Preclinical Studies of the Off-Target Reactivity of AFP₁₅₈-Specific TCR Engineered T Cells

Autologous T cells engineered with T receptor genes (TCR) are being studied to treat cancers. We have recently identified a panel of mouse TCRs specific for the HLA-A0201/alpha fetoprotein epitope (AFP₁₅₈) complex and have shown that human T cells engineered with these TCR genes (TCR-Ts) can eradicate hepatocellular carcinoma (HCC) xenografts in NSG mice. However, due to TCR’s promiscuity, their off-target cross-reactivity must be studied prior to conducting clinical trials. In this study, we conducted in vitro X-scan assay and in silico analysis to determine the off-target cross-reactivity of 3 AFP₁₅₈-specific TCR-Ts. We found that the 3 AFP₁₅₈-specific TCR-Ts could be cross-activated by ENPP1₄₃₆ peptide and that the TCR3-Ts could also be activated by another off-target peptide, RCL1₂₁₅. However, compared to AFP₁₅₈, it requires 250 times more ENPP1₄₃₆ and 10,000 times more RCL1₂₁₅ peptides to achieve the same level of activation. The EC₅₀ of ENPP1₄₃₆ peptide for activating TCR-Ts is approximately 17–33 times higher than AFP₁₅₈. Importantly, the ENPP1+ tumor cells did not activate TCR1-Ts and TCR2-Ts, and only weakly activated TCR3-Ts. The IFNγ produced by TCR3-Ts after ENPP1+ cell stimulation was >22x lower than that after HepG2 cells. And, all TCR-Ts did not kill ENPP1 + tumor cells. Furthermore, ectopic over-expression of ENPP1 protein in HLA-A2+ tumor cells did not activate TCR-Ts. In silico analysis showed that the ENPP1₄₃₆ peptide affinity for HLA-A0201 was ranked 40 times lower than AFP₁₅₈ and the chance of ENPP1₄₃₆ peptide being processed and presented by HLA-A0201 was 100 times less likely than AFP₁₅₈. In contrast, the two off-targets (Titin and MAGE-A3) that did cause severe toxicity in previous trials have the same or higher MHC-binding affinity and the same or higher chance of being processed and presented. In conclusion, our data shows that TCR-Ts can be activated by off-target ENPP1₄₃₆ peptide. But, compared to target AFP₁₅₈, it requires at least 250 times more ENPP1₄₃₆ to achieve the same level of activation. Importantly, ENPP1₄₃₆ peptide in human cells is not processed and presented to a sufficient level to activate the AFP₁₅₈-specific TCR-Ts. Thus, these TCR-Ts, especially the TCR1-Ts and TCR2-Ts, will unlikely cause significant off-target toxicity.