Biomarkers of response and resistance to anti-PD1 immunotherapy in melanoma.

Abstract

Inhibitors targeting the CTLA-4 and PD-1 receptors have greatly improved the survival and outcomes of patients with advanced stage melanoma. There are currently numerous Phase 1-3 clinical trials testing the combination of immune checkpoint inhibitors in metastatic melanoma, including drugs targeting IDO1, LAG3, and TIM3. In order to determine which patients will benefit from a specific therapy, it is vital to first identify predictors of response to immunotherapies. This will allow for the administration of personalised immunotherapies and increase the rate of response for metastatic melanoma patients. While many patients exhibit a response to single-agent or combination immune checkpoint blockade, there exists a subgroup of patients who receive minimal or no benefit from these therapies. These patients often do not respond at all (innate resistance) or relapse after demonstrating an initial response (acquired resistance). For these patients, it is of utmost importance to identify potential mechanisms of resistance and ways in which these signalling molecules or pathways may be targeted in order to elicit an anti-tumour immune response. Therefore, the aim of this thesis is to identify biomarkers of response and mechanisms of resistance to anti-PD-1 monotherapy, or combination anti-PD-1 and anti-CTLA-4 immunotherapy in metastatic melanoma patients. The studies described herein employ various experimental techniques including highly quantitative multiplex immunofluorescence, immunohistochemistry, RNA-sequencing, targeted RNA-sequencing and DNA sequencing on FFPE melanoma specimens, as well as mass cytometry on tumour dissociates. Throughout the studies included in this thesis, I identify potential biomarkers of response to anti-PD-1 based therapies at baseline, including an EOMES+ memory T-cell population associated with significantly longer progression-free survival and tumour shrinkage. I further highlight the application of multiplex immunofluorescence in investigating the spatial distribution of critical immune populations and their potential role as biomarkers of response. Finally, I perform a detailed characterisation of the non-responding patients, and identify pathways associated with resistance to anti-PD-1 based therapies. These findings have significant implications for the treatment and selection of metastatic melanoma patients for anti-PD-1 based therapies.