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Background Immune Checkpoint blockade for the treatment of metastatic melanoma is associated with highly variable clinical outcomes between individuals in terms of both oncological benefit and immune-related adverse events. Early markers of response are urgently sought. Whereas numerous intra-tumoural determinants of sensitivity to immunotherapy are known, the identification of peripheral predictors of response is limited. We aimed to characterize the CD8+ T-cell transcriptomic and clonal changes to treatment across a large cohort of patients in an effort to gain further insight into the peripheral markers of response. Methods We performed paired-end 75bp read RNA-sequencing to assay the peripheral CD8+ response at baseline and across multiple cycles of treatment (n = 105 patients, 69 controls, 315 separate transcriptomes). We validated identified clonal subsets indicative of response using 10X Chromium single cell sequencing (16 samples, 8 patients), flow-cytometry and targeted PCR. Results After adjusting for multiple testing, we identify >5,800 transcripts induced by treatment. These fall into discrete gene modules, with several markedly diverging between combination immunotherapy and anti-PD1 alone. Patients demonstrating a durable radiological response to checkpoint immunotherapy (absence of progression at 6 months) have significantly increased numbers of large peripheral CD8+ circulating clones by day 21 after treatment, compared to non-responders and controls. We replicate this observation in a separately recruited cohort. Large peripheral clones have a distinct gene expression profile, characterized by high expression of CCL5, BCL2L1and NKG7 amongst other genes. Conclusions We identify robust and reproducible predictors of 6 month clinical and radiological responses to immune checkpoint blockade in the transcriptomes of peripheral circulating CD8+ T-cells from metastic melanoma patients after 21 days of treatment. These observations can be used to further our understanding of determinants of patient response, and may provide a mechanism for early treatment stratification of patients with a non-favourable peripheral profile. Legal entity responsible for the study Oxford Radcliffe Biobank. Funding Wellcome Trust, Oxford NIHR Biomedical Research Centre, Cancer Research UK. Disclosure All authors have declared no conflicts of interest. |
