Figure 4. Neoantigen-specific TCR expansion in stimulated T cell cultures.

Peptides generated from the eliminated mutation associated neoantigen candidates were synthesized and used to pulse autologous peripheral T cells for patient CGLU116. T cells were stimulated with respective mutant and wild type peptides and cultured for 10 days, followed by next generation TCR sequencing of expanded T cell cultures. Reactive TCR clonotypes were matched to clones found in infiltrating tumor lymphocytes. Neoantigen-specific TCR reactivity was observed for the mutant peptides associated with mutant HELB^987P>S (SASPLSVV; panel A), SCL26A7^117R>Q (ISANAVEQIV; panel B) and PGAP1^903Y>F (AFGSAHLFR and VIAFGSAHLFR; panel C) compared to their wild type counterparts. An oligoclonal TCR expansion was observed for both mutant (STPSASPLSV) and wild type (STPSASPLPVV) peptides associated with a single base substitution in HELB (panel D). Adjusted p values are given for pairwise comparisons between productive frequencies in peptide stimulated versus unstimulated T cells. Solid bars represent mutant and bars with diagonal pattern denote wild type peptides.