CD8+ T cell dysregulation is a major cause of the failure of immune checkpoint blockade (ICB) therapies. To identify the molecular determinants involved, we used an integrative data analysis approach that leveraged single cell transcriptome data from human tumor materials in the context of ICB treatment, and data from functional genetic screening in T cells assessing gene functions.
First, by integrating and in silico sorting of single-cell data from five cohorts comprising 97 ICB-treated patients, we extracted a total of 161,071 tumor-infiltrating CD8+ T cells and identified two subclusters of potential tumor-reactive T cells: terminal Tex and CD137+ Tex. We then used the Weighted VIPER approach to infer protein activities in these tumor-reactive cells and compared them between ICB-response and non-response groups. Finally, we conducted an intergrative analysis of the differential protein activity data and the data from 20 CRISPR-based genetic screens in T cells.
Our analysis identified several genes, such as PTPN22, MAP4K1, CD5, and DKGZ, known to contribute to T cell exhaustion or impair T cell functions. Among the same cluster of the hits, we identified RASAL3 as a potential modulator that negatively regulates CD8+ T cells in the ICB treatment. Currently, we are evaluating the effect of RASAL3 and other hits in models of T cell-based immunotherapies.