Home NATURALEZA A general system for targeting MHC class II–antigen complex via a single...

A general system for targeting MHC class II–antigen complex via a single adaptable loop

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  • Weiss, S. & Bogen, B. MHC class II-restricted presentation of intracellular antigen. Cell 64, 767–776 (1991).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Axelrod, M. L., Cook, R. S., Johnson, D. B. & Balko, J. M. Biological consequences of MHC-II expression by tumor cells in cancer. Clin. Cancer Res. 25, 2392–2402 (2019).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Nanaware, P. P., Cruz, J., Khaja, M., Shaffer, S. A. & Stern, L. Inhibited MHC class I and MHC class II antigen processing and presentation upon SARS-CoV-2 infection. J. Immunol. 210, 222.02 (2023).

  • Gras, S. CD4+ T cell mediated HLA class II cross-restriction in HIV controllers. J. Immunol. 204, eaat0687 (2020).

    Article 

    Google Scholar
     

  • Zakharova, M. Y., Belyanina, T. A., Sokolov, A. V., Kiselev, I. S. & Mamedov, A. E. The contribution of major histocompatibility complex class II genes to an association with autoimmune diseases. Acta Naturae 11, 4–12 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wieber, K., Zimmer, C. L. & Hertl, M. Detection of autoreactive CD4+ T cells by MHC class II multimers in HLA-linked human autoimmune diseases. J. Clin. Invest. 131, e148674 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Davies, C. S. et al. Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. Microbiome 10, 41 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wosen, J. E., Mukhopadhyay, D., Macaubas, C. & Mellins, E. D. Epithelial MHC class II expression and its role in antigen presentation in the gastrointestinal and respiratory tracts. Front. Immunol. 9, 2144 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Roche, P. A. & Furuta, K. The ins and outs of MHC class II-mediated antigen processing and presentation. Nat. Rev. Immunol. 15, 203–216 (2015).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Pishesha, N., Harmand, T. J. & Ploegh, H. L. A guide to antigen processing and presentation. Nat. Rev. Immunol. 22, 751–764 (2022).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Stern, L. J. & Santambrogio, L. The melting pot of the MHC II peptidome. Curr. Opin. Immunol. 40, 70–77 (2016).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Baulu, E., Gardet, C., Chuvin, N. & Depil, S. TCR-engineered T cell therapy in solid tumors: state of the art and perspectives. Sci. Adv. 9, eadf3700 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Weber, K. S., Donermeyer, D. L., Allen, P. M. & Kranz, D. M. Class II-restricted T cell receptor engineered in vitro for higher affinity retains peptide specificity and function. Proc. Natl Acad. Sci. USA 102, 19033–19038 (2005).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Li, Y., Jiang, W. & Mellins, E. D. TCR-like antibodies targeting autoantigen–MHC complexes: a mini-review. Front. Immunol. 13, 968432 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Poncette, L., Chen, X., Lorenz, F. K. & Blankenstein, T. Effective NY-ESO-1-specific MHC II-restricted T cell receptors from antigen-negative hosts enhance tumor regression. J. Clin. Invest. 129, 324–335 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Spanier, J. A. et al. Tregs with an MHC class II peptide-specific chimeric antigen receptor prevent autoimmune diabetes in mice. J. Clin. Invest. 133, e168601 (2023).

    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hoydahl, L. S., Frick, R., Sandlie, I. & Loset, G. A. Targeting the MHC ligandome by use of TCR-like antibodies. Antibodies 8, 32 (2019).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Wucherpfennig, K. W. & Strominger, J. L. Molecular mimicry in T cell-mediated autoimmunity: viral peptides activate human T cell clones specific for myelin basic protein. Cell 80, 695–705 (1995).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Lunemann, J. D. et al. EBNA1-specific T cells from patients with multiple sclerosis cross react with myelin antigens and co-produce IFN-γ and IL-2. J. Exp. Med. 205, 1763–1773 (2008).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Jardetzky, T. S. et al. Crystallographic analysis of endogenous peptides associated with HLA-DR1 suggests a common, polyproline II-like conformation for bound peptides. Proc. Natl Acad. Sci. USA 93, 734–738 (1996).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hahn, M., Nicholson, M. J., Pyrdol, J. & Wucherpfennig, K. W. Unconventional topology of self peptide–major histocompatibility complex binding by a human autoimmune T cell receptor. Nat. Immunol. 6, 490–496 (2005).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Beringer, D. X. et al. T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex. Nat. Immunol. 16, 1153–1161 (2015).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Cole, D. K. et al. Human TCR-binding affinity is governed by MHC class restriction. J. Immunol. 178, 5727–5734 (2007).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Hennecke, J., Carfi, A. & Wiley, D. C. Structure of a covalently stabilized complex of a human αβ T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1. EMBO J. 19, 5611–5624 (2000).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hennecke, J. & Wiley, D. C. Structure of a complex of the human α/β T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity. J. Exp. Med. 195, 571–581 (2002).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Broughton, S. E. et al. Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease. Immunity 37, 611–621 (2012).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Frick, R. et al. A high-affinity human TCR-like antibody detects celiac disease gluten peptide–MHC complexes and inhibits T cell activation. Sci. Immunol. 6, eabg4925 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hülsmeyer, M. et al. A major histocompatibility complex–peptide-restricted antibody and T cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1–MAGE-A1 in complex with Fab-Hyb3. J. Biol. Chem. 280, 2972–2980 (2005).

    Article 
    PubMed 

    Google Scholar
     

  • Ataie, N. et al. Structure of a TCR-mimic antibody with target predicts pharmacogenetics. J. Mol. Biol. 428, 194–205 (2016).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Starwalt, S. E., Masteller, E. L., Bluestone, J. A. & Kranz, D. M. Directed evolution of a single-chain class II MHC product by yeast display. Protein Eng. 16, 147–156 (2003).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Dahan, R. & Reiter, Y. T-cell-receptor-like antibodies—generation, function and applications. Expert Rev. Mol. Med. 14, e6 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Cao, L. X. et al. Design of protein-binding proteins from the target structure alone. Nature 605, 551–560 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Wang, L. et al. Crystal structure of a complete ternary complex of TCR, superantigen and peptide–MHC. Nat. Struct. Mol. Biol. 14, 169–171 (2007).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Deacy, A. M., Gan, S. K. & Derrick, J. P. Superantigen recognition and interactions: functions, mechanisms and applications. Front. Immunol. 12, 731845 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Hodtsev, A. S., Choi, Y. W., Spanopoulou, E. & Posnett, D. N. Mycoplasma superantigen is a CDR3-dependent ligand for the T cell antigen receptor. J. Exp. Med. 187, 319–327 (1998).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Huang, P. S. et al. RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS ONE 6, e24109 (2011).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Wintjens, R. T., Rooman, M. J. & Wodak, S. J. Automatic classification and analysis of αα-turn motifs in proteins. J. Mol. Biol. 255, 235–253 (1996).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Mandic, M. et al. One NY-ESO-1-derived epitope that promiscuously binds to multiple HLA-DR and HLA-DP4 molecules and stimulates autologous CD4+ T cells from patients with NY-ESO-1-expressing melanoma. J. Immunol. 174, 1751–1759 (2005).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Liu, R., Jiang, W. & Mellins, E. D. Yeast display of MHC-II enables rapid identification of peptide ligands from protein antigens (RIPPA). Cell Mol. Immunol. 18, 1847–1860 (2021).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Jiang, W. & Boder, E. T. High-throughput engineering and analysis of peptide binding to class II MHC. Proc. Natl Acad. Sci. USA 107, 13258–13263 (2010).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kowalsky, C. A. et al. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J. Biol. Chem. 290, 26457–26470 (2015).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kowalsky, C. A. et al. High-resolution sequence-function mapping of full-length proteins. PLoS ONE 10, e0118193 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Holland, C. J., Cole, D. K. & Godkin, A. Re-directing CD4 T cell responses with the flanking residues of MHC class II-bound peptides: the core is not enough. Front. Immunol. 4, 172 (2013).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Mellins, E. D. & Stern, L. J. HLA-DM and HLA-DO, key regulators of MHC-II processing and presentation. Curr. Opin. Immunol. 26, 115–122 (2014).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Abualrous, E. T. et al. MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Nat. Chem. Biol. 19, 1196–1204 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Denzin, L. K., Robbins, N. F., Carboynewcomb, C. & Cresswell, P. Assembly and intracellular transport of HLA-DM and correction of the class II antigen-processing defect in T2 cells. Immunity 1, 595–606 (1994).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Abualrous, E. T., Sticht, J. & Freund, C. Major histocompatibility complex (MHC) class I and class II proteins: impact of polymorphism on antigen presentation. Curr. Opin. Immunol. 70, 95–104 (2021).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Ghosh, P., Amaya, M., Mellins, E. & Wiley, D. C. The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Nature 378, 457–462 (1995).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Oh, D. Y. & Bang, Y. J. HER2-targeted therapies—a role beyond breast cancer. Nat. Rev. Clin. Oncol. 17, 33–48 (2020).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Sulzer, D. et al. Erratum: T cells from patients with Parkinson’s disease recognize α-synuclein peptides. Nature 549, 292 (2017).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kim, C. Y., Quarsten, H., Bergseng, E., Khosla, C. & Sollid, L. M. Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease. Proc. Natl Acad. Sci. USA 101, 4175–4179 (2004).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Nguyen, T. B. et al. Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides. J. Biol. Chem. 292, 9218–9228 (2017).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Kassardjian, A. et al. Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses. Cell Rep. 42, 112391 (2023).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Jensen, K. K. et al. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154, 394–406 (2018).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Van Deventer, J. A. & Wittrup, K. D. Yeast surface display for antibody isolation: library construction, library screening, and affinity maturation. Methods Mol. Biol. 1131, 151–181 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Chen, S. W. et al. Analysis of SPR signal by using optimized Savitzky–Golay filter. Spectrosc. Spect. Anal. 35, 1124–1128 (2015).

    CAS 

    Google Scholar
     

  • Steinle, A. & Schendel, D. J. HLA class I alleles of LCL 721 and 174 × CEM.T2 (T2). Tissue Antigens 44, 268–270 (1994).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Jiang, W. et al. pH-susceptibility of HLA-DO tunes DO/DM ratios to regulate HLA-DM catalytic activity. Sci. Rep. 5, 17333 (2015).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Busch, R., Doebele, R. C., Patil, N. S., Pashine, A. & Mellins, E. D. Accessory molecules for MHC class II peptide loading. Curr. Opin. Immunol. 12, 99–106 (2000).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Alvaro-Benito, M., Wieczorek, M., Sticht, J., Kipar, C. & Freund, C. HLA-DMA polymorphisms differentially affect MHC class II peptide loading. J. Immunol. 194, 803–816 (2015).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Echols, N. et al. Graphical tools for macromolecular crystallography in PHENIX. J. Appl. Crystallogr. 45, 581–586 (2012).

    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar
     

  • Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

    Article 
    PubMed 
    CAS 

    Google Scholar
     

  • Morin, A. et al. Collaboration gets the most out of software. eLife 2, e01456 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jude, K. M. et al Engineered peptide-specific binder in complex with HLA-DR1/CLIP. Worldwide Protein Data Bank https://doi.org/10.2210/pdb8vsj/pdb (2024).



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