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1.
Theranostics ; 14(6): 2290-2303, 2024.
Article in English | MEDLINE | ID: mdl-38646651

ABSTRACT

Background: Neoantigen nanovaccine has been recognized as a promising treatment modality for personalized cancer immunotherapy. However, most current nanovaccines are carrier-dependent and the manufacturing process is complicated, resulting in potential safety concerns and suboptimal codelivery of neoantigens and adjuvants to antigen-presenting cells (APCs). Methods: Here we report a facile and general methodology for nanoassembly of peptide and oligonucleotide by programming neoantigen peptide with a short cationic module at N-terminus to prepare nanovaccine. The programmed peptide can co-assemble with CpG oligonucleotide (TLR9 agonist) into monodispersed nanostructures without the introduction of artificial carrier. Results: We demonstrate that the engineered nanovaccine promoted the codelivery of neoantigen peptides and adjuvants to lymph node-residing APCs and instigated potent neoantigen-specific T-cell responses, eliciting neoantigen-specific antitumor immune responses with negligible systemic toxicity. Furthermore, the antitumor T-cell immunity is profoundly potentiated when combined with anti-PD-1 therapy, leading to significant inhibition or even complete regression of established melanoma and MC-38 colon tumors. Conclusions: Collectively, this work demonstrates the feasibility and effectiveness of personalized cancer nanovaccine preparation with high immunogenicity and good biosafety by programming neoantigen peptide for nanoassembly with oligonucleotides without the aid of artificial carrier.


Subject(s)
Antigens, Neoplasm , Cancer Vaccines , Peptides , Cancer Vaccines/immunology , Cancer Vaccines/administration & dosage , Animals , Mice , Antigens, Neoplasm/immunology , Peptides/immunology , Peptides/chemistry , Mice, Inbred C57BL , Oligodeoxyribonucleotides/administration & dosage , Oligodeoxyribonucleotides/immunology , Oligodeoxyribonucleotides/chemistry , Antigen-Presenting Cells/immunology , Cell Line, Tumor , Immunotherapy/methods , Humans , Female , T-Lymphocytes/immunology , Nanostructures/chemistry , Colonic Neoplasms/immunology , Colonic Neoplasms/therapy , Colonic Neoplasms/drug therapy
2.
Front Immunol ; 15: 1293706, 2024.
Article in English | MEDLINE | ID: mdl-38646540

ABSTRACT

Major histocompatibility complex Class II (MHCII) proteins initiate and regulate immune responses by presentation of antigenic peptides to CD4+ T-cells and self-restriction. The interactions between MHCII and peptides determine the specificity of the immune response and are crucial in immunotherapy and cancer vaccine design. With the ever-increasing amount of MHCII-peptide binding data available, many computational approaches have been developed for MHCII-peptide interaction prediction over the last decade. There is thus an urgent need to provide an up-to-date overview and assessment of these newly developed computational methods. To benchmark the prediction performance of these methods, we constructed an independent dataset containing binding and non-binding peptides to 20 human MHCII protein allotypes from the Immune Epitope Database, covering DP, DR and DQ alleles. After collecting 11 known predictors up to January 2022, we evaluated those available through a webserver or standalone packages on this independent dataset. The benchmarking results show that MixMHC2pred and NetMHCIIpan-4.1 achieve the best performance among all predictors. In general, newly developed methods perform better than older ones due to the rapid expansion of data on which they are trained and the development of deep learning algorithms. Our manuscript not only draws a full picture of the state-of-art of MHCII-peptide binding prediction, but also guides researchers in the choice among the different predictors. More importantly, it will inspire biomedical researchers in both academia and industry for the future developments in this field.


Subject(s)
Antigen Presentation , Computational Biology , Histocompatibility Antigens Class II , Peptides , Humans , Histocompatibility Antigens Class II/immunology , Histocompatibility Antigens Class II/metabolism , Peptides/immunology , Computational Biology/methods , Protein Binding , Deep Learning , Algorithms
3.
Hum Vaccin Immunother ; 20(1): 2337987, 2024 Dec 31.
Article in English | MEDLINE | ID: mdl-38658133

ABSTRACT

There is a growing interest in development of novel vaccines against respiratory tract infections, due to COVID-19 pandemic. Here, we examined mucosal adjuvanticity and the mucosal booster effect of membrane vesicles (MVs) of a novel probiotic E. coli derivative lacking both flagella and potentially carcinogenic colibactin (ΔflhDΔclbP). ΔflhDΔclbP-derived MVs showed rather strong mucosal adjuvanticity as compared to those of a single flagellar mutant strain (ΔflhD-MVs). In addition, glycoengineered ΔflhDΔclbP-MVs displaying serotype-14 pneumococcal capsular polysaccharide (CPS14+MVs) were well-characterized based on biological and physicochemical parameters. Subcutaneous (SC) and intranasal (IN) booster effects of CPS14+MVs on systemic and mucosal immunity were evaluated in mice that have already been subcutaneously prime-immunized with the same MVs. With a two-dose regimen, an IN boost (SC-IN) elicited stronger IgA responses than homologous prime-boost immunization (SC-SC). With a three-dose regimen, serum IgG levels were comparable among all tested regimens. Homologous immunization (SC-SC-SC) elicited the highest IgM responses among all regimens tested, whereas SC-SC-SC failed to elicit IgA responses in blood and saliva. Furthermore, serum IgA and salivary SIgA levels were increased with an increased number of IN doses administrated. Notably, SC-IN-IN induced not only robust IgG response, but also the highest IgA response in both serum and saliva among the groups. The present findings suggest the potential of a heterologous three-dose administration for building both systemic and mucosal immunity, e.g. an SC-IN-IN vaccine regimen could be beneficial. Another important observation was abundant packaging of colibactin in MVs, suggesting increased applicability of ΔflhDΔclbP-MVs in the context of vaccine safety.


Subject(s)
Adjuvants, Immunologic , Escherichia coli , Immunity, Mucosal , Immunization, Secondary , Mice, Inbred BALB C , Polyketides , Probiotics , Animals , Mice , Probiotics/administration & dosage , Escherichia coli/immunology , Immunization, Secondary/methods , Female , Adjuvants, Immunologic/administration & dosage , Immunoglobulin A , Peptides/immunology , Administration, Intranasal , Immunoglobulin G/blood , Immunoglobulin M , COVID-19 Vaccines/immunology , COVID-19 Vaccines/administration & dosage
4.
Science ; 383(6680): 319-325, 2024 01 19.
Article in English | MEDLINE | ID: mdl-38236978

ABSTRACT

Heterozygosity of Human leukocyte antigen (HLA) class I genes is linked to beneficial outcomes after HIV infection, presumably through greater breadth of HIV epitope presentation and cytotoxic T cell response. Distinct allotype pairs, however, differ in the extent to which they bind shared sets of peptides. We developed a functional divergence metric that measures pairwise complementarity of allotype-associated peptide binding profiles. Greater functional divergence for pairs of HLA-A and/or HLA-B allotypes was associated with slower AIDS progression and independently with enhanced viral load control. The metric predicts immune breadth at the peptide level rather than gene level and redefines HLA heterozygosity as a continuum differentially affecting disease outcome. Functional divergence may affect response to additional infections, vaccination, immunotherapy, and other diseases where HLA heterozygote advantage occurs.


Subject(s)
HIV Infections , HLA-B Antigens , Heterozygote , Humans , Alleles , Disease Progression , HIV Infections/genetics , HIV Infections/pathology , HLA-B Antigens/genetics , Peptides/genetics , Peptides/immunology , Male , Female , Young Adult , Adult , Middle Aged , Aged
5.
Nucleic Acids Res ; 52(D1): D1062-D1071, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-38000392

ABSTRACT

The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.


Subject(s)
Databases, Protein , Peptides , Proteomics , Mass Spectrometry , Peptides/chemistry , Peptides/immunology , Protein Processing, Post-Translational , Proteomics/methods , Databases, Protein/standards , Internet , Humans , Animals
6.
Nature ; 625(7995): 593-602, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38093017

ABSTRACT

Emerging data have shown that previously defined noncoding genomes might encode peptides that bind human leukocyte antigen (HLA) as cryptic antigens to stimulate adaptive immunity1,2. However, the significance and mechanisms of action of cryptic antigens in anti-tumour immunity remain unclear. Here mass spectrometry of the HLA class I (HLA-I) peptidome coupled with ribosome sequencing of human breast cancer samples identified HLA-I-binding cryptic antigenic peptides that were noncanonically translated by a tumour-specific circular RNA (circRNA): circFAM53B. The cryptic peptides efficiently primed naive CD4+ and CD8+ T cells in an antigen-specific manner and induced anti-tumour immunity. Clinically, the expression of circFAM53B and its encoded peptides was associated with substantial infiltration of antigen-specific CD8+ T cells and better survival in patients with breast cancer and patients with melanoma. Mechanistically, circFAM53B-encoded peptides had strong binding affinity to both HLA-I and HLA-II molecules. In vivo, administration of vaccines consisting of tumour-specific circRNA or its encoded peptides in mice bearing breast cancer tumours or melanoma induced enhanced infiltration of tumour-antigen-specific cytotoxic T cells, which led to effective tumour control. Overall, our findings reveal that noncanonical translation of circRNAs can drive efficient anti-tumour immunity, which suggests that vaccination exploiting tumour-specific circRNAs may serve as an immunotherapeutic strategy against malignant tumours.


Subject(s)
Breast Neoplasms , Melanoma , Peptides , Protein Biosynthesis , RNA, Circular , Animals , Female , Humans , Mice , Antigens, Neoplasm/immunology , Breast Neoplasms/genetics , Breast Neoplasms/immunology , Breast Neoplasms/mortality , Breast Neoplasms/pathology , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Histocompatibility Antigens Class I/immunology , Histocompatibility Antigens Class II/immunology , Mass Spectrometry , Melanoma/genetics , Melanoma/immunology , Melanoma/mortality , Melanoma/pathology , Peptides/genetics , Peptides/immunology , Ribosome Profiling , RNA, Circular/genetics , RNA, Circular/metabolism , Survival Analysis
7.
Nature ; 623(7988): 820-827, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37938771

ABSTRACT

The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.


Subject(s)
Antigens, Neoplasm , Neuroblastoma , Oncogene Proteins , Peptides , Receptors, Chimeric Antigen , Animals , Humans , Mice , Africa/ethnology , Alleles , Amino Acid Sequence , Carcinogenesis , Cross Reactions , HLA-A Antigens/chemistry , HLA-A Antigens/immunology , Neuroblastoma/genetics , Neuroblastoma/immunology , Neuroblastoma/therapy , Oncogene Proteins/antagonists & inhibitors , Oncogene Proteins/immunology , Peptides/antagonists & inhibitors , Peptides/chemistry , Peptides/immunology , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/therapeutic use
8.
Nature ; 620(7972): 128-136, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37468623

ABSTRACT

Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.


Subject(s)
Alleles , Asymptomatic Infections , COVID-19 , HLA-B Antigens , Humans , COVID-19/genetics , COVID-19/immunology , COVID-19/physiopathology , COVID-19/virology , Epitopes, T-Lymphocyte/immunology , Peptides/immunology , SARS-CoV-2/immunology , HLA-B Antigens/immunology , Cohort Studies , T-Lymphocytes/immunology , Immunodominant Epitopes/immunology , Cross Reactions/immunology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology
9.
Clin Cancer Res ; 29(12): 2250-2265, 2023 06 13.
Article in English | MEDLINE | ID: mdl-36749875

ABSTRACT

PURPOSE: Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from noncanonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. EXPERIMENTAL DESIGN: Peptides presented on HLA-I were identified in 9 patient-derived tumor cell lines from melanoma, gynecologic, and head and neck cancer through proteogenomics. A total of 507 candidate tumor antigens, including nonC-TL, neoantigens, cancer-germline, or melanocyte differentiation antigens, were tested for T-cell recognition of preexisting responses in patients with cancer. Donor peripheral blood lymphocytes (PBL) were in vitro sensitized against 170 selected nonC-TL to isolate antigen-specific T-cell receptors (TCR) and evaluate their therapeutic potential. RESULTS: We found no recognition of the 507 nonC-TL tested by autologous ex vivo expanded tumor-reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However, in vitro sensitization of donor PBL against 170 selected nonC-TL, led to the identification of TCRs specific to three nonC-TL, two of which mapped to the 5' UTR regions of HOXC13 and ZKSCAN1, and one mapping to a noncoding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. CONCLUSIONS: Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies. See related commentary by Fox et al., p. 2173.


Subject(s)
Neoplasms , Proteogenomics , Female , Humans , Ligands , Lighting , Antigens, Neoplasm/immunology , Receptors, Antigen, T-Cell , Peptides/immunology
10.
J Agric Food Chem ; 71(6): 2990-2998, 2023 Feb 15.
Article in English | MEDLINE | ID: mdl-36728846

ABSTRACT

Peanut and tree-nut allergies are frequently comorbid for reasons not completely understood. Vicilin-buried peptides (VBPs) are an emerging family of food allergens whose conserved structural fold could mediate peanut/tree-nut co-allergy. Peptide microarrays were used to identify immunoglobulin E (IgE) epitopes from the N-terminus of the vicilin allergens Ara h 1, Ana o 1, Jug r 2, and Pis v 3 using serum from three patient diagnosis groups: monoallergic to either peanuts or cashew/pistachio, or dual allergic. IgE binding peptides were highly prevalent in the VBP domains AH1.1, AO1.1, JR2.1, and PV3.1, but not in AO1.2, JR2.2, JR2.3, and PV3.2 nor the unstructured regions. The IgE profiles did not correlate with diagnosis group. The structure of the VBPs from cashew and pistachio was solved using solution-NMR. Comparisons of structural features suggest that the VBP scaffold from peanuts and tree-nuts can support cross-reactivity. This may help understand comorbidity and cross-reactivity despite a distant evolutionary origin.


Subject(s)
Anacardium , Arachis , Immunoglobulin E , Juglans , Pistacia , Humans , Allergens/chemistry , Allergens/immunology , Anacardium/chemistry , Arachis/chemistry , Immunoglobulin E/immunology , Juglans/chemistry , Nut Hypersensitivity/diagnosis , Nuts/chemistry , Peptides/chemistry , Peptides/immunology , Pistacia/chemistry , Cross Reactions
12.
Br J Cancer ; 128(9): 1777-1787, 2023 05.
Article in English | MEDLINE | ID: mdl-36823366

ABSTRACT

BACKGROUND: The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. METHODS: Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of naturally presented HLA ligands isolated from tumour tissue samples (n = 40) using immunoaffinity purification. The cohort included 22 HPV-positive (primarily HPV-16) and 18 HPV-negative samples. A benign reference dataset comprised of the HLA ligandomes of benign haematological and tissue datasets was used to identify tumour-associated antigens. RESULTS: MS analysis led to the identification of naturally HLA-presented peptides in OPSCC tumour tissue. In total, 22,769 peptides from 9485 source proteins were detected on HLA class I. For HLA class II, 15,203 peptides from 4634 source proteins were discovered. By comparative profiling against the benign HLA ligandomic datasets, 29 OPSCC-associated HLA class I ligands covering 11 different HLA allotypes and nine HLA class II ligands were selected to create a peptide warehouse. CONCLUSION: Tumour-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi)personalised strategies.


Subject(s)
HLA Antigens , Otorhinolaryngologic Neoplasms , Papillomavirus Infections , Squamous Cell Carcinoma of Head and Neck , Humans , Papillomavirus Infections/immunology , Peptides/immunology , Vaccination , Otorhinolaryngologic Neoplasms/immunology , HLA Antigens/immunology , Antigens, Neoplasm/immunology , Human papillomavirus 16 , Human papillomavirus 18
13.
Int Immunol ; 35(5): 243-253, 2023 05 08.
Article in English | MEDLINE | ID: mdl-36591893

ABSTRACT

Immunogenicity can be evaluated by detecting antibodies (Abs) induced by an antigen. Presently deployed assays, however, do not consider the negative impacts of Ab poly-specificity, which is well established at the monoclonal antibody level. Here, we studied antibody poly-specificity at the serum level (i.e. nonspecific Ab-probe interactions, NSIs), and ended up establishing a new platform for viral peptide immunogenicity evaluation. We first selected three peptides of high, medium and low immunogenicity, using a 'vaccine serum response rate'-based approach (i.e. the gold standard). These three peptides (Pi) in the bovine serum albumin-Pi form were used to immunize chickens, resulting in longitudinal serum samples for screening with a non-cognate peptide library. The signal intensity of Ab-peptide specific binding and 'NSI count' was used to evaluate the viral peptides' immunogenicity. Only the NSI count agreed with the gold standard. The NSI count also provides more informative data on antibody production than the aggregated signal intensity by whole-protein-based indirect enzyme-linked immunosorbent assay.


Subject(s)
Antibody Specificity , Immunoglobulins , Peptides , Viral Proteins , Peptide Library , Immunoglobulins/blood , Animals , Chickens , Newcastle disease virus/immunology , Peptides/immunology , Enzyme-Linked Immunosorbent Assay , Antibody Formation , Viral Proteins/immunology
14.
Nature ; 613(7944): 565-574, 2023 01.
Article in English | MEDLINE | ID: mdl-36410718

ABSTRACT

Programming T cells to distinguish self from non-self is a vital, multi-step process that occurs in the thymus1-4. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific ß chain, is a critical early checkpoint in thymocyte development within the αß T cell lineage5,6. PreTCRs arrayed on CD4-CD8- double-negative thymocytes ligate peptides bound to major histocompatibility complex molecules (pMHC) on thymic stroma, similar to αß T cell receptors that appear on CD4+CD8+ double-positive thymocytes, but via a different molecular docking strategy7-10. Here we show the consequences of these distinct interactions for thymocyte progression using synchronized fetal thymic progenitor cultures that differ in the presence or absence of pMHC on support stroma, and single-cell transcriptomes at key thymocyte developmental transitions. Although major histocompatibility complex (MHC)-negative stroma fosters αß T cell differentiation, the absence of preTCR-pMHC interactions leads to deviant thymocyte transcriptional programming associated with dedifferentiation. Highly proliferative double-negative and double-positive thymocyte subsets emerge, with antecedent characteristics of T cell lymphoblastic and myeloid malignancies. Compensatory upregulation of diverse MHC class Ib proteins in B2m/H2-Ab1 MHC-knockout mice partially safeguards in vivo thymocyte progression, although disseminated double-positive thymic tumours may develop with ageing. Thus, as well as promoting ß chain repertoire broadening for subsequent αß T cell receptor utilization, preTCR-pMHC interactions limit cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduce developmental vulnerabilities.


Subject(s)
Cell Dedifferentiation , Histocompatibility Antigens Class I , Receptors, Antigen, T-Cell , Thymocytes , Animals , Mice , Mice, Knockout , Molecular Docking Simulation , Peptides/immunology , Peptides/metabolism , Thymocytes/cytology , Thymocytes/immunology , Thymus Gland/cytology , Thymus Gland/immunology , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/metabolism , Histocompatibility Antigens Class I/immunology , Histocompatibility Antigens Class I/metabolism
15.
Nature ; 612(7941): 771-777, 2022 12.
Article in English | MEDLINE | ID: mdl-36477533

ABSTRACT

Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public ß-chain variable region-complementary-determining region 3ß (BV9-CDR3ß) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3ß TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.


Subject(s)
Autoimmunity , HLA-B Antigens , Peptides , Receptors, Antigen, T-Cell , Humans , Autoantigens/chemistry , Autoantigens/immunology , Autoantigens/metabolism , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , HLA-B Antigens/immunology , HLA-B Antigens/metabolism , Peptides/chemistry , Peptides/immunology , Peptides/metabolism , Receptors, Antigen, T-Cell/chemistry , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/metabolism , Synovial Fluid/immunology , Spondylitis, Ankylosing/immunology , Uveitis, Anterior/immunology , Peptide Library , Cross Reactions , Amino Acid Motifs
16.
Viruses ; 14(8)2022 07 27.
Article in English | MEDLINE | ID: mdl-36016268

ABSTRACT

Yellow Fever disease is caused by the Yellow Fever virus (YFV), an arbovirus from the Flaviviridae family. The re-emergence of Yellow Fever (YF) was facilitated by the increasing urbanization of sylvatic areas, the wide distribution of the mosquito vector, and the low percentage of people immunized in the Americas, which caused severe outbreaks in recent years, with a high mortality rate. Therefore, serological approaches capable of discerning antibodies generated from the wild-type (YFV-WT) strain between the vaccinal strain (YFV-17DD) could facilitate vaccine coverage surveillance, enabling the development of strategies to avoid new outbreaks. In this study, peptides were designed and subjected to microarray procedures with sera collected from individuals infected by WT-YFV and 17DD-YFV of YFV during the Brazilian outbreak of YFV in 2017/2018. From 222 screened peptides, around ten could potentially integrate serological approaches aiming to differentiate vaccinated individuals from naturally infected individuals. Among those peptides, one was synthesized and validated through ELISA.


Subject(s)
Peptides , Yellow Fever Vaccine , Yellow Fever , Antibodies/blood , Humans , Peptides/blood , Peptides/immunology , Yellow Fever/blood , Yellow Fever/epidemiology , Yellow Fever/prevention & control , Yellow Fever Vaccine/immunology
17.
Front Immunol ; 13: 847092, 2022.
Article in English | MEDLINE | ID: mdl-35967379

ABSTRACT

Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by Vß2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of Vß2-containing TCRs and correlates with an unusual Vα-Vß interface, CDR loop conformations, and Vß2-specific germline contacts with peptides. Vß2 and Ld may represent "specialist" components for antigen recognition that allows for particularly strong and focused T cell responses.


Subject(s)
CD8-Positive T-Lymphocytes , Peptides , Receptors, Antigen, T-Cell, alpha-beta , Receptors, Antigen, T-Cell , CD8-Positive T-Lymphocytes/immunology , Germ Cells/immunology , Histocompatibility Antigen H-2D/immunology , Molecular Conformation , Peptides/immunology , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell, alpha-beta/immunology , Transglutaminases/immunology
18.
Science ; 377(6607): 728-735, 2022 08 12.
Article in English | MEDLINE | ID: mdl-35857439

ABSTRACT

The potential for future coronavirus outbreaks highlights the need to broadly target this group of pathogens. We used an epitope-agnostic approach to identify six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. All six antibodies target the conserved fusion peptide region adjacent to the S2' cleavage site. COV44-62 and COV44-79 broadly neutralize alpha- and betacoronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants BA.2 and BA.4/5, albeit with lower potency than receptor binding domain-specific antibodies. In crystal structures of COV44-62 and COV44-79 antigen-binding fragments with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine residue at the S2' cleavage site. COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings highlight the fusion peptide as a candidate epitope for next-generation coronavirus vaccine development.


Subject(s)
Antibodies, Monoclonal , Antibodies, Viral , Broadly Neutralizing Antibodies , COVID-19 , Epitopes , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Antibodies, Monoclonal/immunology , Antibodies, Viral/immunology , Broadly Neutralizing Antibodies/immunology , COVID-19/immunology , COVID-19/prevention & control , COVID-19 Vaccines/chemistry , COVID-19 Vaccines/immunology , Epitopes/chemistry , Epitopes/immunology , Humans , Peptides/immunology , Protein Conformation, alpha-Helical , Protein Domains , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology
19.
Science ; 377(6607): 735-742, 2022 08 12.
Article in English | MEDLINE | ID: mdl-35857703

ABSTRACT

The coronavirus spike glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus spike proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors. These mAbs recognize the fusion peptide and acquire affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha- and betacoronaviruses, including animal coronaviruses WIV-1 and PDF-2180. Two selected mAbs also neutralize Omicron BA.1 and BA.2 authentic viruses and reduce viral burden and pathology in vivo. Structural and functional analyses showed that the fusion peptide-specific mAbs bound with different modalities to a cryptic epitope hidden in prefusion stabilized spike, which became exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.


Subject(s)
Angiotensin-Converting Enzyme 2 , Antibodies, Monoclonal , Antibodies, Viral , Broadly Neutralizing Antibodies , COVID-19 , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Angiotensin-Converting Enzyme 2/chemistry , Animals , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/isolation & purification , Antibodies, Viral/immunology , Antibodies, Viral/isolation & purification , Broadly Neutralizing Antibodies/immunology , COVID-19/immunology , Humans , Peptides/immunology , Protein Binding , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology
20.
Proc Natl Acad Sci U S A ; 119(29): e2205498119, 2022 07 19.
Article in English | MEDLINE | ID: mdl-35858344

ABSTRACT

HLA class I (HLA-I) allotypes vary widely in their dependence on tapasin (TAPBP), an integral component of the peptide-loading complex, to present peptides on the cell surface. We identified two single-nucleotide polymorphisms that regulate TAPBP messenger RNA (mRNA) expression in Africans, rs111686073 (G/C) and rs59097151 (A/G), located in an AP-2α transcription factor binding site and a microRNA (miR)-4486 binding site, respectively. rs111686073G and rs59097151A induced significantly higher TAPBP mRNA expression relative to the alternative alleles due to higher affinity for AP-2α and abrogation of miR-4486 binding, respectively. These variants associated with lower Plasmodium falciparum parasite prevalence and lower incidence of clinical malaria specifically among individuals carrying tapasin-dependent HLA-I allotypes, presumably by augmenting peptide loading, whereas tapasin-independent allotypes associated with relative protection, regardless of imputed TAPBP mRNA expression levels. Thus, an attenuated course of malaria may occur through enhanced breadth and/or magnitude of antigen presentation, an important consideration when evaluating vaccine efficacy.


Subject(s)
Histocompatibility Antigens Class I , Malaria, Falciparum , Membrane Transport Proteins , Plasmodium falciparum , Binding Sites , Genetic Variation , Histocompatibility Antigens Class I/immunology , Humans , Malaria, Falciparum/genetics , Malaria, Falciparum/immunology , Malaria, Falciparum/parasitology , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , MicroRNAs/metabolism , Peptides/immunology , Plasmodium falciparum/immunology , RNA, Messenger/genetics , Transcription Factor AP-2/metabolism
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