Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

Caushi, Justina X.; Zhang, Jiajia; Ji, Zhicheng; Vaghasia, Ajay; Zhang, Boyang; Hsiue, Emily Han-Chung; Mog, Brian J.; Hou, Wenpin; Justesen, Sune; Blosser, Richard; Tam, Ada; Anagnostou, Valsamo; Cottrell, Tricia R.; Guo, Haidan; Chan, Hok Yee; Singh, Dipika; Thapa, Sampriti; Dykema, Arbor G.; Burman, Poromendro; Choudhury, Begum; Aparicio, Luis; Cheung, Laurene S.; Lanis, Mara; Belcaid, Zineb; El Asmar, Margueritta; Illei, Peter B.; Wang, Rulin; Meyers, Jennifer; Schuebel, Kornel; Gupta, Anuj; Skaist, Alyza; Wheelan, Sarah; Naidoo, Jarushka; Marrone, Kristen A.; Brock, Malcolm; Ha, Jinny; Bush, Errol L.; Park, Bernard J.; Bott, Matthew; Jones, David R.; Reuss, Joshua E.; Velculescu, Victor E.; Chaft, Jamie E.; Kinzler, Kenneth W.; Zhou, Shibin; Vogelstein, Bert; Taube, Janis M.; Hellmann, Matthew D.; Brahmer, Julie R.; Merghoub, Taha; Forde, Patrick M.; Yegnasubramanian, Srinivasan; Ji, Hongkai; Pardoll, Drew M.; Smith, Kellie N.

PD-1 blockade unleashes CD8 T cells(1), 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 antigens(2), 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 assay(3) 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 HOBIT(high) 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.