Methods and compositions for discovery of receptor-ligand specificity by engineered cell entry
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsHoward Y. CHANG, Ansuman SATPATHY, Bingfei YU, Quanming SHI
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Abstract
The present disclosure relates to systems, methods and compositions for decoding ligand-receptor interactions, for delivering nucleic acids and proteins into target cells and for performing single cell multiomics. Disclosed are engineered lentiviruses displaying ligands that deliver cargo into target cells upon cognate receptor-ligand interaction. Also disclosed are compositions and methods including pMHC or antigen epitopes displaying lentiviruses for identifying pMHC/T-cell receptors and antigen/B-cell receptor interactions.
Claims67
An engineered lentivirus comprising:
- a heterologous ligand displayed on a surface of the lentivirus;
- a fusogen comprising a modified viral envelope protein, wherein the fusogen is capable of fusing the lentivirus to a host cell, wherein the host cell comprises an endogenous receptor for the ligand;
- a reporter protein operably linked to a lentiviral structural protein;
- and
- a barcoded RNA.
A method of identifying an immunogenic antigen, the method comprising:
- providing an engineered lentivirus comprising a heterologous receptor protein displayed on the surface of the lentivirus, a fusogen comprising a modified VSV-G viral envelope protein wherein the fusogen is capable of fusing the lentivirus to a host cell, wherein the host cell comprises a native antigen for the receptor, a reporter transgene operably linked to a lentivirus structural protein, and a barcoded RNA, wherein the RNA encodes antigen information;
- combining the lentivirus with the population of cells;
- and
- sorting the population of cells based on the presence of the reporter.
A method of identifying a T-cell receptor and paired pMHC, the method comprising:
- providing an engineered lentivirus comprising a pMHC displayed on virus surface, a fusogen comprising a modified VSV-G viral envelope protein wherein the fusogen is capable of fusing the lentivirus to a host cell, wherein the host cell comprises a T-cell receptor for the PMHC, a reporter transgene operably linked to a lentivirus structural protein, and a barcoded RNA;
- combining the lentivirus with the population of cells;
- and
- sorting the population of cells based on the presence of the reporter thereby identifying the T-cell receptor.
A method of identifying a B-cell receptor or antibody, the method comprising:
- providing an engineered lentivirus comprising an epitope displayed on lentivirus surface wherein the epitope is operably linked with an ICAM1 transmembrane domain, a fusogen comprising a modified VSV-G viral envelope protein wherein the fusogen is capable of fusing the lentivirus to a host cell, wherein the host cell comprises a B-cell receptor for the intracellular epitope, a reporter transgene operably linked to a lentivirus structural protein, and a barcoded RNA;
- combining the lentivirus with the population of B cells;
- and
- sorting the population of cells based on the presence of the reporter thereby identifying the B-cell receptor or antibody.
A method of single-cell multiomics, comprising:
- providing an engineered lentivirus comprising a heterologous ligand displayed on the surface of the lentivirus, a fusogen comprising a modified VSV-G viral envelope protein wherein the fusogen is capable of fusing the lentivirus to a host cell, wherein the host cell comprises an endogenous receptor for the ligand, a reporter transgene operably linked to a lentivirus structural protein, and a RNA, wherein the RNA comprises an antigen sequence and a capture tag for single cell sequencing;
- and
- retrieving transcriptome and phenotype information simultaneously at the single cell level.
Dependencies are inferred from the claim text.