Antigen identification and high-throughput interaction mapping by reprogramming viral entry

Dobson, Connor S.; Reich, Anna N.; Gaglione, Stephanie; Smith, Blake E.; Kim, Ellen J.; Dong, Jiayi; Ronsard, Larance; Okonkwo, Vintus; Lingwood, Daniel; Dougan, Michael; Dougan, Stephanie K.; Birnbaum, Michael E.

Deciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immune receptor repertoires and the landscape of potential antigens. To address this, we present RAPTR (Receptor-Antigen Pairing by Targeted Retroviruses). RAPTR combines viral pseudotyping and molecular engineering approaches to enable one-pot library on library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cells allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable, and compatible with any cell type, making it easily implemented. These techniques provide a suite of new tools for targeted viral entry, molecular engineering, and interaction screens with broad potential applications.