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. 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.

肿瘤浸润淋巴细胞（Tumor infiltrating lymphocytes, TILs）在多种肿瘤类型中与患者生存获益及免疫治疗应答相关。然而，为何部分肿瘤存在高CD8 T细胞浸润而其余肿瘤却无此现象，这一问题至今尚未得到解答。本研究针对维持人类癌症中CD8 T细胞应答的必要条件展开了探究。研究发现，肿瘤内的CD8 T细胞可分为终末分化和干细胞样两个截然不同的细胞群。干细胞样CD8 T细胞在增殖过程中，会分化为更多表达效应分子的终末分化子代细胞。若要让大量T细胞浸润肿瘤，这一效应分化过程的发生至关重要。本研究从人类肿瘤中分离获取上述不同细胞群，并开展了RNA测序与DNA甲基化分析。研究人员从肿瘤中分选得到细胞群，并使用Qiagen AllPrep试剂盒提取RNA与DNA。针对前列腺癌与膀胱癌样本，采用NuGen Ovation试剂盒流程进行RNA测序；膀胱癌样本则使用Clontech Smart-seq2流程完成测序。DNA甲基化测序文库采用Illumina DNA甲基化测序建库流程制备。测序工作在HiSeq 3000或HiSeq X10测序平台上完成。