroups: epi A (CDH1/EPCAM+), epi B (LY6E/EPCAM+), and mesenchymal (VIM+). Novel mesenchymal CTC markers (AXL/CAV1), were determined. CTCs have RNA modules in common with cancer cells from metastatic lymph nodes and from their respective primary tumors, but not with cancer cells from non-metastatic tumors. CTCs of the epi B subgroup share RNA modules from trophectoderm cells of the early embryo. We inferred a progression trajectory connecting, in succession, cell clusters from normal breast, ER+, and metastatic tumors, with the epithelial or mesenchymal CTC subgroups. We uncovered novel subclasses with respective markers for both epithelial and mesenchymal CTCs. For the first time, we show that CTCs share gene signatures specifically with metastatic cancer cells and with the early embryo's trophectoderm. These novel CTC signatures we identified in the CTC/cancer lineage may enable clinical applications for minimal residual disease, longitudinal studies, or even early detection, in carcinomas from breast and other organs.