The majority of cancer patients die of metastatic disease. Currently, immunotherapy is one of the few successful treatment modalities for metastatic disease and can lead to very durable responses in cancer types such as melanoma. Unfortunately, many cancers including breast cancer exhibit resistance to the currently approved immunotherapies and these patients invariably relapse. We hypothesize that innate resistance of subpopulations of cancer cells within a tumour 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 clonal dynamics over time. We introduced a DNA barcode library (ClonTracer) into heterogeneous murine breast cancer cell lines (4T1 and EMT6). These barcodes are then “read” using next-generation sequencing. Following orthotopic transplantation of these barcoded cells, the clonal response of cancer cells to immuno-selection within the primary tumour as well as metastatic tumours was analysed.
We studied the effects of the immune system and immunotherapies on both models by comparing barcode frequency and distribution from tumours grown in wild-type mice compared to immunocompromised NSG mice, and from wild-type mice with or without combination immunotherapy (anti-PD1+anti-CTLA4). In both models we observed immunoediting of specific immuno-sensitive clones and the enrichment of immunotherapy resistant clones, with the same clones being selected for across replicate mice. In the EMT6 model this occurred in the primary setting, whereas in the 4T1 model, which is very aggressive and poorly responsive to immunotherapy, this only occurred in the metastatic setting. We have now isolated clonal immunotherapy resistant 4T1 cell populations (with specific barcodes) and are determining what allows them to evade immune destruction.
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 in breast cancer patients.