Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers
Frank J. Lowery, Sri Krishna, Rami Yossef, Neilesh B. Parikh, Praveen D. Chatani, Nikolaos Zacharakis, Maria R. Parkhurst, Noam Levin, Sivasish Sindiri, Abraham Sachs, Kyle Hitscherich, Zhiya Yu, Nolan R. Vale, Yong‐Chen Lu, Zhili Zheng, Li Jia, Jared J. Gartner, Victoria Hill, Amy R. Copeland, Shirley Nah, Robert V. Masi, Billel Gasmi, Scott Kivitz, Biman C. Paria, Maria Florentin, Sanghyun P. Kim, Ken‐ichi Hanada, Yong F. Li, Lien T. Ngo, Satyajit Ray, Mackenzie L. Shindorf, Shoshana T. Levi, Ryan P. Shepherd, Chris Toy, Anup Y. Parikh, Todd D. Prickett, Michael C. Kelly, Rachel K. Beyer, Stephanie L. Goff, James C. Yang, Paul F. Robbins, Steven A. Rosenberg
Abstract
The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen-specific TCR clonotypes (NeoTCRs) from 10 metastatic human tumors to their single-cell transcriptomes, we identified signatures of CD8 + and CD4 + neoantigen-reactive tumor-infiltrating lymphocytes (TILs). Neoantigen-specific TILs exhibited tumor-specific expansion with dysfunctional phenotypes, distinct from blood-emigrant bystanders and regulatory TILs. Prospective prediction and testing of 73 NeoTCR signature–derived clonotypes demonstrated that half of the tested TCRs recognized tumor antigens or autologous tumors. NeoTCR signatures identified TCRs that target driver neoantigens and nonmutated viral or tumor-associated antigens, suggesting a common metastatic TIL exhaustion program. NeoTCR signatures delineate the landscape of TILs across metastatic tumors, enabling successful TCR prediction based purely on TIL transcriptomic states for use in cancer immunotherapy.