Extended Data Fig. 3: Immunogenicity of tumor-specific antigens.

a) Epitope mapping of preREP TILs from sample CESC-1 (IFNγ Spot Forming Unit (SFU) per 10⁶ cells, mean +/− SD). CD8 neoantigens (in green) and CD8 viral antigen (in blue) were validated by CD137 up-regulation. b) Gating strategy of CD137 up-regulation on CD8 + REP TILs from sample NPC-1 following the stimulation with EBNA-3A viral peptide (RYSIFFDYM). D) Expression level of EBV genes, either detected as expressed (>0 TPM) or tested immunogenic in patient NPC-1. The height of the bars corresponds to the gene expression levels across the samples. The inner bars display the expression pattern of the genes through EBV cycle phases. c) Viral epitope mapping of preREP TILs from sample NPC-1 (IFNγ SFU per 10⁶ cells, mean +/− SD). d) Viral epitope mapping of REP TILs from sample NPC-1 (middle) (IFNγ SFU per 10⁶ cells, mean +/− SD). Flow cytometry data showing the frequency of EBNA-3A (RYSIFFDYM)-reactive CD8 T-cells (left) and the frequency of BALF2 (LVPRTQSVPARDYPH)-reactive CD4 T-cells (right). C-D) CD8 and CD4 reactivities, assessed by CD137 up-regulation, are shown in blue and orange, respectively. e) CD8 HC-TSA reactivity of REP TILs from sample MEL-1 (IFNγ SFU per 10⁶ cells, mean +/− SD). HC-TSA reactivities also validated as tumor-rejecting antigens (by TCR cloning) are shown in red. All peptides were identified by MS. f) Tumor reactivity of antigen-specific TCR clonotypes from sample MEL-1. Reactivity assessed by CD137 up-regulation of TCR-transfected primary activated CD8⁺ T cells following co-culture with autologous tumor cells. Positivity threshold described in the Methods section. (Irr_Ctrl: irrelevant TCR, Mock: transfection with water).