Engineered cell entry links receptor biology with single-cell genomics

Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver ge-netic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discov-ery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.

Automated summary

In this study, we present a lentiviral-mediated cell entry technique called engineered receptor-ligand interaction (ENTER) that enables the display of ligand proteins, delivery of payloads, and recording of receptor specificity. We optimize ENTER to decode interactions between various receptor-ligand pairs and demonstrate its application in T cell receptor-MHC peptides, antibody-antigen, and B cell receptor-antigen interactions. Using RNA sequencing (ENTER-seq), we achieve a single-cell readout of ENTER, allowing for the multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. In addition, ENTER technology enables the systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.