Author response: Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

HLA class I presentation of pathogen-derived peptide ligands is essential for CD8+ T-cell recognition of Toxoplasma gondii infected cells. Currently, little data exist pertaining to peptides that are presented after T. gondii infection. Herein we purify HLA-A*02:01 complexes from T. gondii infected cells and characterize the peptide ligands using LCMS. We identify 195 T. gondii encoded ligands originating from both secreted and cytoplasmic proteins. Surprisingly, T. gondii ligands are significantly longer than uninfected host ligands, and these longer pathogen-derived peptides maintain a canonical N-terminal binding core yet exhibit a C-terminal extension of 1–30 amino acids. Structural analysis demonstrates that binding of extended peptides opens the HLA class I F’ pocket, allowing the C-terminal extension to protrude through one end of the binding groove. In summary, we demonstrate that unrealized structural flexibility makes MHC class I receptive to parasite-derived ligands that exhibit unique C-terminal peptide extensions.

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Decision letter: Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

10.7554/elife.12556.020 ◽

2015 ◽

Keyword(s):

Toxoplasma Gondii ◽

Hla Class I ◽

Peptide Ligands ◽

Class I ◽

Binding Groove

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Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Nature Communications ◽

10.1038/s41467-020-19142-9 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Laura C. Demmers ◽

Kai Kretzschmar ◽

Arne Van Hoeck ◽

Yotam E. Bar-Epraïm ◽

Henk W. P. van den Toorn ◽

...

Keyword(s):

Damage Control ◽

Colorectal Cancer Patient ◽

Human Leukocyte ◽

Hla Class I ◽

Peptide Ligands ◽

Class I ◽

Viable Option ◽

Leukocyte Antigen ◽

Peptide Presentation ◽

Tumor Mutational Burden

Abstract Tumor heterogeneity is a major cause of therapeutic resistance. Immunotherapy may exploit alternative vulnerabilities of drug-resistant cells, where tumor-specific human leukocyte antigen (HLA) peptide ligands are promising leads to invoke targeted anti-tumor responses. Here, we investigate the variability in HLA class I peptide presentation between different clonal cells of the same colorectal cancer patient, using an organoid system. While clone-specific differences in HLA peptide presentation were observed, broad inter-clone variability was even more prevalent (15–25%). By coupling organoid proteomics and HLA peptide ligandomics, we also found that tumor-specific ligands from DNA damage control and tumor suppressor source proteins were prominently presented by tumor cells, coinciding likely with the silencing of such cytoprotective functions. Collectively, these data illustrate the heterogeneous HLA peptide presentation landscape even within one individual, and hint that a multi-peptide vaccination approach against highly conserved tumor suppressors may be a viable option in patients with low tumor-mutational burden.

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The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02

Frontiers in Immunology ◽

10.3389/fimmu.2021.796584 ◽

2021 ◽

Vol 12 ◽

Author(s):

Soumya Mukherjee ◽

Alvaro Sanchez-Bernabeu ◽

Laura C. Demmers ◽

Wei Wu ◽

Albert J. R. Heck

Keyword(s):

Lymphoblastoid Cell Line ◽

Consensus Sequence ◽

Hla Antigens ◽

Hla Class I ◽

Class I ◽

Small Subset ◽

Post Translational Modifications ◽

Peptide Antigens ◽

Binding Groove ◽

Hla Ligandome

Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neoantigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neoantigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from the JY B cell lymphoblastoid cell line, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. This cumulative list of O-GlcNAcylated HLA peptides were derived from normal and cancerous origin, as well as tissue specimen. Remarkably, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. From this list, we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B*07:02 allele. This allele loads peptides with a Proline residue anchor at position 2, and features a binding groove that can accommodate well the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T), essentially explaining why HLA-B*07:02 is a favoured binding allele. The observations drawn from the compiled list, may assist in the prediction of novel O-GlcNAcylated HLA antigens, which will be best presented by patients harbouring HLA-B*07:02 or related alleles that use Proline as anchoring residue.

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Impaired intracellular transport and cell surface expression of nonpolymorphic HLA-E: evidence for inefficient peptide binding.

Journal of Experimental Medicine ◽

10.1084/jem.176.4.1083 ◽

1992 ◽

Vol 176 (4) ◽

pp. 1083-1090 ◽

Cited By ~ 46

Author(s):

M Ulbrecht ◽

J Kellermann ◽

J P Johnson ◽

E H Weiss

Keyword(s):

Cell Surface ◽

Intracellular Transport ◽

Hla Class I ◽

Surface Expression ◽

Myeloma Cell ◽

Peptide Ligands ◽

Class I ◽

Cell Surface Expression ◽

Trimolecular Complex ◽

Beta 2 Microglobulin

The assembly of the classical, polymorphic major histocompatibility complex class I molecules in the endoplasmic reticulum requires the presence of peptide ligands and beta 2-microglobulin (beta 2m). Formation of this trimolecular complex is a prerequisite for efficient transport to the cell surface, where presented peptides are scanned by T lymphocytes. The function of the other class I molecules is in dispute. The human, nonclassical class I gene, HLA-E, was found to be ubiquitously transcribed, whereas cell surface expression was difficult to detect upon transfection. Pulse chase experiments revealed that the HLA-E heavy chain in transfectants, obtained with the murine myeloma cell line P3X63-Ag8.653 (X63), displays a significant reduction in oligosaccharide maturation and intracellular transport compared with HLA-B27 in corresponding transfectants. The accordingly low HLA-E cell surface expression could be significantly enhanced by either reducing the culture temperature or by supplementing the medium with human beta 2m, suggesting inefficient binding of endogenous peptides to HLA-E. To analyze whether HLA-E binds peptides and to identify the corresponding ligands, fractions of acid-extracted material from HLA-E/X63 transfectants were separated by reverse phase HPLC and were tested for their ability to enhance HLA-E cell surface expression. Two fractions specifically increased the HLA class I expression on the HLA-E transfectant clone.

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