Engineered cell entry links receptor biology with single-cell genomics [scRNA-Seq]

Cells communicate with each other via receptor-ligand interactions. Here we describe lentiviral-mediated cell e¬ntry 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 genetic 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- vs intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery. Overall design: Primary T cells isolated directly from patient blood samples or peptide stimulated donor PBMC were stained with a mixture of pMHC displayed ENTER viruses and oligo-barcoded antibodies. GFP+ or GFP- CD8 T cells were sorted and subjected to multiplexed single cell RNA-seq, CITE-seq, TCR-seq, and pMHC antigen profiling on the droplet based 10X Genomics platform