Protocol for the isolation of CD8+ tumor-infiltrating lymphocytes from human tumors and their characterization by single-cell immune profiling and multiome

Abstract

Understanding the heterogenicity of tumor-infiltraing lymphocyte (TIL) populations and the immunobiology in human cancer is a key to establish efficient immunotherapies. Here, we have established a protocol for the characterization of CD8⁺ TILs in tumors by single-cell RNA-seq paired to VDJ profiling and chromatin structure including dissociation of tumor biopsies. We have also provided guidance for subsequent fluorescence-activated cell sorting (FACS), single-cell encapsulation, bioinformatics analysis, and troubleshooting. For complete details on the use and execution of this protocol, please refer to Anadon et al. (2022).

Keywords: Bioinformatics; Cell isolation; Clinical protocol; Flow cytometry/Mass cytometry; Gene expression; RNAseq; Sequence analysis; Sequencing; Single cell.