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.

CD4 ⁺ T 细胞识别 II 类主要组织相容性复合物 (MHC-II) 分子上呈递的肽抗原以执行其功能。 T 细胞受体序列的显着多样性和缺乏 MHC-II 抗原发现方法使得分析 CD4 ⁺ T 细胞的特异性具有挑战性。我们扩展了信号传导和抗原呈递双功能受体平台，以编码呈递共价连接肽 (SABR-II) 的 MHC-II 分子，用于 CD4 ⁺ T 细胞抗原发现。 SABR-II 可以向 CD4 ⁺ T 细胞呈递表位，并在识别后诱导信号传导，从而产生可读的输出。此外，SABR-II 设计在信号传导和部署到 T 细胞和 B 细胞方面是模块化的。在这里，我们证明呈现内源性和非连续表位的 SABR-II 文库可用于 1 型糖尿病背景下的抗原发现。 SABR-II 文库提供了一种快速、灵活、可扩展且通用的方法，可使用实验和计算方法从单细胞 RNA 测序数据中从头识别 CD4 ^{+ T 细胞配体。}