De novo identification of CD4+ T cell epitopes

Paul M Zdinak; Nishtha Trivedi; Stephanie Grebinoski; Jessica Torrey; Eduardo Zarate Martinez; Salome Martinez; Louise Hicks; Rashi Ranjan; Venkata Krishna Kanth Makani; Mary Melissa Roland; Lyubov Kublo; Sanya Arshad; Mark S Anderson; Dario A A Vignali; Alok V Joglekar

doi:10.1038/s41592-024-02255-0

De novo identification of CD4⁺ T cell epitopes

Nat Methods. 2024 Apr 24. doi: 10.1038/s41592-024-02255-0. Online ahead of print.

Authors

Paul M Zdinak^{1

2

3}, Nishtha Trivedi^#^{1

2}, Stephanie Grebinoski^#^{1

3}, Jessica Torrey^{1

2}, Eduardo Zarate Martinez^{1

2

4}, Salome Martinez^{1

2}, Louise Hicks^{1

2}, Rashi Ranjan^{1

2}, Venkata Krishna Kanth Makani^{1

2}, Mary Melissa Roland^{1

2}, Lyubov Kublo^{1

2}, Sanya Arshad^{1

2}, Mark S Anderson⁵, Dario A A Vignali^{1

6

7}, Alok V Joglekar^{8

9

10}

Affiliations

¹ Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
² Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
³ Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
⁴ Microbiology and Immunology Diversity Scholars Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
⁵ Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
⁶ Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
⁷ Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
⁸ Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. joglekar@pitt.edu.
⁹ Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. joglekar@pitt.edu.
¹⁰ Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA. joglekar@pitt.edu.

^# Contributed equally.

PMID: 38658646
DOI: 10.1038/s41592-024-02255-0

Abstract

CD4⁺ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4⁺ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4⁺ T cell antigen discovery. SABR-IIs can present epitopes to CD4⁺ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4⁺ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.

Abstract

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