Mathematical model of CISH knockout predicts increased efficacy in tumor-infiltrating lymphocyte activation with synergistic gene editing

Tumor-infiltrating lymphocyte (TIL) therapy is a type of adoptive cell therapy, where the lymphocytes of a cancer patients tumor are harvested, expanded in vitro using IL-2 stimulation, and then infused back into the patient. However, even with the use of TIL therapy, cancer cells can survive for various reasons, such as poor lymphocyte infiltration into tumors, chronic activation of the T cell receptor and the immunosuppressive tumor microenvironment. Cytokine-inducible SH2-containing (CISH) protein is a negative regulator of T cell activation, and in a recent clinical trial was knocked out in TILs to improve TIL therapy efficacy. In this study, we developed a mechanistic signaling pathway model to theoretically evaluate the efficacy of CISH knockout (CISH KO) in T cell activation and examine potential alternative target genes that can theoretically be targeted using multiplex gene-editing or drugs to further improve T cell activation and function. Our modeling results demonstrate that CISH knockout increases the transcription of activation biomarkers IL-2 and TNF-a, but also inhibitory biomarkers such PD1 and FasL. Using global sensitivity analysis, we also found that GSK3B, which is responsible for the deactivation of the NFAT, is also predicted to further increase T cell activation when knocked out. In addition, we predict that PDCD1, FAS and CTLA4 can be knocked-out in combination with CISH to further enhance T cell activation and prevent exhaustion and apoptosis.