Sequencing of circulating tumor cells (CTC) allows capturing genetic diversity by copy number alterations (CNA) and measuring chromosomal instability (CIN) at single-cell level during cancer treatment and progression.
We analyzed baseline and end-of-treatment primary tumor samples of a cohort of 31 triple-negative breast cancer patients receiving neoadjuvant anthracycline/taxane and prospectively followed with periodical blood draws for CTCs analysis from initial diagnosis to eventual relapse. We used large scale state transition (LST) as a surrogate measure of CIN, and analysed CNAs in 35 CTCs by low-pass WGS and by Targeted NGS in primary tumor samples.
Mean LSTs varied according to the time of collection and the phase of treatment. Globally LSTs dropped during chemotherapy suggesting either a hit of CTCs with higher CIN or the selection of CTCs with a threshold compatible with cell viability for seeding. Notably, LSTs increased after chemotherapy with no sensitive differences between CTCs collected in parallel with the development of overt metastases. CIN was not associated with relapse as CTCs of recurrent patients were evenly distributed according to high (superior to the median value) and low LST. However, CTCs characterized high-LST had significantly more genomic alterations than those with lower LSTs (502 vs 186 P<0.001, Fisher test). The genomic alterations of CTCs which we previously reported to be more similar to residual rather than primary tumor, were overall characterized by more gains than losses. In high-LST CTCs numbers of gains and losses were similar (270 vs 232), whereas CTCs with low LST had less gains than losses (72 vs 114).
Early stage triple-negative breast cancer patients have CTCs featuring high levels of genomic instability at initial diagnosis. CIN and CNA are reduced by chemotherapy. CTCs of progressive cases recover increased levels of CINs and CNA during follow up and at the time of progression, yet relapses are unexpectedly less instable than primary. Levels of CIN are associated with numbers and type of CNA with low-LST CTCs being associated with less CNA events mostly represented by gene loss.
Fondazione IRCCS Istituto Nazionale dei Tumori di Milano.
Italian Association for Cancer Research Foundation (Fondazione AIRC), Grant number IG 21694 to Vera Cappelletti.
C. Reduzzi: Financial Interests, Personal, Research Grant: Menarini Silicon Biosystem. All other authors have declared no conflicts of interest.