Multidimensional single T cell analysis reveals altered T cell biology upon treatment of murine tumor with checkpoint blockade immunotherapy

Abstract

Checkpoint blockade immunotherapy has shown great success in certain types of cancers, but are ineffective in most cancers. We do not understand why these therapies fail. Here, we seek to better understand functional changes in T cells in responsive tumors through single cell TCR sequencing and high dimensional phenotypic analysis within single tumor-infiltrating T cells. Through surgical biopsy, we analyze the same tumor longitudinally before and after treatment, enabling us to track the fate of individual T cell clones. Our data show that the CD4/CD8 ratio decreases upon treatment. T cells expressing inhibitory markers such as PD1, CTLA4, diminish post treatment. We see distinct clusters of effector CD4 and CD8 T cells in treated tumors, including effector CD4 populations with Tfh, Th1 and Th2 phenotypes. CD4 Tregs are greatly diminished upon successful treatment, and diminish through clonal contraction. Furthermore, TCR acts as a unique marker for T cell ancestry, which links T cell function to T cell specificity. Based on TCR clonality, we observe that expanded T cell clones before treatment do not share the same TCRs with expanded T cell clones after treatment. This implies new CD8 T cell clones are recruited into the tumor upon treatment. From our data, we will be able to identify T cell clones that are phenotypically distinct and expanded in responsive tumors which is critical in understanding what makes for a successful T cell response after immunotherapy.