1947P Single cell analysis reveals that CD8+ T cell clone size determines response to immune checkpoint blockade

Abstract

Immune checkpoint blockers (ICB) have markedly improved survival in patients with metastatic melanoma (MM). However, clinical response remains highly variable and peripheral biomarkers are lacking. CD8+ T cells are a key cellular subset mediating the effect of ICB and previous work has demonstrated that the presence of large CD8+ T cell clones in the peripheral blood (>0.5% of the total repertoire) is associated with positive clinical outcomes. We sought to further characterise and explore the clonal characteristics of the peripheral CD8+ T cell response to ICB at a single-cell level. Single cell transcriptome and V(D)J sequencing was performed on CD8+ T cells isolated from the peripheral blood of patients undergoing ICB treatment for MM (n=8) at baseline and 21 days post-treatment. Dimensionality reduction and trajectory inference were subsequently employed to identify and understand the effects of treatment on cellular subpopulations. We identified 7 subsets of CD8+ T cells, defined by distinctive phenotypes. ICB had a heterogenous effect across these subsets, with the greatest and most unique gene expression changes in the effector and effector memory subsets. Such changes were more marked in larger (>0.5% of repertoire) than smaller clones. By grouping cells based on clonal size, we identify that the effects of ICB vary as a function of clonal size, with clones between 0.5-1% of the repertoire having quantitatively fewer, but qualitatively more relevant, gene expression changes than either hyper-expanded (>2%) or small (<0.1%) clones. Further, ICB had a differential effect on clones that expand following treatment, than those that contract, with expanding clones having both a greater magnitude and qualitatively more relevant gene expression changes than contracting clones. Taken together, we describe a discrete subset of cells which uniquely respond to ICB. We identify that all cells are not equally affected by ICB, but a subset defined by clonal size and clonal behaviour demonstrate a marked and distinctive response, potentially representing a key cellular target of therapy. This work will aid the search for a prognostic biomarker and further advances understanding of the molecular mechanisms of ICB.