Non-terminally exhausted tumor-resident memory HBV-specific T cell responses correlate with relapse-free survival in hepatocellular carcinoma

Human lymphocytes were isolated from 46 HCC patients' PBMC, healthy liver margin (HM) and HCC liver tumor (HCC), and probed by a total of 1169 T cell epitopes directly ex vivo using highly multiplexed combinatorial peptide-MHC tetramers strategy and mass cytometry. The pMHC tetramers (restricted to HLA-A*02:01, HLA-A*24:02, HLA-A*11:01 and HLA-B*58:01) library includes 258 HBV, 499 tumor-associated (TA) and 90 bystander virus epitopes, as well as 322 tumor mutation-derived neoantigens. The tetramer positive events were automatically identified and validated by tetramer deconvolution algorithm, and further evaluated manually with the frequency of antigen-specific T cells > 0.002% of total CD8 T cells and a minimum of 4 events (with 2 exceptions that there were 3 events but very strong tetramer signal). All pMHC monomer and the metal-conjugated streptavidin proteins were made in-house. The experiment was performed by using the CyTOF Helios system. This dataset has total of 374 FCS files, including all the detected antigen-specific (241 FCS files) and tetramer negative global (133 FCS files) CD8 T cells. Detailed information can be found in the manuscript and the Supplementary Information and Tables in Cheng et al., 2021, Immunity. FCS file annotation = PatientID-Tissue-Source virus/TA protein-epitope location: Tissue: hepatocellular carcinoma (HCC), healthy liver margin (HM), peripheral blood mononuclear cells (PBMC), healthy liver (HL), healthy fetal liver (HFL). Hepatitis B virus (HBV): HBV surface (envelope) protein (HBV-S), HBV core protein (HBV-C), HBV x protein (HBV-X), HBV polymerase protein (HBV-P) Tumor-associated antigen (TA): SSX2, GPC3, SCCA-1, AFP, TERT, NY-ESO-1, MAGE-1 (not detected), MAGE-3 (not detected) Neoantigen: MT_1 Bystander virus: Epstein–Barr virus (EBV), cytomegalovirus (CMV), influenza A virus (IAV), dengue virus (DENV) Global (tetramer negative) CD8 T cells = CD8TetN本数据集从46例肝细胞癌（Hepatocellular Carcinoma, HCC）患者的外周血单个核细胞（Peripheral Blood Mononuclear Cell, PBMC）、健康肝切缘（Healthy Liver Margin, HM）以及HCC肝肿瘤组织中分离人淋巴细胞，采用高多重组合肽-主要组织相容性复合体（peptide-MHC, pMHC）四聚体策略与质谱流式细胞术（mass cytometry），直接体外检测了共计1169种T细胞表位。 本次使用的pMHC四聚体（受限于HLA-A*02:01、HLA-A*24:02、HLA-A*11:01及HLA-B*58:01亚型）文库包含258种乙型肝炎病毒（Hepatitis B Virus, HBV）表位、499种肿瘤相关（Tumor-associated, TA）表位、90种旁观者病毒表位，以及322种肿瘤突变衍生新抗原（neoantigen）。 四聚体阳性事件通过四聚体反卷积算法自动识别并验证，随后进一步以抗原特异性CD8阳性T细胞占总CD8 T细胞比例>0.002%、且至少包含4个事件为标准进行人工复核（仅2例例外：虽仅含3个事件，但四聚体信号极强）。 所有pMHC单体蛋白与金属标记链霉亲和素蛋白均为实验室自主制备。 本实验采用CyTOF Helios系统完成。 本数据集共计包含374个FCS文件，涵盖所有检测到的抗原特异性CD8 T细胞（241个FCS文件）与四聚体阴性全局CD8 T细胞（133个FCS文件）。 详细信息可参阅Cheng等人2021年发表于《Immunity》的学术论文及其补充材料与附表。 FCS文件命名格式为：PatientID-Tissue-Source virus/TA protein-epitope location。其中组织类型（Tissue）包括：肝细胞癌（HCC）、健康肝切缘（HM）、外周血单个核细胞（PBMC）、健康肝脏（Healthy Liver, HL）、健康胎儿肝脏（Healthy Fetal Liver, HFL）。 乙型肝炎病毒（HBV）相关表位涵盖：HBV表面（包膜）蛋白（HBV-S）、HBV核心蛋白（HBV-C）、HBV X蛋白（HBV-X）、HBV聚合酶蛋白（HBV-P）。 肿瘤相关抗原（TA）包括：SSX2、GPC3、SCCA-1、AFP、TERT、NY-ESO-1、MAGE-1（未检出）、MAGE-3（未检出）。 新抗原（neoantigen）包括：MT_1。 旁观者病毒相关表位涵盖：Epstein-Barr病毒（Epstein–Barr virus, EBV）、巨细胞病毒（Cytomegalovirus, CMV）、甲型流感病毒（Influenza A virus, IAV）、登革病毒（Dengue virus, DENV）。 四聚体阴性全局CD8 T细胞标注为：CD8TetN。