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Engineering primary T cells with chimeric antigen receptors for rewired responses to soluble ligands


The expression of synthetic receptors in primary T cells enables the programming of user-defined responses when designing T-cell therapies. Chimeric antigen receptors (CARs) are synthetic receptors that have demonstrated efficacy in cancer therapy by targeting immobilized antigens on the surface of malignant cells. Recently, we showed they can also rewire T-cell responses to soluble ligands. In contrast to other synthetic receptors, CARs are not only readily engineered by rational design, but also clinically translatable, with robust function in primary human T cells. This protocol discusses design principles for CARs responsive to soluble ligands and delineates steps for producing T cells expressing synthetic receptors. Functional assays for quantifying the ability of CAR T cells to sense and respond to soluble ligands are also presented. This protocol provides a framework for proficient immune-cell researchers to test novel T-cell therapies targeting soluble ligands in <2 weeks.

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Fig. 1: CAR structure and mechanisms for response to soluble ligands.
Fig. 2: Troubleshooting CAR expression and effector activity.
Fig. 3: Steps in the generation of CAR+ primary human T cells from human whole blood.
Fig. 4: Assessing functionality of the TGF-β CAR.
Fig. 5: Degranulation in response to soluble and immobilized target ligand.

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Data availability

The data analyzed to generate what is shown in this manuscript are compiled in the Supplementary Spreadsheet file. Individual examples of gating strategy are shown when appropriate. Data from Fig. 4 and Supplementary Fig. 3 have been used in a prior publication6.


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Several protocols presented reflect discussion and contributions from present and past members of the Chen lab, notably E. Zah, P. Ho, M.-y. Lin, and M. Lorenzini, as well as members of the M. Jensen lab (Seattle Children’s Research Institute). The NFAT reporter Jurkat T-cell line was a gift from A. Weiss (University of California, San Francisco). The NFκB reporter Jurkat T-cell line was a gift from X. Lin (University of Texas MD Anderson Cancer Center). This work was supported by the National Institutes of Health (grant DP5OD012133, UC CAI grant U54HL119893, and UCLA CTSI grant UL1TR001881 to Y.Y.C.). Z.L.C. was supported by an NIH F30 Fellowship (F30CA183528). A.J.H. was supported by the NIH Biotechnology Training in Biomedical Sciences and Engineering Program (T32 GM067555).

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Authors and Affiliations



Z.L.C., A.J.H., and Y.Y.C. conceptualized and wrote the manuscript. Z.L.C. and Y.Y.C. developed the protocol, with additional contributions as reflected in the Acknowledgements section.

Corresponding author

Correspondence to Yvonne Y. Chen.

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Competing interests

Y.Y.C. and Z.L.C. declare competing interests in the form of a patent application whose value may be affected by the publication of this work.

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Peer review information Nature Protocols thanks Carl June, Atsushi Okuma and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Key references using this protocol

Chang, Z. L. et al. Nat. Chem. Biol. 14, 317–324 (2018):

Hou, A. J., Chang, Z. L., Lorenzini, M. H., Zah, E. & Chen, Y. Y. Bioeng. Transl. Med. 3, 75–86 (2018):

Integrated supplementary information

Supplementary Fig. 1 Comparison of quantifying cytokine secreted into supernatant and intracellular cytokine staining.

CD4 TGF-β CAR-T cells were stimulated with 5 ng/mL TGF-β for 24 hours. Side-by-side samples were prepared for analysis of supernatant or intracellular cytokine staining. a, Quantification of IFN-γ and TNF-α levels secreted into supernatant using a cytometric bead array showed comparable IFN-γ and TNF-α production. Data points from n = 3 (without TGF-β) or n = 2 (with TGF-β) samples are shown with means ± 1 standard deviation or total ranges, respectively. b, In contrast, intracellular cytokine staining detected more robust TNF-α production than IFN-γ production, indicating lower sensitivity for IFN-γ staining using the protocol described.

Supplementary Fig. 2 Cell sorting results are impacted by transduction efficiency of starting material.

Cells lines A and B were generated by transduction with a synthetic construct linked via a T2A “self-cleaving” peptide to truncated EGFR (EGFRt). The poorly transduced cell line (Cell Line A) and well-transduced cell line (Cell Line B) were then sorted according to steps 34-41. The poorly transduced starting material yielded an enriched product that was only 68.5% pure, while the well-transduced cell line yielded a 97.1% pure population.

Supplementary Fig. 3 Gating strategy for flow cytometry experiments.

a, An example gating scheme for all flow cytometry experiments is shown. Initial FSC-Area/SSC-Area gates are drawn to remove debris and dead cells. A subsequent FSC-Area/FSC-Height gate demarcates singlet events. b-d, Histograms are shown for flow cytometry of TGF-β CAR-expressing cell lines, gated for viable singlets, demonstrating upregulation of (b) NFAT-driven EGFP, (c) NFκB-driven EGFP, and (d) CD69. Plots in b-d are representative of data used to generate the bar graphs in Fig. 4a–c. bd adapted from ref. 6, Springer Nature.

Supplementary information

Supplementary Information

Supplementary Figs. 1–3.

Reporting Summary

Supplementary Data 1

Supplementary Spreadsheet

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Chang, Z.L., Hou, A.J. & Chen, Y.Y. Engineering primary T cells with chimeric antigen receptors for rewired responses to soluble ligands. Nat Protoc 15, 1507–1524 (2020).

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