Protocol for decoding immune predictors of response to immunotherapy through pan-cancer multiomics analysis

Here, we present a protocol for analyzing T cell dynamics in multiple cancers through single-cell RNA sequencing (scRNA-seq), single-cell immune profiling, and mass cytometry/cytometry by time-of-flight (CyTOF). We describe steps for performing gene-regulatory network analysis to identify key transcription factors and cell-cell interaction analysis to explore immune signaling. This protocol facilitates the identification of T cell subsets associated with immune checkpoint blockade (ICB) response and the development of predictive biomarkers. For complete details on the use and execution of this protocol, please refer to Li et al.1.