Search

Microbial organisms have key roles in numerous physiological processes in the human body and have recently been shown to modify the response to immune checkpoint inhibitors1,2. Here we aim to address the role of microbial organisms and their potential role in immune reactivity against glioblastoma. We demonstrate that HLA molecules of both glioblastoma tissues and tumour cell lines present bacteria-specific peptides. This finding prompted us to examine whether tumour-infiltrating lymphocytes (TILs) recognize tumour-derived bacterial peptides. Bacterial peptides eluted from HLA class II molecules are recognized by TILs, albeit very weakly. Using an unbiased antigen discovery approach to probe the specificity of a TIL CD4+ T cell clone, we show that it recognizes a broad spectrum of peptides from pathogenic bacteria, commensal gut microbiota and also glioblastoma-related tumour antigens. These peptides were also strongly stimulatory for bulk TILs and peripheral blood memory cells, which then respond to tumour-derived target peptides. Our data hint at how bacterial pathogens and bacterial gut microbiota can be involved in specific immune recognition of tumour antigens. The unbiased identification of microbial target antigens for TILs holds promise for future personalized tumour vaccination approaches., Nature, 617 (7962), ISSN:0028-0836, ISSN:1476-4687

Single-cell RNA sequencing data and TCR data from "Autoreactive napsin A-specific T cells are enriched in lung tumors and inflammatory lung lesions during checkpoint blockade", Berner et al. &nbsp

To understand and treat immunology-related diseases, a comprehensive, unbiased characterization of major histocompatibility complex (MHC) peptide ligands is of key importance. Preceding the analysis by mass spectrometry, MHC class I peptide ligands are typically isolated by MHC immunoaffinity chromatography (MHC-IAC) and less often by mild acid elution (MAE). MAE may provide a cheap alternative to MHC-IAC for suspension cells but has been hampered by the high number of contaminating, MHC-unrelated peptides. Here, we optimized MAE, yielding MHC peptide ligand purities of more than 80%. When compared with MHC-IAC, obtained peptides were similar in numbers, identities, and to a large extent intensities, while the percentage of cysteinylated peptides was 5 times higher in MAE. The latter benefitted the discovery of MHC-allotype-specific, distinct cysteinylation frequencies at individual positions of MHC peptide ligands. MAE revealed many MHC ligands with unmodified, N-terminal cysteine residues which get lost in MHC-IAC workflows. The results support the idea that MAE might be particularly valuable for the high-confidence analysis of post-translational modifications by avoiding the exposure of the investigated peptides to enzymes and reactive molecules in the cell lysate. Our improved and carefully documented MAE workflow represents a high-quality, cost-effective alternative to MHC-IAC for suspension cells. ISSN:1535-3893 ISSN:1535-3907

Increased concentrations of circulating chromatin, especially oligo-nucleosomes, are observed in sepsis, cancer and some inflammatory autoimmune diseases like systemic lupus erythematosus (SLE). In SLE, circulating nucleosomes mainly result from increased apoptosis and decreased clearance of apoptotic cells. Once released, nucleosomes behave both as an autoantigen and as a damage-associated molecular pattern (DAMP) by activating several immune cells, especially pro-inflammatory cells. Deoxyribonuclease 1 (DNase1) is a major serum nuclease whose activity is decreased in mouse and human lupus. Likewise, the mitochondrial chaperone tumor necrosis factor (TNF) receptor-associated protein-1 (Trap1) protects against oxidative stress, which is increased in SLE. Here, using wild type, DNase1-deficient and DNase1/Trap1-deficient mice, we demonstrate that DNase1 is a major serum nuclease involved in chromatin degradation, especially when the plasminogen system is activated. In vitro degradation assays show that chromatin digestion is strongly impaired in serum from DNase1/Trap1-deficient mice as compared to wild type mice. In vivo, after injection of purified chromatin, clearance of circulating chromatin is delayed in DNase1/Trap1-deficient mice in comparison to wild type mice. Since defective chromatin clearance may lead to chromatin deposition in tissues and subsequent immune cell activation, spleen cells were stimulated in vitro with chromatin. Splenocytes were activated by chromatin, as shown by interleukin (IL)-12 secretion and CD69 up-regulation. Moreover, cell activation was exacerbated when Trap1 is deficient. Importantly, we also show that cytokines involved in lupus pathogenesis down-regulate Trap1 expression in splenocytes. Therefore, combined low activities of both DNase1 and Trap1 lead to an impaired degradation of chromatin in vitro, delayed chromatin clearance in vivo and enhanced activation of immune cells. This situation may be encountered especially, but not exclusively, in SLE by the negative action of cytokines on Trap1 expression.

Biomaterials play an increasing role in clinical applications and regenerative medicine. A perfectly designed biomaterial should restore the function of damaged tissue without triggering an undesirable immune response, initiate self-regeneration of the surrounding tissue and gradually degrade after implantation. The immune system is well recognized to play a major role in influencing the biocompatibility of implanted medical devices. To obtain a better understanding of the effects of biomaterials on the immune response, we have developed a highly sensitive novel test system capable of examining changes in the immune system by biomaterial. Here, we evaluated for the first time the immunopeptidome, a highly sensitive system that reflects cancer transformation, virus or drug influences and passes these cellular changes directly to T cells, as a test system to examine the effects of contact with materials. Since monocytes are one of the first immune cells reacting to biomaterials, we have tested the influence of different materials on the immunopeptidome of the monocytic THP-1 cell line. The tested materials included stainless steel, aluminum, zinc, high-density polyethylene, polyurethane films containing zinc diethyldithiocarbamate, copper, and zinc sulfate. The incubation with all material types resulted in significantly modulated peptides in the immunopeptidome, which were material-associated. The magnitude of induced changes in the immunopeptidome after the stimulation appeared comparable to that of bacterial lipopolysaccharides (LPS). The source proteins of many detected peptides are associated with cytotoxicity, fibrosis, autoimmunity, inflammation, and cellular stress. Considering all tested materials, it was found that the LPS-induced cytotoxicity-, inflammation- and cellular stress-associated HLA class I peptides were mainly induced by aluminum, whereas HLA class II peptides were mainly induced by stainless steel. These findings provide the first insights into the effects of biomaterials on the immunopeptidome. A more thorough understanding of these effects may enable the design of more biocompatible implant materials using in vitro models in future. Such efforts will provide a deeper understanding of possible immune responses induced by biomaterials such as fibrosis, inflammation, cytotoxicity, and autoimmune reactions.

Background: We previously showed that the bacterial lipopeptide Pam3Cys-Ser-Ser, meanwhile established as a toll-like receptor (TLR) 1/2 ligand, acts as a strong adjuvant for the induction of virus specific CD8+ T cells in mice, when covalently coupled to a synthetic peptide.Case presentation: We now designed a new water-soluble synthetic Pam3Cys-derivative, named XS15 and characterized it in vitro by a TLR2 NF-κB luciferase reporter assay. Further, the capacity of XS15 to activate immune cells and stimulate peptide-specific CD8+ T and NK cells by 6-sulfo LacNAc+ monocytes was assessed by flow cytometry as well as cytokine induction using immunoassays. The induction of a functional immune response after vaccination of a volunteer with viral peptides was assessed by ELISpot assay and flow cytometry in peripheral blood cells and infiltrating cells at the vaccination site, as well as by immunohistochemistry and imaging.XS15 induced strong ex vivo CD8+ and TH1 CD4+ responses in a human volunteer upon a single injection of XS15 mixed to uncoupled peptides in a water-in-oil emulsion (Montanide™ ISA51 VG). A granuloma formed locally at the injection site containing highly activated functional CD4+ and CD8+ effector memory T cells. The total number of vaccine peptide-specific functional T cells was experimentally assessed and estimated to be 3.0 × 105 in the granuloma and 20.5 × 106 in peripheral blood.Conclusion: Thus, in one volunteer we show a granuloma forming by peptides combined with an efficient adjuvant in a water-in-oil-emulsion, inducing antigen specific T cells detectable in circulation and at the vaccination site, after one single vaccination only. The ex vivo T cell responses in peripheral blood were detectable for more than one year and could be strongly boosted by a second vaccination. Hence, XS15 is a promising adjuvant candidate for peptide vaccination, in particular for tumor peptide vaccines in a personalized setting.

Antigen stimulation of T-cell receptors on T cells induces an immediate increase in ligand-binding affinity and clustering in the plasma membrane of beta2-integrins, resulting in a strong binding to intercellular adhesion molecules (ICAMs) on target cells. This firm adhesion, e.g. of cytotoxic T cells to virus-infected or tumor cells with formation of cytotoxic synapses is required for target cell lysis. Therefore, upregulation of integrin-mediated adhesion after stimulation identifies functional effector T cells. Here we present a novel flow cytometry assay to enumerate antigen-specific CD8+ T cells using soluble multimeric ICAM1-Fc-F(ab’)2 fluorescent complexes to identify integrin activation induced after short-term stimulation in vitro. By optimizing and validating this assay we were able to identify pathogen-, tumor- or vaccine-induced CD8+T cells, and show its feasibility for assessing and isolating live, functional antigen-specific CD8+T cells. Performing coexpression analyses, we found that antigen-stimulated cells that expressed cytokines and mobilized CD107a were predominantly highly adherent CD8+T cells. Finally, CD8+ T cells that upregulated integrins were shown to mediate cytolytic activity in an antigen-specific manner. The most striking advantage of this method is the short-time incubation (several minutes) that is necessary to identify and isolate viable antigen-specific cytotoxic T cells by assessing upregulation of T cell adhesiveness, a critical step for elaborating multiple effector functions, including cytotoxicity and cytokine production.

Funder: Deutschen Konsortium für Translationale Krebsforschung; funder-id: http://dx.doi.org/10.13039/501100012353, Funder: Natural and Medical Sciences Institute (D), Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek's disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek's disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek's disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek's disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.

Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek’s disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek’s disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek’s disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek’s disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.

Cancer immunotherapy has presented itself as a promising approach in the treatment of cancers. Actively incorporating the immune system in cancer treatment has proven to be successful in many different therapeutic approaches, ranging from CAR-T therapy or adoptive cellular transfer to peptide or RNA-based vaccines or biologics. One particularly attractive target for modifications in adoptive cellular transfer or adoptive cell therapy is the T cell receptor. This molecule expressed by T cells can bind to major histocompatibility complex molecules on target cells where they present peptide ligands derived from extra- or intracellular proteins by degradation. Successful recognition can lead to activation of the T cell and an immune response. Thus, introducing TCRs with optimal binding affinity for activation that are specific for a particular peptide-MHC known to be expressed on cancer cells has emerged as an attractive strategy. In anti-cancer biologics, TCR variable domains have also been used in place of antibodies in bispecific constructs that combine a tumor targeting moiety with a T cell engager like an anti-CD3 antibody. Here, the goal is to specifically bind to tumor cells and broadly activate T cells within the tumor microenvironment. In both approaches, reaching the optimal affinity may require increasing candidate TCRs affinity through maturation. Since the TCR repertoire seems to have evolutionally evolved to cover the very large number of possible peptide-MHC complexes by cross-reactivity of individual TCRs, these maturations may entail unwanted affinity changes towards peptide-MHCs that are not the intended target and express on healthy tissues as well for example, severely compromising the clinical safety of these approaches. To counteract these tendencies during development of these approaches, strategies were evaluated to determine the binding motif and potential cross-reactivity of either cellularly expressed or soluble TCRs with affinities which can be encountered in the natural TCR repertoire, as well as highly affinity maturated TCRs in soluble bispecific constructs. The different screening strategies were evaluated both with well-established cell biological approaches to determine T cell activation and more recent biochemical methods like bio-layer interferometry to directly measure binding kinetics between TCRs and peptide-HLA molecules. To facilitate screenings with the latter platform, a newly developed empty HLA-A*02:01 mutant stabilized by a disulfide bridge is introduced that greatly facilitates the generation of large peptide-HLA libraries for screenings. The different combinations of screening strategies and measurement method were compared within each TCR group with respect to sensitivity and usefulness. In addition, an approach is demonstrated to convert a determined binding motif into a search motif and used to identify off-target binders for high-affinity bispecific TCR constructs. Krebsimmuntherapien haben sich als vielversprechender Ansatz in der Behandlung von Krebserkrankungen herausgestellt. Ein besonders attraktives Ziel für Modifikationen im Rahmen von adoptiver Zelltherapie ist der T-Zell-Rezeptor (TCR), da dieser über die Erkennung spezifischer Peptid-HLA Komplexe, die Abbauprodukte interner- oder extrazellulärer Proteine präsentieren, Immunantworten unter anderem gegen Tumorzellen auslösen kann. In einer weiteren Anwendung dieses Konzeptes kann der T-Zell-Rezeptor auch in Form eines löslichen bisepzifischen Antikörpers bereitgestellt werden, der eine Tumorzell-bindende Domäne mit einer T-Zell-aktivierenden Domäne wie einem anti-CD3 Antikörper verbindet. In beiden Anwendungsfällen kann es notwendig sein, die Affinität des TCRs durch Maturierung zu erhöhen, um eine optimale Immunantwort auszulösen. Aufgrund der inhärent kreuzreaktiven Natur des TCR Repertoires können solche Eingriffe aber gleichzeitig unerwünschte Affinitätsänderungen gegenüber Peptid-HLA Komplexen hervorrufen, die auf gesunden Zellen exprimiert werden. Um solchen Tendenzen entgegen zu wirken wurden Strategien zur Bestimmung von TCR Bindemotifen und damit Kreuzreaktivitäten für zelluläre exprimierte oder in bispezifischen Konstrukten befindlichen TCRs, sowohl mit zellbiologischen Ansätzen zur Bestimmung der T-Zell Aktivierung als auch mit biochemischen Methoden zur direkten Messung der Bindung zwischen TCR und Peptid-HLA Komplex, untersucht und im Vortrag präsentiert. Um letztere Untersuchungen zu vereinfach wird eine neue entwickelte leere Disulfid-stabilisierte Mutante von HLA-A*02:01 vorgestellt, die die Erstellung großer Peptid-MHC Bibliotheken stark vereinfacht.