The majority of cancer patients die of metastatic disease. Currently, immunotherapy is one of the few successful treatment modalities for metastatic disease. Unfortunately many cancers such as breast cancer exhibit resistance to the currently approved immunotherapies. We hypothesise that innate resistance of cancer cells can explain some of this resistance.
To test whether clonal selection of innately resistant cells can drive resistance to immunotherapy, we used cellular DNA barcoding, a powerful technique that allows for the analysis of cancer cell clonal dynamics over time. We introduced a DNA barcode library (ClonTracer) into murine metastatic breast cancer cells (4T1) so that each cell received a single unique barcode. These barcodes can then be “read” using next-generation sequencing. Following orthotopic mammary transplantation of these barcoded cells, the primary tumour was resected and metastases allowed to develop.
Comparison of wild-type mice with immunocompromised NSG mice demonstrated that the immune system did not affect barcode number in the primary tumours. In contrast there was a significant increase in the number of barcodes detected in the lungs of NSG mice, despite the level of disease burden being identical at ethical endpoint. We then compared control wild-type mice with adjuvant immunotherapy (anti-PD1/anti-CTLA4) treated mice, this revealed that the number of unique metastatic clones was significantly reduced following immunotherapy. Further analysis revealed a subset of highly metastatic clones detected in NSG mice that were reduced in abundance in wild-type mice and completely eliminated following immunotherapy. Conversely, we identified other clones that were highly enriched following immunotherapy. These same clones were detected in replicate mice suggesting that this was a pre-existing phenotype. We are currently identifying what makes these clones more or less susceptible to immune surveillance and immunotherapy.
This study shows that there are subsets of breast cancer cells that are innately more resistant to immunotherapy. We now aim to identify tumour-intrinsic pathways regulating recognition by the immune system that can be targeted to improve immunotherapy response.