Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules

Major Histocompatibility Complex class I (MHC-I) molecules display self, viral or aberrant epitopic peptides to T cell receptors (TCRs), which employ interactions between complementarity-determining regions with both peptide and MHC-I heavy chain ‘framework’ residues to recognize specific Human Leucocyte Antigens (HLAs). The highly polymorphic nature of the HLA peptide-binding groove suggests a malleability of interactions within a common structural scaffold. Here, using structural data from peptide:MHC-I and pMHC:TCR structures, we first identify residues important for peptide and/or TCR binding. We then outline a fixed-backbone computational design approach for engineering synthetic molecules that combine peptide binding and TCR recognition surfaces from existing HLA allotypes. X-ray crystallography demonstrates that chimeric molecules bridging divergent HLA alleles can bind selected peptide antigens in a specified backbone conformation. Finally, in vitro tetramer staining and biophysical binding experiments using chimeric pMHC-I molecules presenting established antigens further demonstrate the requirement of TCR recognition on interactions with HLA framework residues, as opposed to interactions with peptide-centric Chimeric Antigen Receptors (CARs). Our results underscore a novel, structure-guided platform for developing synthetic HLA molecules with desired properties as screening probes for peptide-centric interactions with TCRs and other therapeutic modalities.

[1]  P. Flicek,et al.  The IPD-IMGT/HLA Database , 2022, Nucleic Acids Res..

[2]  E. Newell,et al.  NY-ESO-1-specific redirected T cells with endogenous TCR knockdown mediate tumor response and cytokine release syndrome , 2022, Journal for ImmunoTherapy of Cancer.

[3]  Amber K Weiner,et al.  RETRACTED ARTICLE: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs , 2021, Nature.

[4]  C. Szeto,et al.  The pockets guide to HLA class I molecules , 2021, Biochemical Society transactions.

[5]  Nianzhi Zhang,et al.  The Structure of a Peptide-Loaded Shark MHC Class I Molecule Reveals Features of the Binding between β2-Microglobulin and H Chain Conserved in Evolution , 2021, The Journal of Immunology.

[6]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[7]  H. Juan,et al.  Connecting MHC-I-binding motifs with HLA alleles via deep learning , 2021, Communications Biology.

[8]  K. Rock,et al.  Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation , 2021, Frontiers in Immunology.

[9]  L. Hellman,et al.  Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner , 2021, Proceedings of the National Academy of Sciences.

[10]  Brian D. Weitzner,et al.  Macromolecular modeling and design in Rosetta: recent methods and frameworks , 2020, Nature Methods.

[11]  Morten Nielsen,et al.  NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data , 2020, Nucleic Acids Res..

[12]  B. Jakobsen,et al.  TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide–HLA Complex , 2020, The Journal of Immunology.

[13]  Pemra Ozbek,et al.  Sequence-structure-function relationships in class I MHC: A local frustration perspective , 2019, bioRxiv.

[14]  J. Maris,et al.  High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange , 2019, Nature Communications.

[15]  David F. Boyd,et al.  Human CD8+ T cell cross-reactivity across influenza A, B and C viruses , 2019, Nature Immunology.

[16]  L. Pease,et al.  Breaking tolerance with engineered class I antigen-presenting molecules , 2019, Proceedings of the National Academy of Sciences.

[17]  Alessandro Sette,et al.  The Immune Epitope Database (IEDB): 2018 update , 2018, Nucleic Acids Res..

[18]  Jedd D. Wolchok,et al.  Cancer immunotherapy using checkpoint blockade , 2018, Science.

[19]  J. Utikal,et al.  Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer , 2017, Nature.

[20]  Charles H. Yoon,et al.  An immunogenic personal neoantigen vaccine for patients with melanoma , 2017, Nature.

[21]  P. Parham,et al.  Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles , 2017, PLoS genetics.

[22]  Peter Schuck,et al.  An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role , 2017, Nature Communications.

[23]  Zhiping Weng,et al.  ATLAS: A database linking binding affinities with structures for wild‐type and mutant TCR‐pMHC complexes , 2017, Proteins.

[24]  Thomas E. Royce,et al.  Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II , 2017, Genome research.

[25]  Y. Wang,et al.  Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes. , 2016, Journal of immunological methods.

[26]  J. Oscherwitz The promise and challenge of epitope-focused vaccines , 2016, Human vaccines & immunotherapeutics.

[27]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[28]  Zhiping Weng,et al.  How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire , 2016, Proceedings of the National Academy of Sciences.

[29]  W. Pickl,et al.  On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy) , 2016, International Archives of Allergy and Immunology.

[30]  Robert Weissert,et al.  Antigen Presentation, Autoantigens, and Immune Regulation in Multiple Sclerosis and Other Autoimmune Diseases , 2015, Front. Immunol..

[31]  H. W. V. van Deutekom,et al.  Zooming into the binding groove of HLA molecules: which positions and which substitutions change peptide binding most? , 2015, Immunogenetics.

[32]  W. Winnall,et al.  Bacterial cytoplasmic display platform Retained Display (ReD) identifies stable human germline antibody frameworks. , 2015, Biotechnology journal.

[33]  James McCluskey,et al.  T cell antigen receptor recognition of antigen-presenting molecules. , 2015, Annual review of immunology.

[34]  Ton N. Schumacher,et al.  Adoptive cellular therapy: A race to the finish line , 2015, Science Translational Medicine.

[35]  T. Schumacher,et al.  Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2–Restricted T Cell Epitopes , 2014, The Journal of Immunology.

[36]  Morten Nielsen,et al.  Uncovering the Peptide-Binding Specificities of HLA-C: A General Strategy To Determine the Specificity of Any MHC Class I Molecule , 2014, The Journal of Immunology.

[37]  R. K. Bright,et al.  Overexpressed oncogenic tumor-self antigens , 2014, Human vaccines & immunotherapeutics.

[38]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

[39]  David Baker,et al.  Proof of principle for epitope-focused vaccine design , 2014, Nature.

[40]  E. Adams,et al.  The adaptable major histocompatibility complex (MHC) fold: structure and function of nonclassical and MHC class I-like molecules. , 2013, Annual review of immunology.

[41]  Peter Cresswell,et al.  Pathways of antigen processing. , 2013, Annual review of immunology.

[42]  R. Cagliani,et al.  Pathogen-Driven Selection in the Human Genome , 2013, International Journal of Evolutionary Biology.

[43]  A. Singer,et al.  MHC restriction is imposed on a diverse T cell receptor repertoire by CD4 and CD8 co-receptors during thymic selection. , 2012, Trends in immunology.

[44]  Morten Nielsen,et al.  Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion , 2012, Nucleic Acids Res..

[45]  D. Price,et al.  A Single Autoimmune T Cell Receptor Recognizes More Than a Million Different Peptides* , 2011, The Journal of Biological Chemistry.

[46]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[47]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[48]  L. K. Ely,et al.  The molecular basis of TCR germline bias for MHC is surprisingly simple , 2009, Nature Immunology.

[49]  Philippa Marrack,et al.  Evolutionarily conserved amino acids that control TCR-MHC interaction. , 2008, Annual review of immunology.

[50]  T. Schumacher,et al.  Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7 , 2008, Proceedings of the National Academy of Sciences.

[51]  L. K. Ely,et al.  T cell allorecognition and MHC restriction--A case of Jekyll and Hyde? , 2008, Molecular immunology.

[52]  Bjoern Peters,et al.  HLA class I supertypes: a revised and updated classification , 2008, BMC Immunology.

[53]  A. Sewell,et al.  Different T Cell Receptor Affinity Thresholds and CD8 Coreceptor Dependence Govern Cytotoxic T Lymphocyte Activation and Tetramer Binding Properties* , 2007, Journal of Biological Chemistry.

[54]  T. Schumacher,et al.  Generation of peptide–MHC class I complexes through UV-mediated ligand exchange , 2006, Nature Protocols.

[55]  Robyn L Stanfield,et al.  How TCRs bind MHCs, peptides, and coreceptors. , 2006, Annual review of immunology.

[56]  T. Schumacher,et al.  Design and use of conditional MHC class I ligands , 2006, Nature Medicine.

[57]  E. Andrès,et al.  Clinical and immunological aspects of HLA class I deficiency. , 2005, QJM : monthly journal of the Association of Physicians.

[58]  F. Balloux,et al.  Pathogen-Driven Selection and Worldwide HLA Class I Diversity , 2005, Current Biology.

[59]  Andrew Sewell,et al.  Structural and kinetic basis for heightened immunogenicity of T cell vaccines , 2005, The Journal of experimental medicine.

[60]  L. K. Ely,et al.  Natural HLA Class I Polymorphism Controls the Pathway of Antigen Presentation and Susceptibility to Viral Evasion , 2004, The Journal of experimental medicine.

[61]  M. Bouvier,et al.  Structures of HLA-A*1101 Complexed with Immunodominant Nonamer and Decamer HIV-1 Epitopes Clearly Reveal the Presence of a Middle, Secondary Anchor Residue1 , 2004, The Journal of Immunology.

[62]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[63]  James Robinson,et al.  IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex , 2003, Nucleic Acids Res..

[64]  W. Potts,et al.  MHC heterozygosity confers a selective advantage against multiple-strain infections , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[65]  A. Casrouge,et al.  A Direct Estimate of the Human αβ T Cell Receptor Diversity , 1999 .

[66]  N. G. Saito,et al.  Recognition of an MHC class I-restricted antigenic peptide can be modulated by para-substitution of its buried tyrosine residues in a TCR-specific manner. , 1999, Journal of immunology.

[67]  J. Yewdell,et al.  Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. , 1999, Annual review of immunology.

[68]  D. Margulies,et al.  Three-dimensional structure of H-2Dd complexed with an immunodominant peptide from human immunodeficiency virus envelope glycoprotein 120. , 1998, Journal of molecular biology.

[69]  Philip J. R. Goulder,et al.  Phenotypic Analysis of Antigen-Specific T Lymphocytes , 1996, Science.

[70]  D. Wiley,et al.  HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[71]  H. Rammensee,et al.  Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules , 1991, Nature.

[72]  M. A. Saper,et al.  Structure of the human class I histocompatibility antigen, HLA-A2 , 1987, Nature.