Alyza M. Skaist, Patrick M. Forde, Rulin Wang, Jiajia Zhang, Malcolm V. Brock, Zineb Belcaid, Haidan Guo, Victor E. Velculescu, Joshua E. Reuss, Matthew J. Bott, Matthew D. Hellmann, Sarah J. Wheelan, Boyang Zhang, Kristen A. Marrone, Peter B. Illei, Ajay Vaghasia, Richard L. Blosser, Sune Justesen, Bert Vogelstein, Jamie E. Chaft, Sampriti Thapa, Errol L. Bush, Srinivasan Yegnasubramanian, Janis M. Taube, Julie R. Brahmer, Tricia R. Cottrell, Luis Aparicio, Jennifer Meyers, Kornel E. Schuebel, Hok Yee Chan, Taha Merghoub, Zhicheng Ji, Wenpin Hou, David R. Jones, Margueritta El Asmar, Bernard J. Park, Jarushka Naidoo, Kellie N. Smith, Jinny Ha, Kenneth W. Kinzler, Ada Tam, Dipika Singh, Brian J. Mog, Justina X. Caushi, Shibin Zhou, Valsamo Anagnostou, Hongkai Ji, Emily Han-Chung Hsiue, Mara Lanis, Poromendro Burman, Begum Choudhury, Drew M. Pardoll, Arbor G. Dykema, Anuj Gupta, and Laurene S. Cheung
PD-1 blockade unleashes CD8 T cells1, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction programs in tumour-infiltrating lymphocytes (TIL). However, the majority of TIL do not recognize tumour antigens2, and little is known about transcriptional programs of MANA-specific TIL. Here, we identify MANA-specific T cell clones using the MANA functional expansion of specific T cells assay3 in neoadjuvant anti-PD-1-treated non-small cell lung cancers (NSCLC). We use their T cell receptors as a ‘barcode’ to track and analyse their transcriptional programs in the tumour microenvironment using coupled single-cell RNA sequencing and T cell receptor sequencing. We find both MANA- and virus-specific clones in TIL, regardless of response, and MANA-, influenza- and Epstein–Barr virus-specific TIL each have unique transcriptional programs. Despite exposure to cognate antigen, MANA-specific TIL express an incompletely activated cytolytic program. MANA-specific CD8 T cells have hallmark transcriptional programs of tissue-resident memory (TRM) cells, but low levels of interleukin-7 receptor (IL-7R) and are functionally less responsive to interleukin-7 (IL-7) compared with influenza-specific TRM cells. Compared with those from responding tumours, MANA-specific clones from non-responding tumours express T cell receptors with markedly lower ligand-dependent signalling, are largely confined to HOBIThigh TRM subsets, and coordinately upregulate checkpoints, killer inhibitory receptors and inhibitors of T cell activation. These findings provide important insights for overcoming resistance to PD-1 blockade., Single-cell RNA sequencing and T cell receptor sequencing are combined to identify transcriptional programs specific to mutation-associated neoantigen-specific T cells in non-small cell lung cancers treated with anti-PD-1, providing insights into resistance to PD-1 blockade.