Stem and effector CD8 T-cells from human cancers

Tumor infiltrating lymphocytes (TILs) are associated with a survival benefit in several tumor types and response to immunotherapy. However, the reason some tumors have high CD8 T cell infiltration while others do not remains an unanswered question. In this study, we investigated the requirements for maintaining a CD8 T cell response against human cancer. We find that CD8 T cells within tumors consist of distinct populations of terminally differentiated and stem-like cells. Upon proliferation, stem-like CD8 T cells give rise to more terminally differentiated, effector molecule expressing daughter cells. For many T-cells to infiltrate the tumor, it is critical that this effector differentiation process occur. In this study, we collected these different cell populations from human tumors and performed RNA sequencing and DNA methylation analysis. Overall design: Cell populations were sorted from tumors and RNA and DNA extracted using qiagen all-prep kits. RNA was sequenced using the NuGen ovation protocol for prostate and bladder, and clontech smartseq2 for bladder samples. Dna methylation libraries were prepared using the Illumina DNAmethyseq protocol. Samples were sequenced on a Hiseq 3000, or Hiseq X10.