Engineered cell entry links receptor biology with single-cell genomics

Bingfei Yu; Quanming Shi; Julia A Belk; Kathryn E Yost; Kevin R Parker; Rui Li; Betty B Liu; Huang Huang; Daniel Lingwood; William J Greenleaf; Mark M Davis; Ansuman T Satpathy; Howard Y Chang

doi:10.1016/j.cell.2022.11.016

Engineered cell entry links receptor biology with single-cell genomics

Cell. 2022 Dec 22;185(26):4904-4920.e22. doi: 10.1016/j.cell.2022.11.016. Epub 2022 Dec 13.

Authors

Affiliations

¹ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
² Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
³ Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁴ Department of Genetics, Stanford University, Stanford, CA 94305, USA.
⁵ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
⁶ The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
⁷ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
⁸ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. Electronic address: howchang@stanford.edu.

Abstract

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 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-clonal 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.

Keywords: B cell receptor; T cell receptor; antigen specificity; ligand-receptor pairs; single-cell multiomics; targeted cargo delivery; viral display; virus-like particle.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biology
Epitopes
Genomics
Humans
Ligands
Peptides
Receptors, Antigen, T-Cell* / metabolism
Single-Cell Analysis
Virus Internalization*

Substances

Epitopes
Ligands
Peptides
Receptors, Antigen, T-Cell

Abstract

Publication types

MeSH terms

Substances

Grants and funding