Gene expression differences between TILs that are reactive to tumor cells and TILs that are not reactive

Clinical significance of tumor-infiltrating lymphocytes (TILs) was demonstrated in many tumor types. In the clinical trials, immune check point inhibitors showed significant clinical efficacy in some tumor types with high mutation burden such as melanoma, bladder cancer, and smoking-induced lung cancer, while there were little effects in cancers with lower mutation rates such as breast cancer. Recently, selection and adoptive transfer of autologous mutation-specific TILs showed successful regression of metastatic tumors in an estrogen receptor-positive breast cancer patient. In this study, we analyzed gene expression profiles in cultured TILs that are reactive or non reactive against autologous breast cancer cells. We cultured TILs and cancer cells derived from breast tumor tissues obtained from the surgery. Reactivity of TILs against cancer cells was determined by interferon gamma (IFN-γ) ELISA analysis after co-culture of TILs and cancer cells for 24 hours. The total RNA was purified from cultured TILs (post-REP TILs) using RNeasy kits. The gene expression library is generated by Illumina TruSeq RNA library prep kit and sequenced.