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Nature Biotechnology Feb 2023Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying...
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging. Here we describe the Protein Modification Integrated Search Engine (PROMISE), an antigen discovery pipeline that enables the analysis of 29 different PTM combinations from multiple clinical cohorts and cell lines. We expanded the antigen landscape, uncovering human leukocyte antigen class I binding motifs defined by specific PTMs with haplotype-specific binding preferences and revealing disease-specific modified targets, including thousands of new cancer-specific antigens that can be shared between patients and across cancer types. Furthermore, we uncovered a subset of modified peptides that are specific to cancer tissue and driven by post-translational changes that occurred in the tumor proteome. Our findings highlight principles of PTM-driven antigenicity, which may have broad implications for T cell-mediated therapies in cancer and beyond.
Topics: Humans; Protein Processing, Post-Translational; Peptides; Antigens; Histocompatibility Antigens Class I; Neoplasms
PubMed: 36203013
DOI: 10.1038/s41587-022-01464-2 -
Nature Reviews. Immunology Aug 2003Ever since the emergence of models for the processing and presentation of antigenic determinants by MHC class II molecules, the main view has been that proteins are... (Review)
Review
Ever since the emergence of models for the processing and presentation of antigenic determinants by MHC class II molecules, the main view has been that proteins are unfolded, enzymatically cleaved into peptide lengths of about 12-25 amino acids and then loaded onto MHC class II molecules. There is, however, an alternative model stating that partially intact unfolding antigens are first bound by MHC class II molecules and then trimmed to fragments of a smaller size while remaining bound to the MHC class II molecule. In this analysis, we make the case that a considerable portion of the elutable peptide cargo belongs to this latter class.
Topics: Animals; Antigen Presentation; Antigen-Presenting Cells; Antigens; Epitopes; Histocompatibility Antigens Class II; Humans; Models, Molecular; Peptide Fragments
PubMed: 12974477
DOI: 10.1038/nri1149 -
Hematology. American Society of... 2015Antigen-specific immunotherapies have emerged as important components of curative treatment algorithms for many cancers. In acute myeloid leukemia (AML), success has... (Review)
Review
Antigen-specific immunotherapies have emerged as important components of curative treatment algorithms for many cancers. In acute myeloid leukemia (AML), success has been less obvious. Nonetheless, among the few drugs shown to improve survival in recent randomized trials is the CD33 antibody-drug conjugate gemtuzumab ozogamicin. Significant antileukemic activity is also well documented for radioimmunoconjugates targeting CD33, CD45, or CD66. These therapeutics can intensify conditioning before hematopoietic cell transplantation, but their effect on patient outcomes needs clarification. Emerging data now suggest clinical antileukemic activity of several novel antibodies and perhaps some adoptive T-cell immunotherapies and vaccines. In parallel, numerous other agents targeting a wider variety of antigens are currently being explored. However, the antigenic heterogeneity characteristic of AML is a considerable limitation for all these therapeutics, and many important questions related to the ideal target antigen(s), disease situation in which to use these therapies, most suitable patient populations, exact treatment modalities, and details of supportive care needs remain open. Addressing such questions in upcoming studies will be required to ensure that antigen-directed therapies become an effective tool in AML, a disease for which outcomes with standard "3 + 7"-based chemotherapy have remained unsatisfactory in many patients.
Topics: Algorithms; Aminoglycosides; Antibodies; Antibodies, Monoclonal, Humanized; Antigens; Antineoplastic Agents; Clinical Trials as Topic; Gemtuzumab; Humans; Immunotherapy; Immunotherapy, Adoptive; Immunotoxins; Leukemia, Myeloid, Acute; Radioimmunotherapy; Randomized Controlled Trials as Topic; Sialic Acid Binding Ig-like Lectin 3; Vaccines
PubMed: 26637776
DOI: 10.1182/asheducation-2015.1.584 -
Current Opinion in Organ Transplantation Aug 2014Human leukocyte antigen (HLA) antibodies are now recognized as being specific for epitopes which can be defined structurally with amino acid differences between HLA... (Review)
Review
PURPOSE OF REVIEW
Human leukocyte antigen (HLA) antibodies are now recognized as being specific for epitopes which can be defined structurally with amino acid differences between HLA alleles. This article addresses two general perspectives of HLA epitopes namely antigenicity, that is their reactivity with antibody and immunogenicity, that is their ability of eliciting an antibody response.
RECENT FINDINGS
Single-antigen bead assays have shown that HLA antibodies recognize epitopes that are equivalent to eplets or corresponding to eplets paired with other residue configurations. There is now a website-based Registry of Antibody-Defined HLA Epitopes (http://www.epregistry.com.br). Residue differences within eplet-defined structural epitopes may also explain technique-dependent variations in antibody reactivity determined in Ig-binding, C1q-binding and lymphocytotoxicity assays.HLA antibody responses correlate with the numbers of eplets on mismatched HLA antigens, and the recently proposed nonself-self paradigm of epitope immunogenicity may explain the production of epitope-specific antibodies.
SUMMARY
These findings support the usefulness of HLA matching at the epitope level, including the identification of acceptable mismatches for sensitized patients and permissible mismatching for nonsensitized patients aimed to reduce HLA antibody responses.
Topics: Animals; Antibodies; Antibody Formation; Antibody Specificity; Epitopes; HLA Antigens; Histocompatibility Testing; Humans
PubMed: 25010064
DOI: 10.1097/MOT.0000000000000100 -
Journal of Immunoassay Nov 1995A simple method for determination of binding kinetics of a solid-phase antibody using antigen-beta-galactosidase hybrid protein was evaluated. To minimize conformational...
A simple method for determination of binding kinetics of a solid-phase antibody using antigen-beta-galactosidase hybrid protein was evaluated. To minimize conformational change of the antigen binding site of the antibody when directly binding to a microtiter plate, the microtiter plate was precoated with protein A. The binding and free antigen concentrations were directly obtained from the beta-galactosidase activity. This method can be used for analyses of the equilibrium dissociation constant (KD), and the association (Kass) and dissociation (Kdiss) rate constants. Peptide antigenicity was also analyzed by competitive ELISA using this method. Since both antigen-beta-galactosidase and the peptide used are localized in the fluid-phase, the proper affinity constant (KA) of the peptide can be estimated from the KD value of the antigen-beta-galactosidase-antibody interaction, and from the IC50 value of the peptide.
Topics: Amino Acid Sequence; Antibodies, Monoclonal; Antibody Affinity; Antigen-Antibody Complex; Antigens; Binding, Competitive; Enzyme-Linked Immunosorbent Assay; Kinetics; Molecular Sequence Data; Peptides; Recombinant Fusion Proteins; beta-Galactosidase
PubMed: 8567983
DOI: 10.1080/15321819508013567 -
Gerontology 1990An aging antigen, senescent cell antigen, resides on the 911 amino acid membrane protein band 3. It marks cells for removal by initiating specific IgG binding. The...
Molecular mapping of the active site of an aging antigen: senescent cell antigen requires lysine(s) for antigenicity and is located on an anion-binding segment of band 3 membrane transport protein.
An aging antigen, senescent cell antigen, resides on the 911 amino acid membrane protein band 3. It marks cells for removal by initiating specific IgG binding. The active antigenic sites of the aging antigen have been localized to residues 538-554 and 778-827. Two peptides within these regions interact synergistically to generate a synthetic aging antigen that is an effective inhibitor of senescent cell IgG binding to old cells. We synthesized peptides corresponding to these residues (pep-ANION 1: SKLIKIFQDHPLQKTYN, and pep-COOH: LFKPPKYHPDVPYVKR). These are extracellular regions of band 3 containing lysines which are implicated in anion transport. The contribution of lysine to the antigenicity of the aging antigen and to anion transport was examined by chemically modifying the lysines on both synthetic peptides and whole cells, and by synthesizing peptides in which glycines or arginines were substituted for lysines. Anion transport sites were localized using 16- to 18-mer peptides followed by 6- to 8-mer peptides. Functional studies with the peptide pep-COOH indicate that it contains sulfate-binding sites and inhibits sulfate transport in addition to carrying aging antigenic determinants. Substitution of arginines or glycines for lysines in pep-COOH reduces the sulfate-binding properties of the peptide although significant inhibition still occurs. Residues 812-827 (pep-COOH) and 813-818 (N6, the six amino acids on the amino side of pep-COOH) and 822-839 are inhibitors of anion transport when used in equimolar amounts with sulfate suggesting that these regions may be transport regions in situ. Results of this study indicate that: (a) lysines are required for the integrity of the aging antigenic site; (b) pep-COOH (residues 812-827) is part of senescent cell antigen and an anion-binding site; (c) pep-ANION 1 (538-554), which has been reported to be a transport segment of band 3, does not bind sulfate; (d) residues 588-602 are part of an anion binding/transport segment; (e) band 3 residues 822-839 are part of an anion binding/transport site, and (f) lysines contribute to anion binding but are not the only amino acid(s) required for anion binding and, thus, anion transport.
Topics: 4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid; 4-Acetamido-4'-isothiocyanatostilbene-2,2'-disulfonic Acid; Amino Acid Sequence; Anion Exchange Protein 1, Erythrocyte; Anions; Antigens, Surface; Binding Sites; Epitopes; Erythrocyte Aging; Humans; Lysine; Molecular Sequence Data; Peptide Mapping
PubMed: 1706294
DOI: 10.1159/000213214 -
Biochimica Et Biophysica Acta.... May 2023Invariant natural killer T cells (iNKT cells) can be activated through binding antigenic lipid/CD1d complexes to their TCR. Antigenic lipids are processed, loaded, and... (Review)
Review
Invariant natural killer T cells (iNKT cells) can be activated through binding antigenic lipid/CD1d complexes to their TCR. Antigenic lipids are processed, loaded, and displayed in complex with CD1d by lipid antigen presenting cells (LAPCs). The mechanism of lipid antigen presentation via CD1d is highly conserved with recent work showing adipocytes are LAPCs that, besides having a role in lipid storage, can activate iNKT cells and play an important role in systemic metabolic disease. Recent studies shed light on parameters potentially dictating cytokine output and how obesity-associated metabolic disease may affect such parameters. By following a lipid antigen's journey, we identify five key areas which may dictate cytokine skew: co-stimulation, structural properties of the lipid antigen, stability of lipid antigen/CD1d complexes, intracellular and extracellular pH, and intracellular and extracellular lipid environment. Recent publications indicate that the combination of advanced omics-type approaches and machine learning may be a fruitful way to interconnect these 5 areas, with the ultimate goal to provide new insights for therapeutic exploration.
Topics: Adipocytes; Antigen Presentation; Cytokines; Lipids; Natural Killer T-Cells; Antigens, CD1d
PubMed: 36773690
DOI: 10.1016/j.bbalip.2023.159292 -
Expert Opinion on Biological Therapy Apr 2004Polymeric microparticles with encapsulated antigens have become well-established in the last decade as potent antigen delivery systems and adjuvants, with experience... (Review)
Review
Polymeric microparticles with encapsulated antigens have become well-established in the last decade as potent antigen delivery systems and adjuvants, with experience being reported from many groups. However, the authors have recently shown that an alternative approach involving charged polylactide co-glycolide (PLG) microparticles with surface adsorbed antigen(s) can also be used to deliver antigen into antigen-presenting cell populations. The authors have described the preparation of cationic and anionic PLG microparticles that have been used to adsorb a variety of agents, to include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides. These novel PLG microparticles were prepared using a w/o/w solvent evaporation process in the presence of the anionic surfactants, such as dioctyl sodium sulfosuccinate, or cationic surfactants, such as hexadecyl trimethyl ammonium bromide. Antigen binding to the charged PLG microparticles was influenced by both electrostatic interaction and other mechanisms, including hydrophobic interactions. Adsorption of antigens to microparticles resulted in the induction of significantly enhanced immune responses in comparison with alternative approaches. The surface adsorbed microparticle formulation offers an alternative way of delivering antigens as a vaccine formulation.
Topics: Animals; Antigens; Drug Carriers; Drug Delivery Systems; Humans; Lactic Acid; Microspheres; Polyglycolic Acid; Polylactic Acid-Polyglycolic Acid Copolymer; Polymers; Vaccines, DNA
PubMed: 15102598
DOI: 10.1517/14712598.4.4.483 -
Immunology and Cell Biology Feb 1997The treamendous explosion in the field of MHC research in the last 5 years has significantly advanced our understanding of antigen processing pathways, particularly with... (Review)
Review
The treamendous explosion in the field of MHC research in the last 5 years has significantly advanced our understanding of antigen processing pathways, particularly with regard to details of MHC class II-mediated antigen presentation. MHC class II molecules at the surface of antigen presenting cells present antigenic peptides to CD4+ T helper cells. However for effective cell surface antigen presentation, a number of highly synchronized events must first take place intracellulary. The monomorphic protein, invariant chain (Ii), is a crucial participant in MHC class II antigen presentation. Acting as a molecular chaperone, this molecule escorts the newly synthesized class II heterodimers from the endoplasmic reticulum into the endosomal system. During this manoeuvre, the interaction of li with class II serves to prevent premature association of antigenic peptide. Once the complex reaches the acidic environment of the endosomes, li is proteolytically degraded and dissociates, leaving the class II binding site available for binding antigenic peptide derived from exogenous proteins. The final Ii fragment to be displaced. CLIP (class II-associated invariant chain peptides), must be physically removed from the class II binding groove with assistance from another MHC-encoded molecule, DM. The interaction of DM with class II also aids in the subsequent rapid loading of high-affinity antigen-derived peptides into the MHC class II groove. The stable peptide-loaded complexes are now ready to exit the endocytic compartments to present their peptide antigen to specific T helper cells at the cell surface.
Topics: Animals; Antigen Presentation; Histocompatibility Antigens Class II; Humans
PubMed: 9046437
DOI: 10.1038/icb.1997.11 -
Immunologic Research 1995The human mayor histocompatibility complex class I molecule HLA-A2 preferentially binds peptides that contain Leu at P2 and Val or Leu at the C terminus. The other amino... (Review)
Review
The human mayor histocompatibility complex class I molecule HLA-A2 preferentially binds peptides that contain Leu at P2 and Val or Leu at the C terminus. The other amino acids in the peptide also contribute to binding positively or negatively. It is possible to estimate the binding stability of HLA-A2 complexes containing particular peptides by applying coefficients, deduced from a large amount of binding data, that quantify the relative contribution of each amino acid at each position. In this review, we describe the molecular basis for these coefficients and demonstrate that estimates of binding stability based on the coefficients are generally concordant with experimental measurements of binding affinities. Peptides that contained cysteine were predicted less well, possibly because of complications resulting from peptide dimerization and oxidation. Apparently, peptide binding affinity is largely controlled by the rate of dissociation of the HLA/peptide/beta 2-microglobulin complex, whereas the rate of formation of the complex has less impact on peptide affinity. Although peptides that bind tightly to HLA-A2, including many antigenic peptides bind much more weakly. Therefore, a full understanding of why certain peptides are immunodominant will require further research.
Topics: Amino Acid Sequence; Animals; Binding Sites; H-2 Antigens; HLA Antigens; Histocompatibility Antigens Class I; Humans; Mice; Molecular Sequence Data; Molecular Structure; Peptides; Protein Binding
PubMed: 7561340
DOI: 10.1007/BF02918496