Single cell profiling of circulating tumor cells: Transcriptional intra-patient heterogeneity of endocrine resistant and phenotypic markers

Understanding the heterogenous biology of circulating tumor cells (CTC) might answer key issues of metastatic processes and therapy resistance. We demonstrate single CTC transcriptional profiling, providing insight into intra-patient CTC heterogeneity and allowing comparisons to breast cancer (BC) cell lines.

A 30 transcript PCR panel characterizing different phenotypes e.g. endocrine resistance, stem cell, epithelial and mesenchymal features was designed and tested for single cell profiling using BC cell lines (MCF-7, MCF-7/TAMR, MDA-MB-231). CTCs were enriched from a diagnostic leukapheresis (DLA) product obtained from a patient suffering from metastatic breast cancer (metBC) resistant to endocrine therapy using Parsortix system. RNA of single uncultured and cultured CTCs was extracted, reversely transcribed into cDNA and pre-amplified. Gene expression profiles were generated by multiplex real-time PCR.

Multimarker analysis was possible in single cells with intense signals of KRT19 and ACTB in 61,5% of BC cell lines (n = 13), in 17,9% of uncultured CTCs (n = 39) and in 33% of cultured CTCs (n = 15). Single cell line cells and pools of 5 cells reproducibly clustered together. Transcriptomic profiles of each cell line were consistent with their biomarker patterns (e.g. ER, HER2, VIM). Gene expression profiles of CTCs and cultured CTCs revealed intra-patient heterogeneity but they clustered into subgroups according to EpCAM, CD44, ER, and HER2 expression. Profiles of metBC cell lines and CTCs were only partly congruent – many transcripts were undetectable in CTCs.

Multimarker RNA profiling of single CTCs and cultured CTCs may provide important insights into intra-patient tumoral heterogeneity relevant for therapy resistance.