Cellular Dynamics Upon Immune Checkpoint Inhibition

Abstract Cellular dynamics in the tumor microenvironment upon immune checkpoint inhibition (ICIs) treatment remain largely known. To elucidate these dynamics and associated mechanisms of response and resistance, we analyzed a large-scale single-cell RNA-sequencing dataset of 326 samples from 163 patients across multiple cancer types, with longitudinally site-matched samples. We developed a robust, integration-free deep phenotyping framework, and annotated 1,022,526 cells into 83 granular cell states. Our analysis revealed consistent compositional changes in 19 cell subtypes during ICI treatment, including enhanced adaptive immune responses (e.g., CD8+ IL7R+ central memory T cells, GZMK+ effector memory T cells, germinal center B cells), reduced interferon-responsive immune cells, quiescent CD4+CREM- memory T cells, and angiogenesis tip cells. Co-regulatory network analysis revealed a continuum between two patterns resembling tertiary lymphoid structure maturity. Accumulation of interferon-responsive subtypes was associated with T cell expansion. We further identified a B cell- centric response-specific pattern indicating an enhanced early-phase adaptive immune response favored treatment efficacy, which was subsequently validated through supervised subgroup analysis. Our study presents a comprehensive landscape of TME cellular dynamics during ICI treatment, showcasing the importance of a systems-level understanding in improving patient stratification and advancing personalized cancer immunotherapy.