Tuberculosis (TB) remains one of the deadliest infectious diseases worldwide, posing great social and economic burden to affected countries. Novel vaccine approaches are needed to increase protective immunity against the causative agent Mycobacterium tuberculosis (Mtb) and to reduce the development of active TB disease in latently infected individuals. Donor-unrestricted T cell responses represent such novel potential vaccine targets. HLA-E-restricted T cell responses have been shown to play an important role in protection against TB and other infections, and recent studies have demonstrated that these cells can be primed in vitro. However, the identification of novel pathogen-derived HLA-E binding peptides presented by infected target cells has been limited by the lack of accurate prediction algorithms for HLA-E binding. In this study, we developed an improved HLA-E binding peptide prediction algorithm and implemented it to identify (to our knowledge) novel Mtb-derived peptides with capacity to induce CD8+ T cell activation and that were recognized by specific HLA-E-restricted T cells in Mycobacterium-exposed humans. Altogether, we present a novel algorithm for the identification of pathogen- or self-derived HLA-E-presented peptides.

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Characterization of immune cells is essential to advance our understanding of immunology and flow cytometry is an important tool in this context. Addressing both cellular phenotype and antigen-specific functional responses of the same cells is valuable to achieve a more integrated understanding of immune cell behavior and maximizes information obtained from precious samples. Until recently, panel size was limiting, resulting in panels generally focused on either deep immunophenotyping or functional readouts. Ongoing developments in the field of (spectral) flow cytometry have made panels of 30 + markers more accessible, opening up possibilities for advanced integrated analyses. Here, we optimized immune phenotyping by co-detection of markers covering chemokine receptors, cytokines and specific T cell/peptide tetramer interaction using a 32-color panel. Such panels enable integrated analysis of cellular phenotypes and markers assessing the quality of immune responses and will contribute to our understanding of the immune system.

There is growing interest in HLA‐E‐restricted T‐cell responses as a possible novel, highly conserved, vaccination targets in the context of infectious and malignant diseases. The developing field of HLA multimers for the detection and study of peptide‐specific T cells has allowed the in‐depth study of TCR repertoires and molecular requirements for efficient antigen presentation and T‐cell activation. In this study, we developed a method for efficient peptide thermal exchange on HLA‐E monomers and multimers allowing the high‐throughput production of HLA‐E multimers. We optimized the thermal‐mediated peptide exchange, and flow cytometry staining conditions for the detection of TCR and NKG2A/CD94 receptors, showing that this novel approach can be used for high‐throughput identification and analysis of HLA‐E‐binding peptides which could be involved in T‐cell and NK cell‐mediated immune responses. Importantly, our analysis of NKG2A/CD94 interaction in the presence of modified peptides led to new molecular insights governing the interaction of HLA‐E with this receptor. In particular, our results reveal that interactions of HLA‐E with NKG2A/CD94 and the TCR involve different residues. Altogether, we present a novel HLA‐E multimer technology based on thermal‐mediated peptide exchange allowing us to investigate the molecular requirements for HLA‐E/peptide interaction with its receptors.