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