Marius Messemaker, Connor A Richterich, Jule Wenner, Yiting Ma, Živa Moravec, Rhianne Voogd, Maike Mussmann, Sam de Paauw, Bjørn P Y Kwee, Jeroen Geerligs, Ben Morris, Yaël Winkler, Babet O Springer, Floris T B T van den Brekel, Jos Urbanus, Aurélie Guislain, Nuno Alfaiate, Frank van Diepen, Martijn van Baalen, Benoit P Nicolet, John B A G Haanen, Catherine J Wu, Jani Huuhtanen, Wouter Scheper, Ton N Schumacher
Tumors contain a mixture of T cells with bystander reactivities and reactivities towards different, frequently patient-specific, cancer (neo)antigens. The one-step identification of highly active TCR-antigen pairs in human tumors would be valuable, both as a monitoring tool and to boost T cell reactivities of interest. Here, we develop PAIR-Scan, an HLA-agnostic library-on-library screening technology that identifies functionally active TCR-neoantigen pairs among tens of thousands of candidate pairs in a single step. We demonstrate the value of PAIR-Scan on a range of tumor samples and for the direct identification of TCR-recognized minimal peptides. In addition, we demonstrate that PAIR-Scan correctly ranks TCRs reactive to the same antigen by their relative tumor-killing efficiency. Together, these data demonstrate the value of PAIR-Scan for both the dissection of T cell responses in clinical samples and to generate large-scale datasets for the development of predictive models of TCR reactivity.