Mass cytometric detection of homologous recombination proficiency in circulating tumor cells to predict chemoresistance of metastatic breast cancer patients

Circulating tumor cells (CTCs) can serve as a liquid biopsy to gain insight into treatment responses and metastatic recurrence. Due to their rarity, the analysis of CTCs is challenging and commonly based on immunomagnetic technologies using antibodies against EpCAM. This study used mass cytometry (CyTOF®) for the identification and characterization of CTCs from longitudinally monitored metastatic breast cancer (mBC) patients. Functional analysis focused on DNA damage responses, particularly the DNA repair pathway of homologous recombination (HR) validated in BC cells from the pleura. Fifty-two blood samples from 13 mBC patients were collected for the enumeration of CTCs using CellSearch® technology, isolation of CTCs together with peripheral blood mononuclear cells (PBMCs) and of plasma. Cell-free DNA (cfDNA) from plasma was analyzed by shallow genome sequencing to determine tumor fraction (TF) and HR deficiency (HRD). CTC/PBMC mixtures were phenotyped by CyTOF® using a panel of 13 antibodies including anti-γH2AX, 53BP1, and RAD51. CyTOF® identified CTCs correlating with CellSearch®- and cfDNA-based quantifications, detected DNA damage in CTCs, and the dynamics of their HR status during genotoxic therapies. Our study shows that CyTOF®-based phenotyping of CTCs from mBC patients shows promise as a method to monitor tumor progression and HR proficiency in real time for the identification of chemoresistance.