PT  - JOURNAL ARTICLE
AU  - Bingfei Yu
AU  - Quanming Shi
AU  - Julia A. Belk
AU  - Kathryn E. Yost
AU  - Kevin R. Parker
AU  - Huang Huang
AU  - Daniel Lingwood
AU  - Mark M. Davis
AU  - Ansuman T. Satpathy
AU  - Howard Y. Chang
TI  - Systematic discovery of receptor-ligand biology by engineered cell entry and single-cell genomics
AID  - 10.1101/2021.12.13.472464
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.12.13.472464
4099  - http://biorxiv.org/content/early/2021/12/14/2021.12.13.472464.short
4100  - http://biorxiv.org/content/early/2021/12/14/2021.12.13.472464.full
AB  - Cells communicate with each other via receptor-ligand interactions on the cell surface. Here we describe a technology for lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to decode receptor specificity. Engineered lentiviral particles displaying specific ligands deliver fluorescent proteins into target cells upon cognate receptor-ligand interaction, without genome integration or transgene transcription. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. We develop an effective presentation strategy to capture interactions between B cell receptor (BCR) and intracellular antigen epitopes. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of TCR-antigen specificities, clonality, cell type, and cell states of individual T cells. ENTER-seq of patient blood samples after CMV infection reveals the viral epitopes that drive human effector memory T cell differentiation and inter-clonal phenotypic diversity that targets the same epitope. ENTER enables systematic discovery of receptor specificity, linkage to cell fates, and cell-specific delivery of gene or protein payloads.HIGHLIGHTSENTER displays ligands, deliver cargos, and records receptor specificity.ENTER deorphanizes antigen recognition of TCR and BCR.ENTER-seq maps TCR specificity, clonality and cell state in single cells.ENTER-seq of patient sample decodes antiviral T cell memory.Competing Interest StatementH.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, Cartography Bio, and is an advisor of 10x Genomics, Arsenal Biosciences, and Spring Discovery. A.T.S. is a co-founder of Cartography Bio and Immunai. K.R.P. is a co-founder of Cartography Bio.